9AB1 | pdb_00009ab1

Integrative structure of the human nuclear pore complex nuclear basket: 1-spoke structure

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb9AB1/pdb

Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2026-07-09 Released: 2026-11-04
Deposition Author(s): Obarska-Kosinska, A., Zhu, Y., Geissler, K., Rosenkranz, R.R.E., Yokoyama, N., Kreysing, J.P., Xing, H., Glushkova, D., Kubanska, M.A., Boehm, S., Kraeusslich, H.G., Turonova, B., Liu, F., Beck, M.

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

How the TREX-2 complex associates with the nuclear pore

Obarska-Kosinska, A., Zhu, Y., Geissler, K., Rosenkranz, R.R.E., Yokoyama, N., Kreysing, J.P., Xing, H., Glushkova, D., Kubanska, M.A., Boehm, S., Kraeusslich, H.G., Turonova, B., Liu, F., Beck, M.

(2026) Mol Cell

DOI: https://doi.org/10.1016/j.molcel.2026.10.006

Macromolecule Content

Total Structure Weight: 17,804.97 kDa
Atom Count: 1,001,888
Modeled Residue Count: 128,888
Deposited Residue Count: 138,549
Unique protein chains: 40

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase RanBP2	A [auth 0], B [auth 016], C [auth 024], D [auth 032], E [auth 08]	3,224	Homo sapiens	Mutation(s): 0 Gene Names: RANBP2 EC: 2.3.2
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Find proteins for P49792 (Homo sapiens) Explore P49792 Go to UniProtKB: P49792
PHAROS: P49792 GTEx: ENSG00000153201
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49792
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore membrane glycoprotein 210	F [auth 1] G [auth 116] H [auth 124] I [auth 132] J [auth 140] F [auth 1], G [auth 116], H [auth 124], I [auth 132], J [auth 140], K [auth 148], L [auth 156], M [auth 18]	1,887	Homo sapiens	Mutation(s): 0 Gene Names: NUP210
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Find proteins for Q8TEM1 (Homo sapiens) Explore Q8TEM1 Go to UniProtKB: Q8TEM1
PHAROS: Q8TEM1 GTEx: ENSG00000132182
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TEM1
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein TPR	N [auth 2], O [auth 3], R [auth 5], S [auth 6]	2,363	Homo sapiens	Mutation(s): 0 Gene Names: TPR
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Find proteins for P12270 (Homo sapiens) Explore P12270 Go to UniProtKB: P12270
PHAROS: P12270 GTEx: ENSG00000047410
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12270
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ALADIN	P [auth 4], Q [auth 48]	546	Homo sapiens	Mutation(s): 0 Gene Names: AAAS
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Find proteins for Q9NRG9 (Homo sapiens) Explore Q9NRG9 Go to UniProtKB: Q9NRG9
PHAROS: Q9NRG9 GTEx: ENSG00000094914
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NRG9
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Germinal-center associated nuclear protein	T [auth 7]	1,980	Homo sapiens	Mutation(s): 0 Gene Names: MCM3AP EC: 2.3.1 (UniProt), 2.3.1.48 (UniProt)
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Find proteins for O60318 (Homo sapiens) Explore O60318 Go to UniProtKB: O60318
PHAROS: O60318 GTEx: ENSG00000160294
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UniProt Group	O60318
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup50	U [auth 8] V [auth 816] W [auth 824] X [auth 832] Y [auth 840] U [auth 8], V [auth 816], W [auth 824], X [auth 832], Y [auth 840], Z [auth 88]	468	Homo sapiens	Mutation(s): 0 Gene Names: NUP50
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Find proteins for Q9UKX7 (Homo sapiens) Explore Q9UKX7 Go to UniProtKB: Q9UKX7
PHAROS: Q9UKX7 GTEx: ENSG00000093000
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UniProt Group	Q9UKX7
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup93	AA [auth A] BA [auth A16] CA [auth A24] DA [auth A32] EA [auth A40] AA [auth A], BA [auth A16], CA [auth A24], DA [auth A32], EA [auth A40], FA [auth A48], GA [auth A8]	819	Homo sapiens	Mutation(s): 0 Gene Names: NUP93
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Find proteins for Q8N1F7 (Homo sapiens) Explore Q8N1F7 Go to UniProtKB: Q8N1F7
PHAROS: Q8N1F7 GTEx: ENSG00000102900
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UniProt Group	Q8N1F7
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup188	HA [auth B], IA [auth B8]	1,749	Homo sapiens	Mutation(s): 0 Gene Names: NUP188
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Find proteins for Q5SRE5 (Homo sapiens) Explore Q5SRE5 Go to UniProtKB: Q5SRE5
PHAROS: Q5SRE5 GTEx: ENSG00000095319
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UniProt Group	Q5SRE5
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup205	JA [auth C], KA [auth C16], LA [auth C24], MA [auth C32], NA [auth C8]	2,012	Homo sapiens	Mutation(s): 0 Gene Names: NUP205
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Find proteins for Q92621 (Homo sapiens) Explore Q92621 Go to UniProtKB: Q92621
PHAROS: Q92621 GTEx: ENSG00000155561
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92621
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup155	OA [auth D] PA [auth D16] QA [auth D24] RA [auth D32] SA [auth D40] OA [auth D], PA [auth D16], QA [auth D24], RA [auth D32], SA [auth D40], TA [auth D8]	1,391	Homo sapiens	Mutation(s): 0 Gene Names: NUP155
UniProt & NIH Common Fund Data Resources
Find proteins for O75694 (Homo sapiens) Explore O75694 Go to UniProtKB: O75694
PHAROS: O75694 GTEx: ENSG00000113569
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UniProt Group	O75694
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear envelope protein NDC1	UA [auth E], VA [auth E8]	674	Homo sapiens	Mutation(s): 0 Gene Names: NDC1
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Find proteins for Q9BTX1 (Homo sapiens) Explore Q9BTX1 Go to UniProtKB: Q9BTX1
PHAROS: Q9BTX1 GTEx: ENSG00000058804
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UniProt Group	Q9BTX1
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup35	WA [auth F], XA [auth F24], YA [auth F40], ZA [auth F8]	326	Homo sapiens	Mutation(s): 0 Gene Names: NUP35
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Find proteins for Q8NFH5 (Homo sapiens) Explore Q8NFH5 Go to UniProtKB: Q8NFH5
PHAROS: Q8NFH5 GTEx: ENSG00000163002
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UniProt Group	Q8NFH5
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingomyelin phosphodiesterase 4	AB [auth G], BB [auth G8]	866	Homo sapiens	Mutation(s): 0 Gene Names: SMPD4 EC: 3.1.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXE4 (Homo sapiens) Explore Q9NXE4 Go to UniProtKB: Q9NXE4
PHAROS: Q9NXE4 GTEx: ENSG00000136699
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UniProt Group	Q9NXE4
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup133	CB [auth K], DB [auth K16], EB [auth K24], FB [auth K8]	1,156	Homo sapiens	Mutation(s): 0 Gene Names: NUP133
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Find proteins for Q8WUM0 (Homo sapiens) Explore Q8WUM0 Go to UniProtKB: Q8WUM0
PHAROS: Q8WUM0 GTEx: ENSG00000069248
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UniProt Group	Q8WUM0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup107	GB [auth L], HB [auth L16], IB [auth L24], JB [auth L8]	925	Homo sapiens	Mutation(s): 0 Gene Names: NUP107
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Find proteins for P57740 (Homo sapiens) Explore P57740 Go to UniProtKB: P57740
PHAROS: P57740 GTEx: ENSG00000111581
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UniProt Group	P57740
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup96 (NUP96 part of NUP98-NUP96 precursor, P52948)	KB [auth M], LB [auth M16], MB [auth M24], NB [auth M8]	937	Homo sapiens	Mutation(s): 0 Gene Names: NUP98 EC: 3.4.21
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Find proteins for P52948 (Homo sapiens) Explore P52948 Go to UniProtKB: P52948
PHAROS: P52948 GTEx: ENSG00000110713
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52948
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup160	OB [auth R], PB [auth R16], QB [auth R24], RB [auth R8]	1,436	Homo sapiens	Mutation(s): 0 Gene Names: NUP160
UniProt & NIH Common Fund Data Resources
Find proteins for Q12769 (Homo sapiens) Explore Q12769 Go to UniProtKB: Q12769
PHAROS: Q12769 GTEx: ENSG00000030066
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UniProt Group	Q12769
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup37	SB [auth S], TB [auth S16], UB [auth S24], VB [auth S8]	326	Homo sapiens	Mutation(s): 0 Gene Names: NUP37
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH4 (Homo sapiens) Explore Q8NFH4 Go to UniProtKB: Q8NFH4
PHAROS: Q8NFH4 GTEx: ENSG00000075188
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UniProt Group	Q8NFH4
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup88	WB [auth W], XB [auth W8]	741	Homo sapiens	Mutation(s): 0 Gene Names: NUP88
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Find proteins for Q99567 (Homo sapiens) Explore Q99567 Go to UniProtKB: Q99567
PHAROS: Q99567 GTEx: ENSG00000108559
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UniProt Group	Q99567
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 209	YB [auth X], ZB [auth X8]	561	Homo sapiens	Mutation(s): 0 Gene Names: TMEM209
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SK2 (Homo sapiens) Explore Q96SK2 Go to UniProtKB: Q96SK2
PHAROS: Q96SK2 GTEx: ENSG00000146842
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SK2
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup153	AC [auth Y], BC [auth Y16], CC [auth Y8]	1,475	Homo sapiens	Mutation(s): 0 Gene Names: NUP153
UniProt & NIH Common Fund Data Resources
Find proteins for P49790 (Homo sapiens) Explore P49790 Go to UniProtKB: P49790
PHAROS: P49790 GTEx: ENSG00000124789
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UniProt Group	P49790
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrin-2	DC [auth a]	172	Homo sapiens	Mutation(s): 0 Gene Names: CETN2
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Find proteins for P41208 (Homo sapiens) Explore P41208 Go to UniProtKB: P41208
PHAROS: P41208 GTEx: ENSG00000147400
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UniProt Group	P41208
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription/export complex protein 2 homolog	EC [auth b], FC [auth b16], GC [auth b24], HC [auth b8]	101	Homo sapiens	Mutation(s): 0 Gene Names: ENY2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPA8 (Homo sapiens) Explore Q9NPA8 Go to UniProtKB: Q9NPA8
PHAROS: Q9NPA8 GTEx: ENSG00000120533
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UniProt Group	Q9NPA8
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein 2	IC [auth c]	399	Homo sapiens	Mutation(s): 0 Gene Names: PCID2
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Find proteins for Q5JVF3 (Homo sapiens) Explore Q5JVF3 Go to UniProtKB: Q5JVF3
PHAROS: Q5JVF3 GTEx: ENSG00000126226
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UniProt Group	Q5JVF3
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	JC [auth d]	70	Homo sapiens	Mutation(s): 0 Gene Names: SEM1
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens) Explore P60896 Go to UniProtKB: P60896
PHAROS: P60896 GTEx: ENSG00000127922
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UniProt Group	P60896
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Spliceosome RNA helicase DDX39B	KC [auth e]	428	Homo sapiens	Mutation(s): 0 Gene Names: DDX39B EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q13838 (Homo sapiens) Explore Q13838 Go to UniProtKB: Q13838
PHAROS: Q13838 GTEx: ENSG00000198563
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UniProt Group	Q13838
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX19B	LC [auth f8], OC [auth f]	479	Homo sapiens	Mutation(s): 0 Gene Names: DDX19B EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMR2 (Homo sapiens) Explore Q9UMR2 Go to UniProtKB: Q9UMR2
PHAROS: Q9UMR2 GTEx: ENSG00000157349
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UMR2
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein GLE1	MC [auth g8], PC [auth g]	698	Homo sapiens	Mutation(s): 0 Gene Names: GLE1
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Find proteins for Q53GS7 (Homo sapiens) Explore Q53GS7 Go to UniProtKB: Q53GS7
PHAROS: Q53GS7 GTEx: ENSG00000119392
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UniProt Group	Q53GS7
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup42	NC [auth h8], QC [auth h]	423	Homo sapiens	Mutation(s): 0 Gene Names: NUP42
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Find proteins for O15504 (Homo sapiens) Explore O15504 Go to UniProtKB: O15504
PHAROS: O15504 GTEx: ENSG00000136243
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UniProt Group	O15504
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup54	RC [auth H], SC [auth H16], TC [auth H24], UC [auth H8]	507	Homo sapiens	Mutation(s): 0 Gene Names: NUP54
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3B4 (Homo sapiens) Explore Q7Z3B4 Go to UniProtKB: Q7Z3B4
PHAROS: Q7Z3B4 GTEx: ENSG00000138750
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UniProt Group	Q7Z3B4
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup58	VC [auth I], WC [auth I16], XC [auth I24], YC [auth I8]	599	Homo sapiens	Mutation(s): 0 Gene Names: NUP58
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Find proteins for Q9BVL2 (Homo sapiens) Explore Q9BVL2 Go to UniProtKB: Q9BVL2
PHAROS: Q9BVL2 GTEx: ENSG00000139496
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UniProt Group	Q9BVL2
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98	AD [auth U16], BD [auth U24], CD [auth U8], ZC [auth U]	880	Homo sapiens	Mutation(s): 0 Gene Names: NUP98 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens) Explore P52948 Go to UniProtKB: P52948
PHAROS: P52948 GTEx: ENSG00000110713
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UniProt Group	P52948
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup214	DD [auth V], ED [auth V8]	2,090	Homo sapiens	Mutation(s): 0 Gene Names: NUP214
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Find proteins for P35658 (Homo sapiens) Explore P35658 Go to UniProtKB: P35658
PHAROS: P35658 GTEx: ENSG00000126883
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UniProt Group	P35658
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear envelope pore membrane protein POM 121	FD [auth Z], GD [auth Z8]	1,249	Homo sapiens	Mutation(s): 0 Gene Names: POM121
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Find proteins for Q96HA1 (Homo sapiens) Explore Q96HA1 Go to UniProtKB: Q96HA1
PHAROS: Q96HA1 GTEx: ENSG00000196313
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UniProt Group	Q96HA1
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup62	HD [auth J16] ID [auth J24] JD [auth J32] KD [auth J40] LD [auth J8] HD [auth J16], ID [auth J24], JD [auth J32], KD [auth J40], LD [auth J8], MD [auth J]	522	Homo sapiens	Mutation(s): 0 Gene Names: NUP62
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Find proteins for P37198 (Homo sapiens) Explore P37198 Go to UniProtKB: P37198
PHAROS: P37198 GTEx: ENSG00000213024
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37198
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SEC13 homolog	ND [auth N], OD [auth N16], PD [auth N24], QD [auth N8]	322	Homo sapiens	Mutation(s): 0 Gene Names: SEC13
UniProt & NIH Common Fund Data Resources
Find proteins for P55735 (Homo sapiens) Explore P55735 Go to UniProtKB: P55735
PHAROS: P55735 GTEx: ENSG00000157020
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55735
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin Seh1	RD [auth O], SD [auth O16], TD [auth O24], UD [auth O8]	360	Homo sapiens	Mutation(s): 0 Gene Names: SEH1L
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Find proteins for Q96EE3 (Homo sapiens) Explore Q96EE3 Go to UniProtKB: Q96EE3
PHAROS: Q96EE3 GTEx: ENSG00000085415
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96EE3
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup85	VD [auth P], WD [auth P16], XD [auth P24], YD [auth P8]	656	Homo sapiens	Mutation(s): 0 Gene Names: NUP85
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW27 (Homo sapiens) Explore Q9BW27 Go to UniProtKB: Q9BW27
PHAROS: Q9BW27 GTEx: ENSG00000125450
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UniProt Group	Q9BW27
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Reference Sequence

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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup43	AE [auth Q16], BE [auth Q24], CE [auth Q8], ZD [auth Q]	380	Homo sapiens	Mutation(s): 0 Gene Names: NUP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH3 (Homo sapiens) Explore Q8NFH3 Go to UniProtKB: Q8NFH3
PHAROS: Q8NFH3 GTEx: ENSG00000120253
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NFH3
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Reference Sequence

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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein ELYS	DE [auth T], EE [auth T8]	2,266	Homo sapiens	Mutation(s): 0 Gene Names: AHCTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WYP5 (Homo sapiens) Explore Q8WYP5 Go to UniProtKB: Q8WYP5
PHAROS: Q8WYP5 GTEx: ENSG00000153207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WYP5
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Reference Sequence