9HJU | pdb_00009hju

Structure of 2x Zincore (SEPHS1:QRICH1) binding to ZFP91 on DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression.

Bianchi, D.Borza, R.De Zan, E.Huelsz-Prince, G.Gregoricchio, S.Dekker, M.Fish, A.Mazouzi, A.Kroese, L.J.Linder, S.Hernandez-Quiles, M.Vermeulen, M.Celie, P.H.N.Krimpenfort, P.Song, J.Y.Zwart, W.Wessels, L.Nijman, S.M.B.Perrakis, A.Brummelkamp, T.R.

(2025) Science 389: eadv2861-eadv2861

  • DOI: https://doi.org/10.1126/science.adv2861
  • Primary Citation of Related Structures:  
    9HJT, 9HJU

  • PubMed Abstract: 

    Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting of QRICH1 and SEPHS1, as a ZNF-specific coregulator essential for embryonic development in mice and associated with developmental syndromes in humans. We also identified ZFP91 as a representative Zincore client, binding the conserved promoter motif CTTTAAR. Cryo-electron microscopy of a Zincore-ZFP91-DNA complex revealed a SEPHS1 arginine clamp to recognize the DNA-bound zinc finger domains. This mode of binding explains recognition of different ZNFs and stabilizes ZFP91 onto its cognate DNA motif. Thus, our study identified Zincore as a ZNF-specific coregulator essential for development, involving a distinctive mechanism that locks ZNFs onto DNA and regulates transcription.


  • Organizational Affiliation
    • Oncode Institute, Utrecht, Netherlands.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ZFP91570Homo sapiensMutation(s): 0 
Gene Names: ZFP91ZNF757FKSG11
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JP5 (Homo sapiens)
Explore Q96JP5 
Go to UniProtKB:  Q96JP5
PHAROS:  Q96JP5
GTEx:  ENSG00000186660 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JP5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Selenide, water dikinase 1
B, C, F, G
392Homo sapiensMutation(s): 0 
Gene Names: SEPHS1SELDSPSSPS1
EC: 2.7.9.3
UniProt & NIH Common Fund Data Resources
Find proteins for P49903 (Homo sapiens)
Explore P49903 
Go to UniProtKB:  P49903
PHAROS:  P49903
GTEx:  ENSG00000086475 
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UniProt GroupP49903
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator QRICH1
D, E, H, I
776Homo sapiensMutation(s): 0 
Gene Names: QRICH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2TAL8 (Homo sapiens)
Explore Q2TAL8 
Go to UniProtKB:  Q2TAL8
PHAROS:  Q2TAL8
GTEx:  ENSG00000198218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TAL8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (31-MER)J [auth K]31Homo sapiens
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (31-MER)K [auth L]31Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIXdev_4788

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Oncode InstituteNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references