9I1Q | pdb_00009i1q

HER3 receptor in complex with the Fab fragment of TK-hu A3 monoclonal antibody

PDB DOI: https://doi.org/10.2210/pdb9I1Q/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Cricetulus griseus
Mutation(s): No

Deposited: 2025-01-16 Released: 2025-10-15
Deposition Author(s): Bulfaro, G., Savino, C., Costanzo, A., Fata, F., Vallone, B., Montemiglio, L.C.
Funding Organization(s): Regione Lazio (Italy)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.263 (Depositor), 0.258 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Novel Humanized Anti-HER3 Antibodies: Structural Characterization and Therapeutic Activity.

Muzi, A., Arriga, R., Bulfaro, G., Fata, F., Costanzo, A., Chiarini, V., Cappelletti, M., Ferrara, F.F., Bucci, F., Montemiglio, L.C., Savino, C., Marra, E., Ciliberto, G., Aurisicchio, L., Vallone, B., Roscilli, G.

(2025) Antibodies (Basel) 14

PubMed: 41133678 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/antib14040084
Primary Citation of Related Structures:
9I1Q

PubMed Abstract:
The ErbB protein family plays a critical role in the progression of various solid tumors, and HER3 has been implicated in resistance mechanisms to multiple cancer therapies due to its ability to form heterodimers with other ErbB receptors, thereby activating pathways that promote tumor growth and survival. This study aimed to generate and characterize humanized monoclonal antibodies against HER3 to inhibit its function and evaluate their potential as therapeutic agents. Murine monoclonal antibodies TK-A3 and TK-A4 were humanized and tested for binding to ErbB3 and competition with neuregulin-1β (NRG). Specificity was assessed by ELISA, and epitope identified by X-ray crystallography. Downstream signaling was analyzed by western blot for phosphorylated ErbB3, Akt, and MAPK. Antitumor activity was evaluated in vitro and in a pancreatic cancer xenograft model. A toxicology study was also conducted. TK-hu A3 and TK-hu A4 bound specifically to ErbB3 without cross-reactivity to other ErbB receptors. The ErbB3-TK-hu A3 Fab structure revealed the binding epitope. Both antibodies competed with NRG, inhibiting ErbB3, Akt, and MAPK phosphorylation in a dose-dependent manner. They suppressed cancer cell survival in vitro, and TK-hu A3 significantly delayed tumor growth in vivo. The toxicology study indicated good tolerability. TK-hu A3 emerged as the lead candidate, showing specific HER3 targeting, strong pathway inhibition, and antitumor efficacy in vivo. Beyond standalone use, it could support novel strategies such as T-cell engagers, ADCs, CAR-T, and bispecific antibodies. These findings highlight TK-hu A3 as a promising therapy for HER3-positive, treatment-resistant cancers, meriting further development.

Organizational Affiliation

Takis s.r.l., 00128 Rome, Italy.

Macromolecule Content

Total Structure Weight: 481 kDa
Atom Count: 31,872
Modeled Residue Count: 4,062
Deposited Residue Count: 4,300
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-3	A, B, C, D	632	Homo sapiens	Mutation(s): 0 Gene Names: ERBB3, HER3 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens) Explore P21860 Go to UniProtKB: P21860
PHAROS: P21860 GTEx: ENSG00000065361
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21860
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P21860-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain hA3-Fab	E, F, G, H	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain hA3-Fab	I, J, K, L	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O	3		N-Glycosylation	Interactions Focus chain M Focus chain O Interactions & Density Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	4		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P, Q	2		N-Glycosylation	Interactions Focus chain P Focus chain Q Interactions & Density Focus chain P Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] EA [auth C] FA [auth C] AA [auth B], BA [auth B], CA [auth B], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], KA [auth D], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], QA [auth D], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain JA [auth C] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth H] SDF format, chain UA [auth H] SDF format, chain VA [auth I] SDF format, chain WA [auth I] SDF format, chain XA [auth L] MOL2 format, chain DA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth L] mmCIF format, chain DA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth L]	DA [auth B] JA [auth C] RA [auth D] SA [auth D] TA [auth H] DA [auth B], JA [auth C], RA [auth D], SA [auth D], TA [auth H], UA [auth H], VA [auth I], WA [auth I], XA [auth L]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain JA [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth L] Interactions & Density Focus chain DA [auth B] Focus chain JA [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth L]