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Structure of Zanidatamab bound to HER2

Method: ELECTRON MICROSCOPY Dmax: 135.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor tyrosine-protein kinase erbB-2

Homo sapiens

UniProt P04626

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain X； UniProt 23–644 Not recorded Zanidatamab Heavy Chain A × 1 Zanidatamab Light Chain A × 1 Zanidatamab Heavy Chain B × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.50 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8FFJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1MW4 Solution structure of the human Grb7-SH2 domain in complex with a 10 amino acid peptide pY1139 Deposited 2002-09-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1135–1144（10 aa） Fragment：SH2 domain binding site
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1
NMR sample composition 0.7mM Grb7 SH2 U-15N, 13C, 50mM acetate | 90% H2O/10% D2O
Resolution not provided
1N8Z Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab Deposited 2002-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 23–629（607 aa） Fragment：extracellular domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20-30% PEG 5000 MME, 0.1M MES pH6.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.52 Å R-free 0.284
1QR1 POOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A LACK OF INTERACTIONS IN THE CENTER OF THE PEPTIDE Deposited 1999-06-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 654–662（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 2.40 Å R-free 0.284
1QR1 POOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A LACK OF INTERACTIONS IN THE CENTER OF THE PEPTIDE Deposited 1999-06-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 654–662（9 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Resolution 2.40 Å R-free 0.284
1S78 Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex Deposited 2004-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–646（624 aa） Fragment：extracellular domain (residues 23-646)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 3350, ammonium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.268
1S78 Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex Deposited 2004-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 23–646（624 aa） Fragment：extracellular domain (residues 23-646)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 3350, ammonium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.268
2A91 Crystal structure of ErbB2 domains 1-3 Deposited 2005-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–530（509 aa） Fragment：residues 1-510 + FLAG peptide
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；PEG 1500, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.264
2JWA ErbB2 transmembrane segment dimer spatial structure Deposited 2007-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 641–684（44 aa） Fragment：UNP residues 641-684
Chain B 641–684（44 aa） Fragment：UNP residues 641-684
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；313 K；Pressure ambient
NMR sample composition 2.0mM [U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.0mM [U-13C; U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0mM [U-13C; U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 1.0mM ErbB2, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KS1 Heterodimeric association of Transmembrane domains of ErbB1 and ErbB2 receptors Enabling Kinase Activation Deposited 2009-12-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 641–684（44 aa） Fragment：ErbB2TM domain, UNP residues 641-684
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；313 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] ErbB1TM-1, 1 mM [U-100% 15N] ErbB2TM-2, 12 mM DMPC-3, 48 mM DHPC-4, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] ErbB1TM-5, 1 mM ErbB2TM-6, 12 mM [U-2H] DMPC-7, 48 mM [U-2H] DHPC-8, 100% D2O | 100% D2O
NMR sample composition 1 mM ErbB1TM-9, 1 mM [U-100% 13C; U-100% 15N] ErbB2TM-10, 12 mM [U-2H] DMPC-11, 48 mM [U-2H] DHPC-12, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] ErbB1TM-13, 1 mM ErbB2TM-14, 12 mM [U-2H] DMPC-15, 48 mM [U-2H] DHPC-16, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2L4K Water refined solution structure of the human Grb7-SH2 domain in complex with the 10 amino acid peptide pY1139 Deposited 2010-10-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1135–1144（10 aa） Fragment：unp residues 1135-1144
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Pressure ambient
NMR sample composition 0.6-0.8 mM [U-100% 13C; U-100% 15N] Grb7-SH2 domain-1, 0.6-0.8 mM [U-100% 13C; U-100% 15N] pY1139 peptide-2, 52.2 mM acetic acid-3, 100 mM sodium chloride-4, 5 mM DTT-5, 1 mM EDTA-6, 0.9 mM sodium azide-7, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N2A Spatial structure of HER2/ErbB2 dimeric transmembrane domain in the presence of cytoplasmic juxtamembrane domains Deposited 2015-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 644–700（57 aa） Fragment：transmembrane domain (UNP residues 644-700)
Chain B 644–700（57 aa） Fragment：transmembrane domain (UNP residues 644-700)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.5；318 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 4 mM [U-100% 2H] DPC, 1 mM [U-100% 13C; U-100% 15N] labeled protein, 1 mM unlabeled protein, 50 mM sodium acetate, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM [U-100% 2H] DPC, 1 mM [U-100% 13C; U-100% 15N] labeled protein, 50 mM sodium acetate, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM [U-100% 2H] DPC, 1 mM [U-100% 13C; U-100% 15N] labeled protein, 50 mM sodium acetate, 0.1 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3BE1 Dual specific bH1 Fab in complex with the extracellular domain of HER2/ErbB-2 Deposited 2007-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–646（624 aa） Fragment：sequence database residues 23-646
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；Crystals of the Fab/HER2 complex were obtained by mixing protein solution (11 mg/ml protein, 25 mM Tris-HCl pH 8 and 150 mM sodium chloride) with crystallization buffer containing 25% w/v PEG2000, 0.1M MES pH 6.5. Before data collection the crystals were flash frozen in liquid nitrogen with 20% Ethylene Glycol as cryo-protectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.90 Å R-free 0.277
3H3B Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain Deposited 2009-04-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–214（192 aa） Fragment：extracellular domain, UNP residues 23-214
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；15% polyethylene glycol 4000, 100mM 3-(1-pyridino)-1-propane sulfonate, 100mM Na cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.45 Å R-free 0.255
3H3B Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21 in complex with residues 1-192 of ErbB2 extracellular domain Deposited 2009-04-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–214（192 aa） Fragment：extracellular domain, UNP residues 23-214
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；15% polyethylene glycol 4000, 100mM 3-(1-pyridino)-1-propane sulfonate, 100mM Na cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.45 Å R-free 0.255
3MZW HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342 Deposited 2010-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–646（624 aa） Fragment：Extracellular domain residues 23-646
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；279 K；0.05M sodium chloride, 7.5% PEG3350, 0.1M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.90 Å R-free 0.278
3N85 Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment Deposited 2010-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 23–646（624 aa） Fragment：UNP residues 23-646
Not recorded CL CHLORIDE ION × 3 SO4 SULFATE ION × 48 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；NaCl, Na/K-phosphate, Li-sulfate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.20 Å R-free 0.230
3PP0 Crystal Structure of the Kinase domain of Human HER2 (erbB2). Deposited 2010-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 706–1009（304 aa） Fragment：kinase domain, residues 706-1009
Mutation：M706A, Q711L, M712L 03Q 2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethoxy}ethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200mM di-Ammonium Tartrate, 100 mM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.25 Å R-free 0.260
3PP0 Crystal Structure of the Kinase domain of Human HER2 (erbB2). Deposited 2010-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 706–1009（304 aa） Fragment：kinase domain, residues 706-1009
Mutation：M706A, Q711L, M712L 03Q 2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethoxy}ethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200mM di-Ammonium Tartrate, 100 mM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.25 Å R-free 0.260
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded 03P N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded 03P N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 713–1028（316 aa） Fragment：UNP residues 713-1028
Chain B 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded 03P N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3RCD HER2 Kinase Domain Complexed with TAK-285 Deposited 2011-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 713–1028（316 aa） Fragment：UNP residues 713-1028
Chain D 713–1028（316 aa） Fragment：UNP residues 713-1028
Not recorded 03P N-{2-[4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethyl}-3-hydroxy-3-methylbutanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3550, 200MM DI-AMMONIUM TARTRATE, 100 MM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.21 Å R-free 0.294
3WLW Molecular Architecture of the ErbB2 Extracellular Domain Homodimer Deposited 2013-11-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–586（564 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；0.1M Ammonium acetate, 0.1M BIS-TRIS pH 5.7, 13% w/v Polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.09 Å R-free 0.269
3WLW Molecular Architecture of the ErbB2 Extracellular Domain Homodimer Deposited 2013-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 23–586（564 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；0.1M Ammonium acetate, 0.1M BIS-TRIS pH 5.7, 13% w/v Polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.09 Å R-free 0.269
3WSQ Structure of HER2 with an Fab Deposited 2014-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–586（564 aa） Fragment：UNP residues 23-586
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.1M sodium malonate pH 7.0, 0.1M HEPES 7.0, 0.5% v/v Jeffamine ED-2001, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.50 Å R-free 0.258
4HRL Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via Binding to the Extracellular Domain of HER2 Deposited 2012-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–219（196 aa） Fragment：N-terminal extracellular domain I, UNP RESIDUES 24-219
Mutation：N46D, N102D, N165D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；293 K；0.2M ammonium acetate, 0.1M sodium citrate, 30% PEG 4000, pH 5.6, vapor diffusion, temperature 293K
Resolution 2.55 Å R-free 0.253
4HRM Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via Binding to the Extracellular Domain of HER2 Deposited 2012-10-28 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 24–219（196 aa） Fragment：N-terminal extracellular domain I, UNP RESIDUES 24-219
Chain C 24–219（196 aa） Fragment：N-terminal extracellular domain I, UNP RESIDUES 24-219
Mutation：N46D, N102D, N165D Mutation：N46D, N102D, N165D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；0.2 M sodium chloride, 0.1 M phosphate citrate, 20% PEG 8000, pH 4.2, vapor diffusion, temperature 293K
Resolution 3.20 Å R-free 0.339
4HRN Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via Binding to the Extracellular Domain of HER2 Deposited 2012-10-28 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 529–625（97 aa） Fragment：Domain IV, UNP RESIDUES 529-625
Chain D 529–625（97 aa） Fragment：Domain IV, UNP RESIDUES 529-625
Mutation：N8D, N49D Mutation：N8D, N49D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；293 K；0.05M succinic acid, 29% ammonium sulfate, pH 4.0, vapor diffusion, temperature 293K
Resolution 2.65 Å R-free 0.249
4HRN Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via Binding to the Extracellular Domain of HER2 Deposited 2012-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 529–625（97 aa） Fragment：Domain IV, UNP RESIDUES 529-625
Mutation：N8D, N49D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；293 K；0.05M succinic acid, 29% ammonium sulfate, pH 4.0, vapor diffusion, temperature 293K
Resolution 2.65 Å R-free 0.249
4HRN Structural Basis for Eliciting a Cytotoxic Effect in HER2-Overexpressing Cancer Cells via Binding to the Extracellular Domain of HER2 Deposited 2012-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 529–625（97 aa） Fragment：Domain IV, UNP RESIDUES 529-625
Mutation：N8D, N49D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；293 K；0.05M succinic acid, 29% ammonium sulfate, pH 4.0, vapor diffusion, temperature 293K
Resolution 2.65 Å R-free 0.249
4NND Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites Deposited 2013-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1109–1114（6 aa） Fragment：phosphorylated peptide (UNP residues 1109-1114)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.1 M HEPES, 25% PEG3350, 6% Jeffamine M-600, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.291
4NND Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites Deposited 2013-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1109–1114（6 aa） Fragment：phosphorylated peptide (UNP residues 1109-1114)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.1 M HEPES, 25% PEG3350, 6% Jeffamine M-600, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.291
4NND Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites Deposited 2013-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1109–1114（6 aa） Fragment：phosphorylated peptide (UNP residues 1109-1114)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.1 M HEPES, 25% PEG3350, 6% Jeffamine M-600, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.291
4NND Structural basis of PTPN18 fingerprint on distinct HER2 tyrosine phosphorylation sites Deposited 2013-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1109–1114（6 aa） Fragment：phosphorylated peptide (UNP residues 1109-1114)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.1 M HEPES, 25% PEG3350, 6% Jeffamine M-600, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.291
5K33 Crystal structure of extracellular domain of HER2 in complex with Fcab STAB19 Deposited 2016-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 23–629（607 aa）
Not recorded GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.05 M MES, 10% w/v PEG3350
Resolution 3.30 Å R-free 0.271
5KWG Crystal structure of extracellular domain of HER2 in complex with Fcab H10-03-6 Deposited 2016-07-18 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 23–653（631 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；50 mM Citric acid, 18% (w/v) PEG 3350
Resolution 4.30 Å R-free 0.369
5MY6 Crystal structure of a HER2-Nb complex Deposited 2017-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–645（622 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；293.15 K；100 mM HEPES pH 7.25, 10% 2-propanol, 22% PEG 4000
Resolution 2.25 Å R-free 0.220
5O4G HER2 in complex with Fab MF3958 Deposited 2017-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 23–628（606 aa） Fragment：UNP residues 23-628
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M MES pH 6.0, 15% PEG 6000
Resolution 3.00 Å R-free 0.271
5OB4 NMR spatial structure of HER2 TM domain dimer in DPC micelles. Deposited 2017-06-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–74（44 aa） Fragment：UNP residues 31-74
Chain B 31–74（44 aa） Fragment：UNP residues 31-74
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 30；Pressure AMBIENT
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] HER2TM, 2.5 mM HER2TM, 200 mM [U-99% 2H] DPC, 20 mM potassium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6ATT 39S Fab bound to HER2 ecd Deposited 2017-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–652（630 aa） Fragment：UNP residues 23-652
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；PEG8000, ethylene glycol, MES buffer
Resolution 3.77 Å R-free 0.289
6BGT Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain Deposited 2017-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–652（652 aa） Fragment：UNP residues 1-652
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；100 mM MES, pH 6.5, 18% PEG3350, 10% glycerol
Resolution 2.70 Å R-free 0.247
6J71 HuA21-scFv in complex with the extracellular domain(ECD) of HER2 Deposited 2019-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–639（618 aa）
Not recorded BMA beta-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M MES monohydrate pH 6.5, 12% (w/v) PEG 20,000
Resolution 2.92 Å R-free 0.267
6LBX Crystal structure of HER2 Domain IV and Rb-H2 Deposited 2019-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 531–626（96 aa） Fragment：Domain IV
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；290 K；0.1M Sodium Citrate/Citric Acid (pH 5.5), 20% PEG 3000
Resolution 2.03 Å R-free 0.228
6OGE Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex Deposited 2019-04-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 23–644（622 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7JXH HER2 in complex with JBJ-08-178-01 Deposited 2020-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 703–1024（322 aa） Fragment：kinase domain
Not recorded VOY (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350
Resolution 3.27 Å R-free 0.285
7MN5 Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain Deposited 2021-04-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1029（1029 aa） Fragment：Extracellular Domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7MN6 Structure of the HER2 S310F/HER3/NRG1b Heterodimer Extracellular Domain Deposited 2021-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1029（1029 aa） Fragment：Extracellular Domain
Mutation：S310F NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7MN8 Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain bound to Trastuzumab Fab Deposited 2021-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–1029（1029 aa）
Mutation：S310F NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7PCD HER2 IN COMPLEX WITH A COVALENT INHIBITOR Deposited 2021-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–1029（327 aa） Fragment：NONE
Not recorded 70I 1-[4-[4-[[3,5-bis(chloranyl)-4-([1,2,4]triazolo[1,5-a]pyridin-7-yloxy)phenyl]amino]pyrimido[5,4-d]pyrimidin-6-yl]piperazin-1-yl]-4-(3-fluoranylazetidin-1-yl)butan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.75；293 K；18% PEG3350, 50mM ammonium tartrate, 150mM sodium tartrate and 100mM BIS-TRIS
Resolution 1.77 Å R-free 0.241
7QVK NM-02 in complex with HER2-ECD Deposited 2022-01-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 23–646（624 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；13% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol
Resolution 3.10 Å R-free 0.330
8HGO The EGF-bound EGFR/HER2 ectodomain complex Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–693（693 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM Hepes, 150mM NaCl, 0.02%DDM-0.002%CHS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8HGP The EREG-bound EGFR/HER2 ectodomain complex Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–693（693 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
8JYR Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I Deposited 2023-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–216（194 aa） Fragment：domain I
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate pH5.5, 20% w/v PEG3000
Resolution 1.69 Å R-free 0.209
8PWH Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex Deposited 2023-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 23–646（624 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8Q6J Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex Deposited 2023-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 23–646（624 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8U4K Structure of the HER2/HER4/BTC Heterodimer Extracellular Domain Deposited 2023-09-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 24–629（606 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
8U4L Structure of the HER2/HER4/NRG1b Heterodimer Extracellular Domain Deposited 2023-09-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 24–629（606 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8U8X crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase domain in complex with inhibitor compound 27 Deposited 2023-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 694–1029（336 aa） Fragment：kinase domain
Mutation：YVMA inserted after residue 84 W9N 1-{(1R,3r,5S)-3-[(3M)-4-methyl-3-{3-methyl-4-[(1-methyl-1H-benzimidazol-5-yl)oxy]phenyl}-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-8-azabicyclo[3.2.1]octan-8-yl}propan-1-one × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；8% PEG 3350, 0.1M Tris pH8.5, 0.5M NaCl
Resolution 1.69 Å R-free 0.203
8VB5 Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with tucatinib Deposited 2023-12-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 703–1029（327 aa）
Not recorded A1AAC Tucatinib × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bicine pH 8.5, 11% w/v PEG 1500, 0.5mM Tucatinib
Resolution 1.48 Å R-free 0.187
8VQD HER2 S310F in complex with TL1 Fab Deposited 2024-01-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–652（630 aa）
Mutation：S310F No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 150mM NaCl, 0.7mM fluorinated octyl maltoside
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out with blot force 5, blot time 4 s
Resolution 2.61 Å
8VQE Homodimeric structure of HER2 S310F extracellular region Deposited 2024-01-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–652（630 aa）
Chain B 23–652（630 aa）
Mutation：S310F Mutation：S310F No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 150mM NaCl, 0.7mM Fluorinated octyl maltoside
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified
Resolution 2.67 Å
9IUT Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide Deposited 2024-07-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 611–618（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M MgCl2, 0.1 M Bis-Tris pH 5.7, 25% w/v PEG 3350
Resolution 2.09 Å R-free 0.236
9IUT Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide Deposited 2024-07-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 611–618（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M MgCl2, 0.1 M Bis-Tris pH 5.7, 25% w/v PEG 3350
Resolution 2.09 Å R-free 0.236
9L1S Structure of the HER2 (S310F) - pertuzumab (T30S/D31A) complex Deposited 2024-12-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–652（630 aa）
Mutation：S310F No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9MTE CryoEM structure of extracellular domain of human HER2 complexed with two nano-bodies 27A05 and 47D05 Deposited 2025-01-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 23–652（630 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Hepes pH7.5, 150 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；BF4 Bt4
Resolution 2.66 Å
9MTX CryoEM structure of extracellular domain of human HER2 complexed with nano-bodies 29E09 Deposited 2025-01-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–652（630 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM Hepes pH7.5, 150 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9QBF HER2/ErbB2 extracellular domain (ECD) in compact conformation in complex with trastuzumab (TZB) antibody Deposited 2025-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–1029（1007 aa）
Mutation：Del1-22,Del1030-1255,C789S,C805S,C965S. No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QBG HER2/ErbB2 extracellular domain (ECD) in extended conformation in complex with trastuzumab (TZB) antibody Deposited 2025-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–1029（1007 aa）
Mutation：Del1-22,Del1030-1255,C789S,C805S,C965S. No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9QBH HER2/ErbB2 extracellular domain (ECD) from a near full-length construct solubilized in amphipols. Deposited 2025-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–1029（1007 aa）
Mutation：Del1-22,Del1030-1255,C789S,C805S,C965S. No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.77 Å
9T3R Structure of human HER2 in complex with EPS232 Fab Deposited 2025-10-29 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–652（630 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9T3S Structure of human HER2 in complex with EPS226 Fab Deposited 2025-10-29 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–652（630 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

57 other PDB entries and 80 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERBB2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain X； PDBConstruct 1–622； UniProt 23–644

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8ffj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ffj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ffj
Deposition date deposition_date2022-12-08
Structure title titleStructure of Zanidatamab bound to HER2
Keywords keywordsAntibody, biparatopic, TRANSFERASE-IMMUNE SYSTEM complex; TRANSFERASE/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.31 Å
Radius of gyration Rg (electron density) rg_electron40.98 Å
Forward intensity I(0) i0265684000.00
Molecular weight molecular_weight127910.0 kDa
Excluded volume excluded_volume158140 ų
Envelope volume envelope_volume227620 ų
Hydration-shell volume shell_volume48743 ų
Envelope diameter envelope_diameter138.3 Å
Shell Rg shell_rg43.44 Å
Envelope Rg envelope_rg40.46 Å
Shape Rg shape_rg40.94 Å
Total Rg total_rg41.26 Å
Total atoms total_atoms17582
Residues n_residues1164
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax135.2 Å
Rg (real space) rg_real41.34 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real2.6570e+08
I(0) uncertainty (real space) i0_real_error4.0110e+06
Rg (reciprocal space) rg_reciprocal41.31 Å
I(0) (reciprocal space) i0_reciprocal265700000.0000
Solution quality estimate total_estimate0.8901
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.8 Å
Skewness Skewness skewness0.271
Kurtosis Kurtosis kurtosis-0.547
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16890000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.736
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)