5o4o

HER3 in complex with Fab MF3178

Method: X-RAY DIFFRACTION D_max: 148.8 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor tyrosine-protein kinase erbB-3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 2 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–643	Not recorded	MF3178 FAB light chain × 1 MF3178 FAB heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M bis tris propane pH 8.5, 0.2 M potassium thyocianate and 20% w/v PEG 3350	Resolution 3.40 Å R-free 0.261

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 5O4O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M6B Structure of the HER3 (ERBB3) Extracellular Domain Deposited 2002-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–640（621 aa） Fragment：Extracellular Domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；pH 9.0, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.60 Å R-free 0.294
1M6B Structure of the HER3 (ERBB3) Extracellular Domain Deposited 2002-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–640（621 aa） Fragment：Extracellular Domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；pH 9.0, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.60 Å R-free 0.294
2L9U Spatial structure of dimeric ErbB3 transmembrane domain Deposited 2011-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 639–670（32 aa） Fragment：UNP RESIDUES 640-670 Chain B 639–670（32 aa） Fragment：UNP RESIDUES 640-670	Mutation：K639R Mutation：K639R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；313 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] ErbB3tm-1, 1 mM ErbB3tm-2, 80 mM [U-99% 2H] DPC-3, 1 mM sodium azide-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] ErbB3tm-5, 1 mM ErbB3tm-6, 80 mM [U-99% 2H] DPC-7, 1 mM sodium azide-8, 100% D2O \| 100% D2O	Resolution not provided
3KEX Crystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3 (HER3) Deposited 2009-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 698–1019（322 aa） Fragment：UNP residues 698-1019 Chain B 698–1019（322 aa） Fragment：UNP residues 698-1019	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5mM AMP-PNP, 2mM MgCl2, 1mM DTT, 1mM TCEP, 0.1M Tris pH8.5, 0.2M lithium sulfate, 25% w/v PEG 3350 supplemented with 0.2% w/v 1,2- Diaminocyclohexane sulfate, 0.2% w/v Diloxanite Furoate, 0.2% w/v Fumaric Acid, 0.2% w/v Spermine, 0.2% w/v Sulfaguanidine, 0.02M Hepes sodium pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.283
3KEX Crystal structure of the catalytically inactive kinase domain of the human epidermal growth factor receptor 3 (HER3) Deposited 2009-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 698–1019（322 aa） Fragment：UNP residues 698-1019 Chain B 698–1019（322 aa） Fragment：UNP residues 698-1019	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5mM AMP-PNP, 2mM MgCl2, 1mM DTT, 1mM TCEP, 0.1M Tris pH8.5, 0.2M lithium sulfate, 25% w/v PEG 3350 supplemented with 0.2% w/v 1,2- Diaminocyclohexane sulfate, 0.2% w/v Diloxanite Furoate, 0.2% w/v Fumaric Acid, 0.2% w/v Spermine, 0.2% w/v Sulfaguanidine, 0.02M Hepes sodium pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.283
3LMG Crystal structure of the ERBB3 kinase domain in complex with AMP-PNP Deposited 2010-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 684–1020（337 aa） Fragment：Tyrosine Kinase Domain (UNP residues 684-1020)	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；50 mM MOPS pH7.4, 27% (w/v) PEG8000, 0.17 M ammonium sulfate and 15%(v/v) glycerol in well solution and 5mM MgCl2 and 1mM AMP-PNP in protein solution, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.285
3LMG Crystal structure of the ERBB3 kinase domain in complex with AMP-PNP Deposited 2010-01-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 684–1020（337 aa） Fragment：Tyrosine Kinase Domain (UNP residues 684-1020)	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；50 mM MOPS pH7.4, 27% (w/v) PEG8000, 0.17 M ammonium sulfate and 15%(v/v) glycerol in well solution and 5mM MgCl2 and 1mM AMP-PNP in protein solution, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.285
3P11 anti-EGFR/HER3 Fab DL11 in complex with domains I-III of the HER3 extracellular region Deposited 2010-09-29	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 A 20–532（513 aa） Fragment：domains I-III, UNP residues 20-532	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；295 K；PEG 1500, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.70 Å R-free 0.323
4LEO Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular domains of human Her3 (ERBB3) Deposited 2013-06-26	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 C 20–631（612 aa） Fragment：UNP residues 20-631	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350 , pH pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.64 Å R-free 0.258
4P59 HER3 extracellular domain in complex with Fab fragment of MOR09825 Deposited 2014-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–646（627 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM bis-tris pH 6.5, 16% (w/v) PEG 10000	Resolution 3.40 Å R-free 0.250
4RIW Crystal structure of an EGFR/HER3 kinase domain heterodimer Deposited 2014-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7 mg/mL protein, 0.1M HEPES pH 7.5, 14% PEG-6000, 0.2M magnesium chloride, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.287
4RIW Crystal structure of an EGFR/HER3 kinase domain heterodimer Deposited 2014-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；7 mg/mL protein, 0.1M HEPES pH 7.5, 14% PEG-6000, 0.2M magnesium chloride, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.287
4RIX Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-Q790R mutation Deposited 2014-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Mutation：Q790R	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10 mg/mL protein, 0.1M HEPES pH 7.5, 15% PEG-5000 MME, 5mM magnesium chloride, 0.5M ammonium acetate, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.258
4RIX Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-Q790R mutation Deposited 2014-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Mutation：Q790R	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10 mg/mL protein, 0.1M HEPES pH 7.5, 15% PEG-5000 MME, 5mM magnesium chloride, 0.5M ammonium acetate, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.258
4RIY Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-E909G mutation Deposited 2014-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Mutation：E909G	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10 mg/mL protein, 0.1M HEPES pH 7.5, 15% PEG-5000 MME, 5mM magnesium chloride, 0.5M ammonium acetate, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.98 Å R-free 0.267
4RIY Crystal structure of an EGFR/HER3 kinase domain heterodimer containing the cancer-associated HER3-E909G mutation Deposited 2014-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 698–1020（323 aa） Fragment：KINASE DOMAIN, UNP residues 698-1020	Mutation：E909G	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10 mg/mL protein, 0.1M HEPES pH 7.5, 15% PEG-5000 MME, 5mM magnesium chloride, 0.5M ammonium acetate, 2mM AMP-PNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.98 Å R-free 0.267
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–641（622 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–641（622 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–641（622 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 20–641（622 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5O7P HER3 in complex with Fab MF3178 Deposited 2017-06-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–643（643 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M bis tris propane pH 7.5, 0.15 sodium citrate, 20% w/v PEG 3350	Resolution 4.50 Å R-free 0.296
6KBI Crystal structure of ErbB3 N418Q mutant Deposited 2019-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–639（620 aa） Chain B 20–639（620 aa）	Mutation：N418Q Mutation：N418Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M lithium sulfate, 0.1 M Tris buffer (pH 8.5) and 11% (w/v) PEG4000.	Resolution 3.00 Å R-free 0.278
6OP9 HER3 pseudokinase domain bound to bosutinib Deposited 2019-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 674–1001（328 aa）	Not recorded	DB8 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；10% PEG 20000, 0.1M MES, pH 6.7	Resolution 2.50 Å R-free 0.230
7BHE DARPin_D5/Her3 domain 4 complex, monoclinic crystals Deposited 2021-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 500–643（144 aa）	Not recorded	GOL GLYCEROL × 2 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.83；293 K；0.1 M Na citrate, 12% PEG4000, 0.2 M Li sulfate	Resolution 2.30 Å R-free 0.254
7BHE DARPin_D5/Her3 domain 4 complex, monoclinic crystals Deposited 2021-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 500–643（144 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.83；293 K；0.1 M Na citrate, 12% PEG4000, 0.2 M Li sulfate	Resolution 2.30 Å R-free 0.254
7BHF DARPin_D5/Her3 domain 4 complex, orthorhombic crystals Deposited 2021-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 441–571（131 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.74；293 K；0.1 M Na citrate, 10% PEG4000, 0.2 M Li sulfate	Resolution 2.00 Å R-free 0.243
7BHF DARPin_D5/Her3 domain 4 complex, orthorhombic crystals Deposited 2021-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 441–571（131 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.74；293 K；0.1 M Na citrate, 10% PEG4000, 0.2 M Li sulfate	Resolution 2.00 Å R-free 0.243
7D85 Crystal structure of anti-ErbB3 Fab ISU104 in complex with human ErbB3 extracellular domain 3 Deposited 2020-10-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 328–519（192 aa） Fragment：extracellular domain 3	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium acetate, 20%(w/v) PEG 3350	Resolution 2.50 Å R-free 0.258
7D85 Crystal structure of anti-ErbB3 Fab ISU104 in complex with human ErbB3 extracellular domain 3 Deposited 2020-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 328–519（192 aa） Fragment：extracellular domain 3	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Sodium acetate, 20%(w/v) PEG 3350	Resolution 2.50 Å R-free 0.258
7MN5 Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain Deposited 2021-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1021（1021 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1021（1021 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 3.09 Å
7MN8 Structure of the HER2/HER3/NRG1b Heterodimer Extracellular Domain bound to Trastuzumab Fab Deposited 2021-04-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1021（1021 aa）	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 3.45 Å
8YRY HER3 in complex with FAb Hu3f8 Deposited 2024-03-22	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 71–205（135 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
9I1Q HER3 receptor in complex with the Fab fragment of TK-hu A3 monoclonal antibody Deposited 2025-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–643（624 aa） Chain C 20–643（624 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M KSCN, 0.1 M BIS-TRIS propane pH 8.5, 14% PEG 3350	Resolution 2.80 Å R-free 0.263
9I1Q HER3 receptor in complex with the Fab fragment of TK-hu A3 monoclonal antibody Deposited 2025-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 20–643（624 aa） Chain D 20–643（624 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 SCN THIOCYANATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M KSCN, 0.1 M BIS-TRIS propane pH 8.5, 14% PEG 3350	Resolution 2.80 Å R-free 0.263

22 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERBB3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–643； UniProt 1–643

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5o4o
Deposition date deposition_date	2017-05-30
Structure title title	HER3 in complex with Fab MF3178
Keywords keywords	HER3 ectodomain, complex, Fab, immune system; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.89 Å
Radius of gyration Rg (electron density) rg_electron	41.19 Å
Forward intensity I(0) i0	125170000.00
Molecular weight molecular_weight	86509.0 kDa
Excluded volume excluded_volume	106820 Å³
Envelope volume envelope_volume	161380 Å³
Hydration-shell volume shell_volume	36089 Å³
Envelope diameter envelope_diameter	152.4 Å
Shell Rg shell_rg	40.93 Å
Envelope Rg envelope_rg	41.41 Å
Shape Rg shape_rg	41.11 Å
Total Rg total_rg	41.40 Å
Total atoms total_atoms	6065
Residues n_residues	776
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	148.8 Å
Rg (real space) rg_real	41.40 Å
Rg uncertainty (real space) rg_real_error	2.13 Å
I(0) (real space) i0_real	1.2520e+08
I(0) uncertainty (real space) i0_real_error	2.6360e+06
Rg (reciprocal space) rg_reciprocal	40.90 Å
I(0) (reciprocal space) i0_reciprocal	125100000.0000
Solution quality estimate total_estimate	0.7466
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.607
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7247000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.549; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.350; Smooth: 0.704

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MF3178 FAB light chain
Molecular weight formula_weight	23283.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6065

DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	MF3178 FAB heavy chain
Molecular weight formula_weight	26981.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGWSCIILFLVLLLAQPAMAQVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARDHGSRHFWSYWGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCAAA

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Receptor tyrosine-protein kinase erbB-3
Molecular weight formula_weight	71601.3 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRANDALQVLGLLFSLARGSEVGNSQAVCPGTLNGLSVTGDAENQYQTLYKLYERCEVVMGNLEIVLTGHNADLSFLQWIREVTGYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVMLNYNTNSSHALRQLRLTQLTEILSGGVYIEKNDKLCHMDTIDWRDIVRDRDAEIVVKDNGRSCPPCHEVCKGRCWGPGSEDCQTLTKTICAPQCNGHCFGPNPNQCCHDECAGGCSGPQDTDCFACRHFNDSGACVPRCPQPLVYNKLTFQLEPNPHTKYQYGGVCVASCPHNFVVDQTSCVRACPPDKMEVDKNGLKMCEPCGGLCPKACEGTGSGSRFQTVDSSNIDGFVNCTKILGNLDFLITGLNGDPWHKIPALDPEKLNVFRTVREITGYLNIQSWPPHMHNFSVFSNLTTIGGRSLYNRGFSLLIMKNLNVTSLGFRSLKEISAGRIYISANRQLCYHHSLNWTKVLRGPTEERLDIKHNRPRRDCVAEGKVCDPLCSSGGCWGPGPGQCLSCRNYSRGGVCVTHCNFLNGEPREFAHEAECFSCHPECQPMEGTATCNGSGSDTCAQCAHFRDGPHCVSSCPHGVLGAKGPIYKYPDVQNECRPCHENCTQGCKGPELQDCLGQTLVLIGKTHLTHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5o4oA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o4oA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o4oB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	64.380 Å
Unit-cell length b length_b	144.020 Å
Unit-cell length c length_c	218.756 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	59.971 Å
R factor r_factor	0.2171
R_work r_work	0.2148
R_free r_free	0.2610

fit	/app/data/saxs_computation/o4/5o4o/5o4o.fit
pddf	/app/data/pr_computation/o4/5o4o/5o4o.pr.out
profile	/app/data/saxs_computation/o4/5o4o/5o4o.dat

HER3 in complex with Fab MF3178

1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor tyrosine-protein kinase erbB-3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)