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7xq8

Structure of human B-cell antigen receptor of the IgM isotype

Method: ELECTRON MICROSCOPY Dmax: 213.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu

Homo sapiens

UniProt P01871-2

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–474 Chain v； UniProt 1–474 Not recorded Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant × 2 （P01834） B-cell antigen receptor complex-associated protein alpha chain × 1 （P11912） B-cell antigen receptor complex-associated protein beta chain × 1 （P40259） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 7XQ8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7QDO Cryo-EM structure of human monomeric IgM-Fc Deposited 2021-11-27 Different construct 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 105–446（342 aa）
Chain B 105–446（342 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XT6 Structure of a membrane protein M3 Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 109–472（364 aa）
Chain D 109–472（364 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.63 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGHM-2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 141–614； UniProt 1–474 Author chain v； PDBConstruct 141–614； UniProt 1–474

Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant

Homo sapiens

UniProt P01834

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain L； UniProt 1–107 Chain R； UniProt 1–107 Not recorded Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01871-2） B-cell antigen receptor complex-associated protein alpha chain × 1 （P11912） B-cell antigen receptor complex-associated protein beta chain × 1 （P40259） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 7XQ8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A4J DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR Deposited 1998-01-30 Different construct Different mutation/modification 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 L 1–104（104 aa） Fragment：FAB
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；19% PEG 8K, 20% GLYCEROL, 200MM MG(CH3COO)2, 10MM CDS04 100MM BISTRIS PH 6.0
Resolution 2.10 Å R-free 0.292
1A4J DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR Deposited 1998-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa） Fragment：FAB
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；19% PEG 8K, 20% GLYCEROL, 200MM MG(CH3COO)2, 10MM CDS04 100MM BISTRIS PH 6.0
Resolution 2.10 Å R-free 0.292
1A4K DIELS ALDER CATALYTIC ANTIBODY WITH TRANSITION STATE ANALOGUE Deposited 1998-01-30 Different construct Different mutation/modification 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 L 1–104（104 aa） Fragment：FAB
Not recorded CD CADMIUM ION × 2 FRA [4-(4-ACETYLAMINO-PHENYL)-3,5-DIOXO-4-AZA-TRICYCLO[5.2.2.0 2,6]UNDEC-1-YLCARBAMOYLOXY]-ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；17% PEG 8K, 200MM (NH4)2SO4, 10MM CDS0 100MM TRIS PH 8.0
Resolution 2.40 Å R-free 0.291
1A4K DIELS ALDER CATALYTIC ANTIBODY WITH TRANSITION STATE ANALOGUE Deposited 1998-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa） Fragment：FAB
Not recorded CD CADMIUM ION × 2 FRA [4-(4-ACETYLAMINO-PHENYL)-3,5-DIOXO-4-AZA-TRICYCLO[5.2.2.0 2,6]UNDEC-1-YLCARBAMOYLOXY]-ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；17% PEG 8K, 200MM (NH4)2SO4, 10MM CDS0 100MM TRIS PH 8.0
Resolution 2.40 Å R-free 0.291
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Chain L 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.285
1D5I UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；75mM Hepes pH 7.0 9% PEG 4000 150 mM Ammonium Sulfate 20% 1,4 butanediol 100 mM Cadmium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.263
1D6V CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION Deposited 1999-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–104（104 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Not recorded CD CADMIUM ION × 4 HOP (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；9% polyethylene glycol 4000 250mM ammonium sulfate 80mM Cadmium Chloride 75mM Hepes 20% 1,4 butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K
Resolution 2.00 Å R-free 0.264
1HKL FREE AND LIGANDED FORM OF AN ESTEROLYTIC CATALYTIC ANTIBODY Deposited 1996-12-20 Different construct Different mutation/modification 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 L 23–236（214 aa） Fragment：VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.68 Å R-free 0.244
1I7Z ANTIBODY GNC92H2 BOUND TO LIGAND Deposited 2001-03-12 Different construct Different mutation/modification 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 A 1–106（106 aa）
Not recorded COC COCAINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.265
1I7Z ANTIBODY GNC92H2 BOUND TO LIGAND Deposited 2001-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–106（106 aa）
Not recorded COC COCAINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.265
1MIM IGG FAB FRAGMENT (CD25-BINDING) Deposited 1995-12-04 Different construct Different mutation/modification 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 L 135–348（214 aa） Fragment：IGG FAB
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1UCB STRUCTURE OF UNCOMPLEXED FAB COMPARED TO COMPLEX (1CLY, 1CLZ) Deposited 1996-02-06 Different construct Different mutation/modification 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 L 1–106（106 aa） Fragment：MOUSE VH AND VL DOMAINS, HUMAN CL KAPPA AND CH1 IGG1 DOMAINS
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M SODIUM ACETATE (PH 4.6), 0.1 M AMMONIUM SULFATE, 15 % PEG 8000.
Resolution 2.50 Å R-free 0.276
3O11 Anti-beta-amyloid antibody c706 fab in space group c2 Deposited 2010-07-20 Different construct Different mutation/modification 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 L 1–106（106 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；293 K；0.1 M CITRATE PH 3.5, 18% PEG 8000 CRYO CONDITIONS, 0.1 M CITRATE PH 3.5, 25% PEG 8000, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.304
3O11 Anti-beta-amyloid antibody c706 fab in space group c2 Deposited 2010-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–106（106 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；293 K；0.1 M CITRATE PH 3.5, 18% PEG 8000 CRYO CONDITIONS, 0.1 M CITRATE PH 3.5, 25% PEG 8000, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.80 Å R-free 0.304
3QCT Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab fragment Deposited 2011-01-17 Different construct Different mutation/modification 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 L 1–105（105 aa）
Not recorded SO4 SULFATE ION × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES sodium pH 7.5, 2% PEG 400 (v/v), and 1.75 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.15 Å R-free 0.287
3QCU Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0) Deposited 2011-01-17 Different construct Different mutation/modification 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 L 1–105（105 aa）
Not recorded NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.98 Å R-free 0.252
3QCU Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0) Deposited 2011-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–105（105 aa）
Not recorded NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；0.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.98 Å R-free 0.252
3QCV Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (18:2) Deposited 2011-01-17 Different construct Different mutation/modification 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 L 1–105（105 aa）
Not recorded 18L (2R)-2-hydroxy-3-(phosphonooxy)propyl (9Z,12Z)-octadeca-9,12-dienoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.51 Å R-free 0.266
3QCV Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (18:2) Deposited 2011-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–105（105 aa）
Not recorded 18L (2R)-2-hydroxy-3-(phosphonooxy)propyl (9Z,12Z)-octadeca-9,12-dienoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.51 Å R-free 0.266
3U0W AD related murine antibody Fragment Deposited 2011-09-29 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100mM citric acid, 20%(v/v) 2-propanol, 20%(w/v) PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.235
3U7W Crystal structure of NIH45-46 Fab Deposited 2011-10-14 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；12% polyethylene glycol 20,000, 0.1 M sodium acetate pH 5.0, 0.1 M sodium/potassium tartrate, 0.02 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.238
3U7Y Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV Deposited 2011-10-14 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded FLC CITRATE ANION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；12% isopropanol, 10% polyethylene glycol 10,000, 0.1 M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.45 Å R-free 0.256
3VH8 KIR3DL1 in complex with HLA-B*5701 Deposited 2011-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 93–101（9 aa） Fragment：UNP residues 93-101
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；16% PEG 3350, 2% tacsimate pH 5.0, 0.1M tri-sodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.80 Å R-free 0.237
3VH8 KIR3DL1 in complex with HLA-B*5701 Deposited 2011-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 93–101（9 aa） Fragment：UNP residues 93-101
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；16% PEG 3350, 2% tacsimate pH 5.0, 0.1M tri-sodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.80 Å R-free 0.237
3X11 Crystal structure of HLA-B*57:01.I80N.L82R.R83G Deposited 2014-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 93–101（9 aa） Fragment：UNP residues 93-101
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；12-20% PEG4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate pH 5.4., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.15 Å R-free 0.231
3X12 Crystal structure of HLA-B*57:01.I80N Deposited 2014-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 93–101（9 aa） Fragment：UNP residues 1-9
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；12-20% PEG4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate pH 5.4., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.219
4D9R Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D Deposited 2012-01-11 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Resolution 2.42 Å R-free 0.251
4D9R Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D Deposited 2012-01-11 Different construct Different mutation/modification 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 D 1–106（106 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Resolution 2.42 Å R-free 0.251
4YDV STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–106（106 aa） Fragment：HIV ANTIBODY 7B2 LIGHT CHAIN,HIV ANTIBODY 7B2 LIGHT CHAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；298 K；6% PEG 20,000, 5% 2-PROPANOL, 0.1 M CITRIC ACID PH 3.5
Resolution 2.70 Å R-free 0.223
4YDV STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS Deposited 2015-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–106（106 aa） Fragment：HIV ANTIBODY 7B2 LIGHT CHAIN,HIV ANTIBODY 7B2 LIGHT CHAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；298 K；6% PEG 20,000, 5% 2-PROPANOL, 0.1 M CITRIC ACID PH 3.5
Resolution 2.70 Å R-free 0.223
5B38 KIR3DL1*005 in complex with HLA-B*57:01 Deposited 2016-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 93–101（9 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；14 to 18% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6
Resolution 2.30 Å R-free 0.251
5B39 KIR3DL1*015 in complex with HLA-B*57:01 Deposited 2016-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 93–101（9 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；14 to 18% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6
Resolution 2.50 Å R-free 0.229
5C7K Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195 Deposited 2015-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 1–106（106 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；280 K；0.05 M lithium sulfate, 0.05 M sodium sulfate, 26% (w/v) PEG 400 and 0.1 M Tris-HCl pH 8.3
Resolution 4.60 Å R-free 0.295
5ESV Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256. Deposited 2015-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–106（106 aa）
Chain D 1–106（106 aa）
Chain L 1–106（106 aa）
Not recorded ZN ZINC ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG8000, .1M CaCl, 20% MPD, .1M Na Acetate pH 5.5, frozen in 15% sucrose as cryoprotectant
Resolution 3.10 Å R-free 0.259
5ESZ Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244 Deposited 2015-11-17 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；54% isopropanol .1M Tris pH 8.5 Cryo used was 15% 2R3R
Resolution 4.19 Å R-free 0.282
5ESZ Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244 Deposited 2015-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain L 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；54% isopropanol .1M Tris pH 8.5 Cryo used was 15% 2R3R
Resolution 4.19 Å R-free 0.282
5ESZ Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244 Deposited 2015-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；54% isopropanol .1M Tris pH 8.5 Cryo used was 15% 2R3R
Resolution 4.19 Å R-free 0.282
5ESZ Crystal Structure of Broadly Neutralizing Antibody CH04, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade AE Strain A244 Deposited 2015-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；54% isopropanol .1M Tris pH 8.5 Cryo used was 15% 2R3R
Resolution 4.19 Å R-free 0.282
5EWI Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90 Deposited 2015-11-20 Different construct Different mutation/modification 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 L 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；14% PEG400, 13% PEG8000, 0.1M Tris pH 8.5, 0.1M MgCl, No Cryo
Resolution 1.60 Å R-free 0.202
5VEB Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6 Deposited 2017-04-04 Different construct Different mutation/modification 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 B 1–107（107 aa）
Not recorded A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate
Resolution 2.34 Å R-free 0.252
5VEB Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6 Deposited 2017-04-04 Different construct Different mutation/modification 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 L 1–107（107 aa）
Not recorded A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate
Resolution 2.34 Å R-free 0.252
5VIY BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195 Deposited 2017-04-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 1–107（107 aa）
Chain I 1–107（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.20 Å
6AU5 Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant Deposited 2017-08-30 Different construct Different mutation/modification 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 1–106（106 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, pH 4.0, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.227
6AU5 Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant Deposited 2017-08-30 Different construct Different mutation/modification 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 C 1–106（106 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, pH 4.0, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.227
6AXP Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant Deposited 2017-09-07 Different construct Different mutation/modification 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 1–106（106 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate pH 4.0, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.228
6AXP Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant Deposited 2017-09-07 Different construct Different mutation/modification 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 C 1–106（106 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate pH 4.0, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.228
6AYN Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant Deposited 2017-09-08 Different construct Different mutation/modification 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 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.222
6AYN Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant Deposited 2017-09-08 Different construct Different mutation/modification 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 C 1–106（106 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.6 M ammonium sulfate
Resolution 2.48 Å R-free 0.222
6AZK Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant Deposited 2017-09-11 Different construct Different mutation/modification 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 1–106（106 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.8 M ammonium sulfate
Resolution 2.48 Å R-free 0.213
6AZK Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant Deposited 2017-09-11 Different construct Different mutation/modification 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 C 1–106（106 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.8 M ammonium sulfate
Resolution 2.48 Å R-free 0.213
6AZL Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope variant Deposited 2017-09-11 Different construct Different mutation/modification 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 1–106（106 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5.5, 1.8 M ammonium sulfate
Resolution 2.48 Å R-free 0.216
6AZL Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope variant Deposited 2017-09-11 Different construct Different mutation/modification 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 C 1–106（106 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5.5, 1.8 M ammonium sulfate
Resolution 2.48 Å R-free 0.216
6B9Y Trastuzumab Fab v3 in complex with 5-phenyl meditope variant Deposited 2017-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 15% PEG3350, 24 mM NaCl
Resolution 2.14 Å R-free 0.218
6B9Z Trastuzumab Fab v3 Deposited 2017-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG3350
Resolution 1.82 Å R-free 0.189
6BAE Trastuzumab Fab v3 in complex with CQFDLSTRRLKC Deposited 2017-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 24 mM NaCl, 15% PEG 3350
Resolution 2.14 Å R-free 0.224
6BAH Trastuzumab Fab v3 with 5-diphenyl meditope variant Deposited 2017-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG 3350
Resolution 1.90 Å R-free 0.194
6OGE Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex Deposited 2019-04-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–107（107 aa）
Chain D 1–107（107 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
6OKP B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074 Deposited 2019-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain N 1–107（107 aa）
Chain P 1–107（107 aa）
Chain R 1–107（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids
Resolution 3.28 Å
7CZY S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B Deposited 2020-09-09 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain K 1–107（107 aa）
Chain N 1–107（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7CZZ S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B Deposited 2020-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain K 1–107（107 aa）
Chain M 1–107（107 aa）
Chain N 1–107（107 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8C1C Structure of IgE bound to the ectodomain of FceRIa Deposited 2022-12-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain L 1–107（107 aa）
Chain Y 1–107（107 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 4.10 Å
8DAO Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79 Deposited 2022-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000
Resolution 2.80 Å R-free 0.284
8DAO Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79 Deposited 2022-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–107（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000
Resolution 2.80 Å R-free 0.284

44 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IGKC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain L； PDBConstruct 144–250； UniProt 1–107 Author chain R； PDBConstruct 144–250； UniProt 1–107

B-cell antigen receptor complex-associated protein alpha chain

Homo sapiens

UniProt P11912

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–226 Not recorded Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01871-2） Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant × 2 （P01834） B-cell antigen receptor complex-associated protein beta chain × 1 （P40259） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 7XQ8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7WSO Structure of a membrane protein G Deposited 2022-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 33–169（137 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.03 Å
7WSP Structure of a membrane protein M Deposited 2022-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 33–169（137 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 4.09 Å
7XT6 Structure of a membrane protein M3 Deposited 2022-05-16 Different construct 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 33–169（137 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.63 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD79A_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–226； UniProt 1–226

B-cell antigen receptor complex-associated protein beta chain

Homo sapiens

UniProt P40259

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 1–229 Not recorded Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu × 2 （P01871-2） Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant × 2 （P01834） B-cell antigen receptor complex-associated protein alpha chain × 1 （P11912） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 7XQ8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3KG5 Crystal structure of human Ig-beta homodimer Deposited 2009-10-28 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 26–159（134 aa） Fragment：extracellular domain
Chain B 26–159（134 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K
Resolution 3.20 Å R-free 0.263
3KG5 Crystal structure of human Ig-beta homodimer Deposited 2009-10-28 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 26–159（134 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K
Resolution 3.20 Å R-free 0.263
3KG5 Crystal structure of human Ig-beta homodimer Deposited 2009-10-28 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 B 26–159（134 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4；298 K；0.6M Na formate, 100mM Na Acetate, pH 4.0, VAPOR DIFFUSION, temperature 298K
Resolution 3.20 Å R-free 0.263
7WSO Structure of a membrane protein G Deposited 2022-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 44–182（139 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.03 Å
7WSP Structure of a membrane protein M Deposited 2022-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 44–182（139 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 4.09 Å
7XT6 Structure of a membrane protein M3 Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 44–182（139 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.63 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD79B_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–229； UniProt 1–229

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 7xq8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7xq8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7xq8
Deposition date deposition_date2022-05-07
Structure title titleStructure of human B-cell antigen receptor of the IgM isotype
Keywords keywordsimmunology, B cell signalling, adaptive immunity, antibody, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier62.90 Å
Radius of gyration Rg (electron density) rg_electron64.28 Å
Forward intensity I(0) i0522732000.00
Molecular weight molecular_weight176090.0 kDa
Excluded volume excluded_volume213800 ų
Envelope volume envelope_volume414520 ų
Hydration-shell volume shell_volume58686 ų
Envelope diameter envelope_diameter240.5 Å
Shell Rg shell_rg56.86 Å
Envelope Rg envelope_rg63.14 Å
Shape Rg shape_rg64.42 Å
Total Rg total_rg63.64 Å
Total atoms total_atoms12452
Residues n_residues1873
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 dmax213.2 Å
Rg (real space) rg_real63.69 Å
Rg uncertainty (real space) rg_real_error2.17 Å
I(0) (real space) i0_real5.2230e+08
I(0) uncertainty (real space) i0_real_error1.0360e+07
Rg (reciprocal space) rg_reciprocal62.02 Å
I(0) (reciprocal space) i0_reciprocal521100000.0000
Solution quality estimate total_estimate0.8231
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.6 Å
Skewness Skewness skewness0.493
Kurtosis Kurtosis kurtosis-0.467
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0035
Highest regularization parameter α highest_alpha26670000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.733; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.800; Smooth: 0.698
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)