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- PDB-6v6w: Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) i... -

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Basic information

Entry
Database: PDB / ID: 6v6w
TitleCrystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 Fab Heavy chain
  • 35O22 Fab Light chain
  • B11 DSS Fab heavy chain
  • B11 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 gp160 / glycan supersite / human antibody / immune system / viral-protein complex / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.5 Å
AuthorsKumar, S. / Wilson, I.A.
CitationJournal: Sci Adv / Year: 2020
Title: A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite
Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / ...Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / Ge, X. / Su, B. / Landais, E. / Sok, D. / Zwick, M.B. / He, L. / Zhu, J. / Wilson, I.A. / Shao, Y.
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 35O22 Fab Heavy chain
E: 35O22 Fab Light chain
G: Envelope glycoprotein gp120
I: B11 DSS Fab heavy chain
J: B11 Fab light chain
T: Envelope glycoprotein gp41
A: 35O22 Fab Heavy chain
B: 35O22 Fab Light chain
C: Envelope glycoprotein gp120
F: B11 DSS Fab heavy chain
H: B11 Fab light chain
K: Envelope glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,68342
Polymers335,20612
Non-polymers9,47730
Water0
1
D: 35O22 Fab Heavy chain
E: 35O22 Fab Light chain
G: Envelope glycoprotein gp120
I: B11 DSS Fab heavy chain
J: B11 Fab light chain
T: Envelope glycoprotein gp41
hetero molecules

D: 35O22 Fab Heavy chain
E: 35O22 Fab Light chain
G: Envelope glycoprotein gp120
I: B11 DSS Fab heavy chain
J: B11 Fab light chain
T: Envelope glycoprotein gp41
hetero molecules

D: 35O22 Fab Heavy chain
E: 35O22 Fab Light chain
G: Envelope glycoprotein gp120
I: B11 DSS Fab heavy chain
J: B11 Fab light chain
T: Envelope glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,02563
Polymers502,81018
Non-polymers14,21545
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
A: 35O22 Fab Heavy chain
B: 35O22 Fab Light chain
C: Envelope glycoprotein gp120
F: B11 DSS Fab heavy chain
H: B11 Fab light chain
K: Envelope glycoprotein gp41
hetero molecules

A: 35O22 Fab Heavy chain
B: 35O22 Fab Light chain
C: Envelope glycoprotein gp120
F: B11 DSS Fab heavy chain
H: B11 Fab light chain
K: Envelope glycoprotein gp41
hetero molecules

A: 35O22 Fab Heavy chain
B: 35O22 Fab Light chain
C: Envelope glycoprotein gp120
F: B11 DSS Fab heavy chain
H: B11 Fab light chain
K: Envelope glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,02563
Polymers502,81018
Non-polymers14,21545
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)148.534, 148.534, 843.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A1 - 222
211chain 'D'D1 - 222
112chain 'B'B2 - 9
122chain 'B'B11 - 210
212chain 'E'E2 - 9
222chain 'E'E11 - 210
113chain 'C'C33 - 140
123chain 'C'C149 - 185
133chain 'C'C188 - 309
143chain 'C'C312 - 401
153chain 'C'C410 - 508
163chain 'C'C515 - 516
173chain 'C'C534 - 538
183chain 'C'C541 - 542
193chain 'C'C545
1103chain 'C'C547
1113chain 'C'C553
1123chain 'C'C588
1133chain 'C'C598
1143chain 'C'C611
1153chain 'C'C613
213chain 'G'G33 - 140
223chain 'G'G149 - 185
233chain 'G'G188 - 309
243chain 'G'G312 - 401
253chain 'G'G410 - 508
263chain 'G'G515 - 516
273chain 'G'G534 - 538
283chain 'G'G541 - 542
293chain 'G'G545
2103chain 'G'G547
2113chain 'G'G553
2123chain 'G'G588
2133chain 'G'G598
2143chain 'G'G611
2153chain 'G'G613
114chain 'F'F1 - 96
124chain 'F'F100 - 129
134chain 'F'F132 - 216
214chain 'I'I1 - 96
224chain 'I'I100 - 129
234chain 'I'I132 - 216
115chain 'H'H1 - 211
215chain 'J'J1 - 211
116chain 'K'K518 - 547
126chain 'K'K569 - 664
136chain 'K'K666 - 667
146chain 'K'K669
216chain 'T'T518 - 547
226chain 'T'T569 - 664
236chain 'T'T666 - 667
246chain 'T'T669

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Envelope glycoprotein ... , 2 types, 4 molecules GCTK

#3: Protein Envelope glycoprotein gp120 /


Mass: 53737.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#6: Protein Envelope glycoprotein gp41 / Env polyprotein


Mass: 15702.743 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S9

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Antibody , 4 types, 8 molecules DAEBIFJH

#1: Antibody 35O22 Fab Heavy chain


Mass: 26171.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Antibody 35O22 Fab Light chain


Mass: 23318.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#4: Antibody B11 DSS Fab heavy chain


Mass: 25227.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#5: Antibody B11 Fab light chain


Mass: 23444.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Sugars , 4 types, 30 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 12% 1-propanol, 0.1M MES (pH=6.5), 20% polyethylene glycol monomethyl ether 5000, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 6.5→50 Å / Num. obs: 13313 / % possible obs: 97.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 233.87 Å2 / CC1/2: 0.85 / Rpim(I) all: 0.09 / Net I/σ(I): 1
Reflection shellResolution: 6.5→6.62 Å / Num. unique obs: 638 / CC1/2: 0.62 / Rpim(I) all: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
HKL-2000data scaling
HKL-2000data processing
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UTK

6utk


Resolution: 6.5→46.72 Å / SU ML: 1.3366 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 42.6069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3552 666 5.02 %
Rwork0.3089 12592 -
obs0.3112 13258 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 279.19 Å2
Refinement stepCycle: LAST / Resolution: 6.5→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23434 0 0 0 23434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003423968
X-RAY DIFFRACTIONf_angle_d0.642832614
X-RAY DIFFRACTIONf_chiral_restr0.09363792
X-RAY DIFFRACTIONf_plane_restr0.00534126
X-RAY DIFFRACTIONf_dihedral_angle_d13.54958844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5-70.44421340.37062507X-RAY DIFFRACTION97.02
7-7.70.37291340.34552562X-RAY DIFFRACTION98.97
7.7-8.810.33011320.29462450X-RAY DIFFRACTION94.47
8.81-11.080.31871330.26422543X-RAY DIFFRACTION98.6
11.08-46.720.36151330.31932530X-RAY DIFFRACTION96.87

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