[English] 日本語
Yorodumi
- PDB-6v6w: Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) i... -

+
Open data


ID or keywords:

Loading...

-
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


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

-
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

-
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)

-
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


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more