[English] 日本語
Yorodumi
- PDB-5cd3: Structure of immature VRC01-class antibody DRVIA7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cd3
TitleStructure of immature VRC01-class antibody DRVIA7
Components
  • DRVIA7 Heavy Chain
  • DRVIA7 Light Chain
KeywordsIMMUNE SYSTEM / VRC01 / HIV-1 / CD4 binding site / gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKong, L. / Wilson, I.A.
CitationJournal: Immunity / Year: 2016
Title: Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / ...Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / Yanling Hao / Yi Feng / Fernando Garces / Richard Wilson / Kaifan Dai / Sijy O'Dell / Krisha McKee / John R Mascola / Andrew B Ward / Richard T Wyatt / Yuxing Li / Ian A Wilson / Jiang Zhu / Yiming Shao /
Abstract: VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain ...VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain elusive. We demonstrated how VRC01-class antibodies emerged in a Chinese donor by antigen-specific single B cell sorting, structural and functional studies, and longitudinal antibody and virus repertoire analyses. A monoclonal antibody DRVIA7 with modest neutralizing breadth was isolated that displayed a subset of VRC01 signatures. X-ray and EM structures revealed a VRC01-like angle of approach, but less favorable interactions between the DRVIA7 light-chain CDR1 and the N terminus with N276 and V5 glycans of gp120. Although the DRVIA7 lineage was unable to acquire broad neutralization, longitudinal analysis revealed a repertoire-encoded VRC01 light-chain CDR3 signature and VRC01-like neutralizing heavy-chain precursors that rapidly matured within 2 years. Thus, light chain accommodation of the glycan shield should be taken into account in vaccine design targeting this conserved site of vulnerability.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: DRVIA7 Heavy Chain
H: DRVIA7 Light Chain
A: DRVIA7 Heavy Chain
B: DRVIA7 Light Chain
C: DRVIA7 Heavy Chain
D: DRVIA7 Light Chain
E: DRVIA7 Heavy Chain
F: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)189,0248
Polymers189,0248
Non-polymers00
Water00
1
G: DRVIA7 Heavy Chain
H: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area19970 Å2
MethodPISA
2
A: DRVIA7 Heavy Chain
B: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area20010 Å2
MethodPISA
3
C: DRVIA7 Heavy Chain
D: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area19890 Å2
MethodPISA
4
E: DRVIA7 Heavy Chain
F: DRVIA7 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-24 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.829, 73.747, 101.158
Angle α, β, γ (deg.)89.84, 89.40, 89.95
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody
DRVIA7 Heavy Chain


Mass: 24048.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody
DRVIA7 Light Chain


Mass: 23207.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.16 M ammonium sulfate, 20% (w/v) PEG 4000, 20% (v/v) glycerol and 0.08 M sodium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 41586 / % possible obs: 98.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 3.84
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.1 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.542 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 2109 5.08 %
Rwork0.2341 --
obs0.2367 41505 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13172 0 0 0 13172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513500
X-RAY DIFFRACTIONf_angle_d1.22618332
X-RAY DIFFRACTIONf_dihedral_angle_d13.6424872
X-RAY DIFFRACTIONf_chiral_restr0.0512052
X-RAY DIFFRACTIONf_plane_restr0.0062348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.96510.35991510.28372443X-RAY DIFFRACTION91
2.9651-3.03920.31381250.28442693X-RAY DIFFRACTION98
3.0392-3.12140.36781460.28552635X-RAY DIFFRACTION98
3.1214-3.21320.29611550.27592670X-RAY DIFFRACTION98
3.2132-3.31690.33411410.27112682X-RAY DIFFRACTION98
3.3169-3.43540.30781310.25962632X-RAY DIFFRACTION98
3.4354-3.57290.33021340.24862678X-RAY DIFFRACTION98
3.5729-3.73550.28671410.25012653X-RAY DIFFRACTION98
3.7355-3.93230.28421280.23122693X-RAY DIFFRACTION98
3.9323-4.17860.26141460.22032638X-RAY DIFFRACTION98
4.1786-4.5010.26421430.19152640X-RAY DIFFRACTION97
4.501-4.95360.23851520.18912616X-RAY DIFFRACTION97
4.9536-5.66950.25551450.20522604X-RAY DIFFRACTION96
5.6695-7.13960.25251290.2392604X-RAY DIFFRACTION95
7.1396-49.54890.24721420.21052515X-RAY DIFFRACTION93

+
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