[English] 日本語
Yorodumi
- PDB-5v6m: Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v6m
TitleCrystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB
Components
  • Envelope glycoprotein gp120 V3 peptide of Con B sequence
  • Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
  • Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / V3 / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Dectin-2 family / 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 / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...Dectin-2 family / 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 / positive regulation of cell growth / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074286 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: J. Virol. / Year: 2018
Title: Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120.
Authors: Pan, R. / Qin, Y. / Banasik, M. / Lees, W. / Shepherd, A.J. / Cho, M.W. / Kong, X.P.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
H: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3
P: Envelope glycoprotein gp120 V3 peptide of Con B sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4024
Polymers47,3623
Non-polymers401
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-47 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.846, 83.870, 90.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-693-

HOH

21H-697-

HOH

-
Components

#1: Antibody Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3


Mass: 23384.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A3


Mass: 22305.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens
#3: Protein/peptide Envelope glycoprotein gp120 V3 peptide of Con B sequence


Mass: 1671.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P20871*PLUS
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 32% polyethylene glycol 6000, 1 M LiCL, 0.1 M Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.978637 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978637 Å / Relative weight: 1
ReflectionResolution: 1.9→39.9 Å / Num. obs: 38386 / % possible obs: 99.8 % / Redundancy: 13.3 % / Net I/σ(I): 31.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 6070 / CC1/2: 0.94 / Rsym value: 0.46 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXmodel building
PHENIXphasing
PHENIX1.11.1_2575refinement
RefinementResolution: 1.9→39.861 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2243 1917 4.99 %
Rwork0.1785 --
obs0.1808 38386 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 1 668 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063391
X-RAY DIFFRACTIONf_angle_d0.8554625
X-RAY DIFFRACTIONf_dihedral_angle_d13.5542019
X-RAY DIFFRACTIONf_chiral_restr0.057534
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.29971340.23072505X-RAY DIFFRACTION98
1.9475-2.00020.27511270.20982553X-RAY DIFFRACTION100
2.0002-2.0590.23991300.20072588X-RAY DIFFRACTION100
2.059-2.12550.24051330.20212583X-RAY DIFFRACTION100
2.1255-2.20150.26931500.19222561X-RAY DIFFRACTION100
2.2015-2.28960.22111280.19242585X-RAY DIFFRACTION100
2.2896-2.39380.26831460.19992573X-RAY DIFFRACTION100
2.3938-2.520.27461280.22627X-RAY DIFFRACTION100
2.52-2.67780.2731320.20252584X-RAY DIFFRACTION100
2.6778-2.88450.25081430.20212599X-RAY DIFFRACTION100
2.8845-3.17470.22111410.18972613X-RAY DIFFRACTION100
3.1747-3.63380.19661350.16322649X-RAY DIFFRACTION100
3.6338-4.57720.1891380.14552671X-RAY DIFFRACTION100
4.5772-39.86980.18851520.15312778X-RAY DIFFRACTION100

+
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