[English] 日本語
Yorodumi
- PDB-4jo2: Crystal structure of rabbit mAb R56 Fab in complex with V3 crown ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jo2
TitleCrystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 Consensus A gp120
Components
  • gp120
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Ig / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / Gp120
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2013
Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans.
Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47512
Polymers94,2356
Non-polymers2406
Water8,629479
1
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers47,1173
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-60 kcal/mol
Surface area18850 Å2
MethodPISA
2
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers47,1173
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-61 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 74.350, 84.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain


Mass: 22782.014 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain


Mass: 21882.527 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide gp120


Mass: 2452.747 Da / Num. of mol.: 2
Fragment: third variable region (V3) crown (UNP residues 30-52)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / References: UniProt: Q9YXH5
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG6000, 1 M lithium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→26.465 Å / Num. obs: 30171 / % possible obs: 99.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.127 / Rsym value: 0.161 / Net I/σ(I): 8.93
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.64 / Rsym value: 0.587 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
Blu-Icelikedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.465 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 1565 5.19 %RANDOM
Rwork0.1895 ---
all0.1934 51241 --
obs0.1934 30171 99.72 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.275 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4203 Å20 Å20.1222 Å2
2--1.0763 Å2-0 Å2
3----0.6561 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 6 479 6815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086478
X-RAY DIFFRACTIONf_angle_d1.1478836
X-RAY DIFFRACTIONf_dihedral_angle_d14.7172240
X-RAY DIFFRACTIONf_chiral_restr0.071054
X-RAY DIFFRACTIONf_plane_restr0.0051134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.28341360.20082841X-RAY DIFFRACTION100
2.5893-2.69290.32441460.21922852X-RAY DIFFRACTION100
2.6929-2.81530.32031610.21492831X-RAY DIFFRACTION100
2.8153-2.96350.27211680.20522830X-RAY DIFFRACTION100
2.9635-3.14890.31121540.19722890X-RAY DIFFRACTION100
3.1489-3.39160.27711570.20392824X-RAY DIFFRACTION100
3.3916-3.73210.24131540.19272871X-RAY DIFFRACTION100
3.7321-4.27020.22971900.16422853X-RAY DIFFRACTION100
4.2702-5.37250.22431430.14982901X-RAY DIFFRACTION100
5.3725-26.46660.26931560.2052913X-RAY DIFFRACTION99

+
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