[English] 日本語
Yorodumi
- PDB-3mlx: Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with an MN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mlx
TitleCrystal structure of anti-HIV-1 V3 Fab 3074 in complex with an MN V3 peptide
Components
  • HIV-1 gp120 third variable region (V3) crown
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
KeywordsIMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction
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 / 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 ...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 / 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 / identical protein binding
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 speciesHomo sapiens (human)
HIV-1 M:B_MN (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKong, X.-P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Conserved structural elements in the V3 crown of HIV-1 gp120.
Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionApr 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)98,5826
Polymers98,5826
Non-polymers00
Water13,529751
1
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,2913
Polymers49,2913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-30 kcal/mol
Surface area20110 Å2
MethodPISA
2
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,2913
Polymers49,2913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-28 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.870, 128.796, 60.189
Angle α, β, γ (deg.)90.000, 92.660, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain


Mass: 22301.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain


Mass: 24277.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 third variable region (V3) crown


Mass: 2711.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HIV-1 M:B_MN (virus) / References: UniProt: P05877
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M NH4 citrate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2008
Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→500 Å / Num. obs: 71846 / % possible obs: 96.5 % / Rmerge(I) obs: 0.138 / Χ2: 0.829 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.970.37163630.2486.3
1.97-2.050.31568330.29492.3
2.05-2.140.2670990.38695.7
2.14-2.250.2272540.46397.1
2.25-2.390.19772380.5898
2.39-2.580.17273130.6898.4
2.58-2.840.15173790.96498.9
2.84-3.250.13773931.12799.3
3.25-4.090.12874341.52699.6
4.09-500.11475401.45899.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.228 6794 9.5 %
Rwork0.192 --
obs-67118 93.7 %
Solvent computationBsol: 51.706 Å2
Displacement parametersBiso max: 80.2 Å2 / Biso mean: 26.547 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1-5.664 Å20 Å22.165 Å2
2---6.634 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6780 0 0 751 7531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.432
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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