[English] 日本語
Yorodumi
- PDB-4ywg: Crystal structure of 830A in complex with V1V2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ywg
TitleCrystal structure of 830A in complex with V1V2
Components
  • Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
  • Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
  • Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
KeywordsViral protein/Immune system / HIV-1 gp120 / the V1V2 Region / antibody / complex structure / Viral protein-Immune system complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll ...Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsPan, R. / Kong, X.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI084119 United States
CitationJournal: J.Virol. / Year: 2015
Title: The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel.
Authors: Pan, R. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jul 27, 2016Group: Data collection
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
H: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
G: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
M: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
I: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
Q: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99012
Polymers122,6626
Non-polymers1,3276
Water00
1
L: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
H: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
G: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9956
Polymers61,3313
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-15 kcal/mol
Surface area27220 Å2
MethodPISA
2
M: Light chain of anti-HIV-1 gp120 V1V2 antibody 830A
I: Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A
Q: Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9956
Polymers61,3313
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-19 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.725, 159.168, 170.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Light chain of anti-HIV-1 gp120 V1V2 antibody 830A


Mass: 23692.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of anti-HIV-1 gp120 V1V2 antibody 830A


Mass: 23976.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293S / Production host: Homo sapiens (human)
#3: Protein Scaffold HIV-1 gp120 V1V2 region derived from strain ZM109


Mass: 13662.056 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: Q6TCP8*PLUS
#4: 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.: 6
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16.5% polyethylene glycol 8000 and 0.1 M Tris pH 8.5
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.998→49.029 Å / Num. obs: 35990 / % possible obs: 99.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.16
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.26 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDM

3kdm


Resolution: 2.998→49.029 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 1623 4.91 %
Rwork0.219 --
obs0.2228 35968 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.998→49.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 84 0 8149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098346
X-RAY DIFFRACTIONf_angle_d1.41711358
X-RAY DIFFRACTIONf_dihedral_angle_d17.7332934
X-RAY DIFFRACTIONf_chiral_restr0.0521321
X-RAY DIFFRACTIONf_plane_restr0.0071430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9983-3.04120.41631300.39672608X-RAY DIFFRACTION97
3.0412-3.08660.45181450.37922686X-RAY DIFFRACTION99
3.0866-3.13480.40841370.34462711X-RAY DIFFRACTION100
3.1348-3.18620.42611300.32922692X-RAY DIFFRACTION100
3.1862-3.24110.37971640.31812695X-RAY DIFFRACTION100
3.2411-3.30.36471270.30672678X-RAY DIFFRACTION100
3.3-3.36350.36141530.30042714X-RAY DIFFRACTION100
3.3635-3.43210.37921310.29212695X-RAY DIFFRACTION100
3.4321-3.50670.36421510.27382666X-RAY DIFFRACTION100
3.5067-3.58830.32721310.26082733X-RAY DIFFRACTION100
3.5883-3.6780.3661440.24882631X-RAY DIFFRACTION100
3.678-3.77740.31371410.22942723X-RAY DIFFRACTION100
3.7774-3.88850.27141280.2382718X-RAY DIFFRACTION100
3.8885-4.01390.27821610.22282675X-RAY DIFFRACTION100
4.0139-4.15730.26691360.21212689X-RAY DIFFRACTION100
4.1573-4.32370.24991310.19272739X-RAY DIFFRACTION100
4.3237-4.52030.27031540.18762651X-RAY DIFFRACTION100
4.5203-4.75850.28281190.19092719X-RAY DIFFRACTION100
4.7585-5.05630.28371290.19122697X-RAY DIFFRACTION99
5.0563-5.44630.3161460.19532669X-RAY DIFFRACTION99
5.4463-5.99350.27571320.20762675X-RAY DIFFRACTION99
5.9935-6.85870.31441480.21442684X-RAY DIFFRACTION99
6.8587-8.63360.26191240.19682685X-RAY DIFFRACTION99
8.6336-49.03550.25191330.18332543X-RAY DIFFRACTION94

+
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://pdbjlvh1.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