[English] 日本語
Yorodumi
- PDB-3jwo: Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jwo
TitleStructure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility
Components
  • FAB 48D Heavy CHAIN
  • FAB 48D LIGHT CHAIN
  • HIV-1 GP120 ENVELOPE GLYCOPROTEIN
  • T-cell surface glycoprotein CD4
KeywordsVIRAL PROTEIN / HIV-1 VIRAL SPIKE / MOLECULAR MOTION / PROTEIN ARCHITECTURE / RECEPTOR-TRIGGERED ENTRY / TYPE 1 FUSION PROTEIN / CELL MEMBRANE / DISULFIDE BOND / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / interleukin-15-mediated signaling pathway / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / interleukin-15-mediated signaling pathway / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / positive regulation of kinase activity / Nef Mediated CD4 Down-regulation / Alpha-defensins / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / T cell activation / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / MHC class II protein complex binding / Clathrin-mediated endocytosis / signaling receptor activity / virus receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin / Immunoglobulin domain / Beta Complex / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.51 Å
AuthorsPancera, M. / Majeed, S. / Huang, C.C. / Kwon, Y.D. / Zhou, T. / Robinson, J.E. / Sodroski, J. / Wyatt, R. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.
Authors: Pancera, M. / Majeed, S. / Ban, Y.E. / Chen, L. / Huang, C.C. / Kong, L. / Kwon, Y.D. / Stuckey, J. / Zhou, T. / Robinson, J.E. / Schief, W.R. / Sodroski, J. / Wyatt, R. / Kwong, P.D.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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
A: HIV-1 GP120 ENVELOPE GLYCOPROTEIN
C: T-cell surface glycoprotein CD4
L: FAB 48D LIGHT CHAIN
H: FAB 48D Heavy CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,91915
Polymers106,3404
Non-polymers2,57911
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint8 kcal/mol
Surface area45770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.000, 190.000, 103.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 2 types, 2 molecules AC

#1: Protein HIV-1 GP120 ENVELOPE GLYCOPROTEIN


Mass: 39655.910 Da / Num. of mol.: 1 / Mutation: T257S, S375W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HXBC2 / Plasmid: pMT / Production host: DROSOPHILA MELANOGASTER (fruit fly) / Strain (production host): FRUIT FLY
#2: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20419.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01730

-
Antibody , 2 types, 2 molecules LH

#3: Antibody FAB 48D LIGHT CHAIN


Mass: 22749.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified herpesvirus
#4: Antibody FAB 48D Heavy CHAIN


Mass: 23515.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified herpesvirus

-
Sugars , 2 types, 11 molecules

#5: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 10
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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 5.3% PEG8000, 0.2M Calcium acetate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 20271 / % possible obs: 87.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.217 / Net I/σ(I): 8.06
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 1.3 / % possible all: 41.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3JWD

3jwd


Resolution: 3.51→41.09 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 3.51 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1842 9.09 %
Rwork0.257 --
obs0.258 20271 83.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.1 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 141.66 Å2
Baniso -1Baniso -2Baniso -3
1--21.939 Å2-0 Å20 Å2
2---21.939 Å20 Å2
3---43.878 Å2
Refinement stepCycle: LAST / Resolution: 3.51→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7433 0 164 0 7597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047782
X-RAY DIFFRACTIONf_angle_d0.86110566
X-RAY DIFFRACTIONf_dihedral_angle_d14.4252815
X-RAY DIFFRACTIONf_chiral_restr0.0511223
X-RAY DIFFRACTIONf_plane_restr0.0041333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.6040.4750.354714X-RAY DIFFRACTION43
3.604-3.710.391800.333876X-RAY DIFFRACTION53
3.71-3.8290.3241100.3191087X-RAY DIFFRACTION65
3.829-3.9660.3291240.3011245X-RAY DIFFRACTION75
3.966-4.1250.2751460.2751403X-RAY DIFFRACTION84
4.125-4.3120.2421430.2621499X-RAY DIFFRACTION90
4.312-4.5390.2591590.2351575X-RAY DIFFRACTION94
4.539-4.8230.2271610.221607X-RAY DIFFRACTION96
4.823-5.1950.2281610.2231615X-RAY DIFFRACTION95
5.195-5.7170.2521660.2321649X-RAY DIFFRACTION97
5.717-6.5410.291640.2471645X-RAY DIFFRACTION96
6.541-8.230.2681690.251700X-RAY DIFFRACTION98
8.23-41.0910.2631840.241814X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.53050.04810.28111.7208-0.18190.8536-0.06350.1448-0.01990.14690.1309-0.0956-0.004-0.039-0.04830.65340.06110.02320.8558-0.04950.973631.239299.98482.7753
21.6436-0.38390.6786-1.575-0.52241.0459-0.15870.0532-0.29570.18450.3829-0.2279-0.223-0.0197-0.16541.06630.0942-0.19140.8844-0.04681.390147.411881.361217.3561
30.2744-0.2597-0.08443.4358-0.44410.5061-0.2251-0.01720.16450.5407-0.5261-1.088-0.19180.08850.62691.53710.1863-0.16421.24320.03851.613462.74551.85624.8424
4-0.08071.3961-0.66712.2089-0.74862.1682-0.01380.11550.2810.17690.28690.37330.1322-0.6799-0.26861.2692-0.25170.13791.32260.17831.5627-2.327767.248517.7981
53.43751.8066-0.63192.6499-2.17321.350.21170.14620.17340.77990.19440.2164-0.5895-0.0032-0.35881.5427-0.12380.34861.46950.35421.8585-3.294541.453842.3159
60.5317-1.3075-0.32851.9418-1.88242.06970.1279-0.1244-0.2702-0.6655-0.05080.17340.63970.3741-0.05551.3401-0.00910.12921.14210.22731.283719.072460.3317.084
73.44122.0105-0.33854.1126-1.22030.2628-1.095-0.3626-2.1145-1.98370.5138-0.08620.2320.10910.52872.129-0.03610.50871.53110.69852.81193.280532.16330.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA34 - 948
2X-RAY DIFFRACTION2chain C and resid 1000:1097C1000 - 1097
3X-RAY DIFFRACTION3chain C and resid 1098:1183C1098 - 1183
4X-RAY DIFFRACTION4chain L and resid 1:106L1 - 106
5X-RAY DIFFRACTION5chain L and resid 107:211L107 - 211
6X-RAY DIFFRACTION6chain H and resid 1:119H1 - 119
7X-RAY DIFFRACTION7chain H and resid 120:221H120 - 221

+
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