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- PDB-3jwo: Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Ar... -

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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 / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...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 / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / 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 / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling 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 viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / cell adhesion / positive regulation of protein phosphorylation / immune response / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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