[English] 日本語
Yorodumi
- PDB-1gc1: HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gc1
TitleHIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY
Components
  • (ANTIBODY 17B) x 2
  • CD4
  • ENVELOPE PROTEIN GP120
KeywordsViral protein/receptor/Immune system / COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB) / HIV-1 EXTERIOR ENVELOPE GP120 / T-CELL SURFACE GLYCOPROTEIN CD4 / ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B / GLYCOSYLATED PROTEIN / Viral protein-receptor-Immune system COMPLEX
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding / positive regulation of kinase activity / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of establishment of T cell polarity / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / response to vitamin D / extracellular matrix structural constituent / Other interleukin signaling / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of calcium ion transport into cytosol / macrophage differentiation / Generation of second messenger molecules / immunoglobulin binding / T cell differentiation / Co-inhibition by PD-1 / Binding and entry of HIV virion / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / actin filament organization / host cell endosome membrane / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Assembly Of The HIV Virion / Budding and maturation of HIV virion / positive regulation of protein phosphorylation / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / response to estradiol / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / response to ethanol / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / positive regulation of MAPK cascade / viral protein processing / immune response / membrane raft / receptor ligand activity / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / 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 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR, DENSITY MODIFICATION / Resolution: 2.5 Å
AuthorsKwong, P.D. / Wyatt, R. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A.
CitationJournal: Nature / Year: 1998
Title: Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.
Authors: Kwong, P.D. / Wyatt, R. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A.
History
DepositionJun 15, 1998Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Jun 28, 2017Group: Database references / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_site / struct_site_gen
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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: ENVELOPE PROTEIN GP120
C: CD4
L: ANTIBODY 17B
H: ANTIBODY 17B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,80315
Polymers103,7854
Non-polymers3,01811
Water10,863603
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.640, 88.130, 196.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

-
Antibody , 3 types, 3 molecules CLH

#2: Antibody CD4


Mass: 20503.260 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT / Mutation: S184N, I185T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01730
#3: Antibody ANTIBODY 17B


Mass: 23368.818 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Details: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120
Source: (gene. exp.) Homo sapiens (human)
Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: Mus musculus (house mouse)
#4: Antibody ANTIBODY 17B


Mass: 24483.471 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Details: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120
Source: (gene. exp.) Homo sapiens (human)
Description: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: Mus musculus (house mouse)

-
Protein / Non-polymers , 2 types, 604 molecules G

#1: Protein ENVELOPE PROTEIN GP120


Mass: 35429.160 Da / Num. of mol.: 1 / Fragment: CORE
Mutation: (GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: CLADE B
Description: SECRETED FROM DROSOPHILA SCHNEIDER 2 LINES UNDER CONTROL OF AN INDUCIBLE METALLOTHIONEIN PROMOTER
Gene: env / Organ: OVARY / Variant: HXBC2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04578
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 11 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(6+1)][a-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.: 7
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion / pH: 7
Details: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0. ...Details: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, vapor diffusion
PH range: 6.4-7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop / Details: Kwong, P.D., (1999) J. Biol. Chem., 274, 4115.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 Msodium citrate1drop
30.02 MNa HEPES1drop
410 %isopropanol1drop
510.5 %mPEG50001drop
60.0075 %SeaPrep agarose1drop
70.35 M1reservoirNaCl
80.1 Msodium citrate1reservoir
90.02 MHEPES1reservoir
1010 %isopropanol1reservoir
1110.5 %mPEG50001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.00614
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00614 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 37724 / % possible obs: 86 % / Observed criterion σ(I): -0.5 / Redundancy: 3 % / Rsym value: 0.093 / Net I/σ(I): 9.17
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.56 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.247 / % possible all: 62.8
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 113966 / Rmerge(I) obs: 0.093

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR, DENSITY MODIFICATION
Starting model: PDB ENTRIES 1HIL, 1CDH AND 3CD4

1hil

1cdh

3cd4


Resolution: 2.5→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1430 5 %RANDOM
Rwork0.2103 ---
obs0.2103 28620 74.9 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 194 603 7877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.331
X-RAY DIFFRACTIONx_mcangle_it2.311.5
X-RAY DIFFRACTIONx_scbond_it1.971.5
X-RAY DIFFRACTIONx_scangle_it3.012
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3878 92 5.7 %
Rwork0.2876 1518 -
obs--42.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM3_MOD.CHOTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMCSDX.MISCTOPH3.CHO
X-RAY DIFFRACTION3PARAMCSDX_MOD.PROTOPHCSDX.MISC
X-RAY DIFFRACTION4PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3026
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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