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- PDB-2ny3: HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S3... -

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Basic information

Entry
Database: PDB / ID: 2ny3
TitleHIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4 and Antibody 17b
Components
  • (ANTIBODY 17B, ...) x 2
  • ENVELOPE GLYCOPROTEIN GP120
  • T-cell surface glycoprotein CD4
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / antibody / CD4 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
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 / membrane fusion involved in viral entry into host cell / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...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 / membrane fusion involved in viral entry into host cell / positive regulation of kinase activity / 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 / regulation of T cell activation / Other interleukin signaling / extracellular matrix structural constituent / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / macrophage differentiation / regulation of calcium ion transport / Generation of second messenger molecules / T cell differentiation / Co-inhibition by PD-1 / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / positive regulation of T cell activation / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / virus receptor activity / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / 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 MAPK cascade / cell adhesion / immune response / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / external side of plasma membrane / lipid binding / viral envelope / 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 / extracellular region / 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 / : ...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 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Beta Complex / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose / T-cell surface glycoprotein CD4 / Ig-like domain-containing protein / IGK@ protein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. ...Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D.
CitationJournal: Nature / Year: 2007
Title: Structural definition of a conserved neutralization epitope on HIV-1 gp120.
Authors: Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN GP120
B: T-cell surface glycoprotein CD4
C: ANTIBODY 17B, LIGHT CHAIN
D: ANTIBODY 17B, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,56818
Polymers103,3504
Non-polymers3,21814
Water11,980665
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.740, 88.197, 197.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ENVELOPE GLYCOPROTEIN GP120


Mass: 35073.785 Da / Num. of mol.: 1 / Fragment: CORE / Mutation: K231C, T257S, E267C, S334A, S375W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXBc2 / Plasmid: CMVR / Cell line (production host): EMBRYONIC CELL LINE 293 / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: Q993A8
#2: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 20419.252 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P01730

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Antibody , 2 types, 2 molecules CD

#3: Antibody ANTIBODY 17B, LIGHT CHAIN


Mass: 23399.898 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner
Production host: Homo sapiens (human) / References: UniProt: Q6P5S8
#4: Antibody ANTIBODY 17B, HEAVY CHAIN


Mass: 24457.387 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner
Production host: Homo sapiens (human) / References: UniProt: Q6N030

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Sugars , 2 types, 14 molecules

#5: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}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.: 13 / Source method: obtained synthetically / 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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Non-polymers , 1 types, 665 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 8.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Feb 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 85338 / Num. obs: 81583 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.072.60.496185.9
2.07-2.153.10.478188.8
2.15-2.253.90.475190.7
2.25-2.374.80.459194.8
2.37-2.525.60.413197
2.52-2.715.90.273199
2.71-2.996.20.171199.9
2.99-3.426.60.102199.9
3.42-4.316.90.0691100
4.31-506.80.056199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GC1

1gc1


Resolution: 2→44.11 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.317 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were ...Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were inspected to identify radiation-induced disulfide breakage, and the refined models were adjusted to reflect the initial, radiation-damage free structure. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24284 3926 5 %RANDOM
Rwork0.20314 ---
obs0.20513 74341 91.63 %-
all-85416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 205 665 7966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9810173
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1985917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80425306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.938151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261531
X-RAY DIFFRACTIONr_chiral_restr0.0620.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025481
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.32997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.55055
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.51085
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.539
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.65524686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08337428
X-RAY DIFFRACTIONr_scbond_it0.62723133
X-RAY DIFFRACTIONr_scangle_it1.01432745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 232 -
Rwork0.238 4429 -
obs--74.85 %
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)
12.161-1.63720.34187.4604-0.42691.33430.06360.0915-0.4566-0.121-0.05720.42420.1758-0.0136-0.0065-0.118-0.0377-0.0154-0.1164-0.0463-0.061423.635-26.5879.448
21.782-0.732-0.06622.87350.07141.8295-0.1281-0.1468-0.07880.38120.0761-0.26820.04440.170.0521-0.1258-0.0017-0.0419-0.20370.0296-0.16836.617-15.50691.009
35.40831.1492-1.94981.9119-1.16382.22370.02890.2979-0.1639-0.4897-0.0593-0.411-0.04990.05840.03040.02040.01790.1365-0.12610.0331-0.054944.059-7.7567.825
43.20951.6669-0.187.1539-1.02643.55-0.1631-0.2866-0.33030.1037-0.08060.23860.3435-0.31260.2437-0.1015-0.03410.0569-0.04550.0276-0.139761.34917.25556.098
51.7994-1.2754-0.31083.630.9291.4898-0.0661-0.2232-0.07120.2733-0.03950.22440.1131-0.15140.1056-0.15830.01240.0066-0.1223-0.0056-0.24282.94622.56690.642
61.5814-0.82440.19462.3152-1.40857.17360.15070.17040.2694-0.2670.04120.2855-0.2826-0.6521-0.1919-0.12960.069-0.0655-0.049-0.0388-0.0699-12.11250.25773.548
70.9459-0.98361.20182.4011-1.40052.76510.04560.0569-0.044-0.1094-0.0874-0.12220.16930.14710.0417-0.18460.0296-0.0034-0.191-0.0026-0.235215.17418.50973.336
82.81220.57760.57554.78333.05964.39290.058-0.04820.642-0.40660.0649-0.0824-0.62960.2297-0.1229-0.0712-0.01480.0001-0.1643-0.0471-0.05294.09951.93169.622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA83 - 2541 - 108
2X-RAY DIFFRACTION1AA475 - 491300 - 316
3X-RAY DIFFRACTION2AA255 - 474109 - 299
4X-RAY DIFFRACTION3BB1001 - 10972 - 98
5X-RAY DIFFRACTION4BB1098 - 118199 - 182
6X-RAY DIFFRACTION5CC2001 - 21101 - 110
7X-RAY DIFFRACTION6CC2111 - 2214111 - 214
8X-RAY DIFFRACTION7DD3001 - 31271 - 127
9X-RAY DIFFRACTION8DD3128 - 3229128 - 229

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