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- PDB-3idx: Crystal structure of HIV-gp120 core in complex with CD4-binding s... -

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Basic information

Entry
Database: PDB / ID: 3idx
TitleCrystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222
Components
  • Fab b13 heavy chain
  • Fab b13 light chain
  • HIV-1 HxBc2 gp120 core
KeywordsIMMUNE SYSTEM / HIV-1 / antibody / gp120 / b13 / Envelope glycan protein / CD4-binding site / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Envelope protein / Fusion protein / Host-virus interaction / Membrane / Transmembrane / Viral immunoevasion / Virion
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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 / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, L. / Kwon, Y.D. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. ...Chen, L. / Kwon, Y.D. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Nabel, G.J. / Posner, M. / Sodroski, J. / Wyatt, R. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Science / Year: 2009
Title: Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120.
Authors: Chen, L. / Do Kwon, Y. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D. ...Authors: Chen, L. / Do Kwon, Y. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z.Y. / Zhang, M.Y. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Nabel, G.J. / Posner, M.R. / Sodroski, J. / Wyatt, R. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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
G: HIV-1 HxBc2 gp120 core
H: Fab b13 heavy chain
L: Fab b13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06926
Polymers83,5773
Non-polymers4,49223
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.609, 203.964, 109.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11G-1002-

SO4

DetailsAntigen/antibody complex: the biological assembly is chain G in complex with chain H and L

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab b13 heavy chain


Mass: 24810.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Fab b13 light chain


Mass: 23639.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 17 molecules G

#1: Protein HIV-1 HxBc2 gp120 core


Mass: 35126.867 Da / Num. of mol.: 1
Mutation: M95W, T257S, S375W, A443M, W96C, V275C, I109C, Q428C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HxBc2 / Gene: env / Plasmid: pcDNA3.1(-) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P04578*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.: 16
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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Non-polymers , 4 types, 240 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8 % PEG 8000, 6.5 % Isopropanol, 200 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 42470 / Num. obs: 34810 / % possible obs: 81 % / Redundancy: 8.5 % / Rsym value: 0.081 / Net I/σ(I): 37.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.51 / % possible all: 35

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BBJ

1bbj


Resolution: 2.5→39.2184 Å / SU ML: -0 / σ(F): 1.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1776 5.13 %random
Rwork0.1783 ---
obs0.1814 34645 78.98 %-
all-34358 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.167 Å2 / ksol: 0.324 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→39.2184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 278 233 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056181
X-RAY DIFFRACTIONf_angle_d0.8748371
X-RAY DIFFRACTIONf_dihedral_angle_d15.3942254
X-RAY DIFFRACTIONf_chiral_restr0.053956
X-RAY DIFFRACTIONf_plane_restr0.0041046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56760.2839390.2663930X-RAY DIFFRACTION29
2.5676-2.64320.3346600.2781326X-RAY DIFFRACTION42
2.6432-2.72850.3508840.2951653X-RAY DIFFRACTION52
2.7285-2.8260.32851010.26491926X-RAY DIFFRACTION61
2.826-2.93910.35781230.26132249X-RAY DIFFRACTION71
2.9391-3.07280.3081370.25242613X-RAY DIFFRACTION82
3.0728-3.23470.2871740.23582841X-RAY DIFFRACTION90
3.2347-3.43730.28281920.21173097X-RAY DIFFRACTION98
3.4373-3.70250.27591840.1843172X-RAY DIFFRACTION100
3.7025-4.07470.23991670.15933198X-RAY DIFFRACTION100
4.0747-4.66350.17231590.13063244X-RAY DIFFRACTION100
4.6635-5.87240.20961750.13493261X-RAY DIFFRACTION100
5.8724-39.21840.21681810.17973359X-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)
11.1273-0.2582-0.797-0.5244-0.00693.780.03080.0109-0.25480.04910.05780.06840.26640.2227-0.04170.8944-0.0311-0.00190.5586-0.010.668516.4577-6.371298.4811
21.7851.1150.29180.6383-0.60870.9910.029-0.03590.06920.0319-0.1246-0.08470.10790.18770.06790.9126-0.0310.08160.70110.01170.727728.8038.81893.4517
32.60771.89060.08873.44251.46934.3274-0.41420.3025-0.323-0.21830.49950.0138-0.04720.2994-0.01210.944-0.29220.0150.58570.00130.593922.305519.158165.4141
43.85630.39220.3829-1.55050.49873.12990.8117-0.093-0.91540.2808-0.0305-0.35831.2849-0.0228-0.6321.2947-0.2288-0.06280.7675-0.18071.089441.812528.041640.1419
51.49281.2605-0.14063.1491-0.7582.3687-0.18550.04030.1642-0.0260.30660.2541-0.4107-0.0097-0.08761.0943-0.31410.05460.6308-0.05260.792328.027839.258170.7166
62.09370.51151.7261.7212.34513.3751-0.05930.10460.2525-1.02150.2515-0.0511-1.30990.0183-0.22641.8269-0.48990.27260.7595-0.08970.775338.360642.740434.6303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 83:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:128
4X-RAY DIFFRACTION4chain H and resid 129:231
5X-RAY DIFFRACTION5chain L and resid 1:109
6X-RAY DIFFRACTION6chain L and resid 110:214

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