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

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Basic information

Entry
Database: PDB / ID: 3idy
TitleCrystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221
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: 3.2 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 ...Data collection / Database references / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type
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
A: HIV-1 HxBc2 gp120 core
B: Fab b13 heavy chain
C: Fab b13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,44435
Polymers167,1546
Non-polymers6,29029
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.168, 204.316, 216.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain G and (resseq 83:119 or resseq 205:299 or resseq...
211chain A and (resseq 83:119 or resseq 205:299 or resseq...
112chain H and (resseq 1:101 or resid 110:231 ) and (not element H)
212chain B and (resseq 1:101 or resid 110:231 ) and (not element H)
113chain L and (resseq 1:29 or resseq 31:212 ) and (not element H)
213chain C and (resseq 1:29 or resseq 31:212 ) and (not element H)

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is an Antigen-Antibody complex that contains chain G in complex with chain H and L or chain A in complex with chain B and C.

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Components

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Antibody , 2 types, 4 molecules HBLC

#2: Antibody Fab b13 heavy chain


Mass: 24810.910 Da / Num. of mol.: 2
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.: 2
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, 30 molecules GA

#1: Protein HIV-1 HxBc2 gp120 core


Mass: 35126.867 Da / Num. of mol.: 2
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.: 28
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 , 2 types, 153 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
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: 3.2→50 Å / Num. obs: 35856 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Rsym value: 0.099 / Net I/σ(I): 21.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.45 / % possible all: 34

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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 3IDX

3idx


Resolution: 3.2→43.204 Å / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1778 5.03 %random
Rwork0.1955 ---
obs0.1977 35358 47.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.972 Å2 / ksol: 0.287 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→43.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11489 0 397 152 12038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412184
X-RAY DIFFRACTIONf_angle_d0.79616518
X-RAY DIFFRACTIONf_dihedral_angle_d15.9114424
X-RAY DIFFRACTIONf_chiral_restr0.0511895
X-RAY DIFFRACTIONf_plane_restr0.0042084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G2166X-RAY DIFFRACTIONPOSITIONAL
12A2166X-RAY DIFFRACTIONPOSITIONAL0.021
21H1662X-RAY DIFFRACTIONPOSITIONAL
22B1662X-RAY DIFFRACTIONPOSITIONAL0.013
31L1630X-RAY DIFFRACTIONPOSITIONAL
32C1630X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28660.3897590.28561249X-RAY DIFFRACTION23
3.2866-3.38330.304920.27261815X-RAY DIFFRACTION33
3.3833-3.49240.2931240.24652233X-RAY DIFFRACTION41
3.4924-3.61720.28121350.2252565X-RAY DIFFRACTION47
3.6172-3.76190.27491390.20852732X-RAY DIFFRACTION50
3.7619-3.9330.22641550.19262822X-RAY DIFFRACTION51
3.933-4.14020.2131580.17192795X-RAY DIFFRACTION52
4.1402-4.39940.18141340.16272886X-RAY DIFFRACTION52
4.3994-4.73870.20541530.14682841X-RAY DIFFRACTION52
4.7387-5.21480.20661530.14492875X-RAY DIFFRACTION52
5.2148-5.96780.23261530.16332873X-RAY DIFFRACTION53
5.9678-7.51230.24981450.20382931X-RAY DIFFRACTION53
7.5123-43.20830.23311780.21932963X-RAY DIFFRACTION54
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.96920.1442-0.2274-0.7162-0.29812.9942-0.17950.2881-0.3859-0.0066-0.14390.00430.08730.2210.26810.91860.08630.24811.02940.07941.074675.689849.579121.014
22.11880.8261-0.42741.9199-1.16881.0316-0.0926-0.0682-0.10290.177-0.1099-0.2282-0.07540.51270.22180.8725-0.02130.081.41980.11950.886
34.63111.42920.24555.50352.27170.8216-0.3960.0431-0.2159-0.56920.7279-0.1566-0.14730.4277-0.22840.9543-0.317-0.02320.7283-0.04730.4347
42.71622.4790.17821.8682.92484.760.59930.1321-0.65741.3308-0.239-0.54451.8477-0.4149-0.18261.8282-0.1033-0.00451.3569-0.24161.4177
52.31411.5251-2.57785.29941.94584.3450.09620.3851-0.0223-0.42280.25310.142-0.7959-0.1132-0.27660.967-0.21570.10861.0669-0.13260.7036
61.9310.84620.77541.32860.6493-3.9443-0.06230.2560.2478-1.08960.2814-0.131-0.769-0.2872-0.21632.0558-0.290.35141.5749-0.13410.7969
70.88750.1012-0.02350.3665-1.0583.8151-0.3364-0.3920.099-0.11140.16370.02590.1371-0.46980.17631.07270.08410.00081.256-0.05990.9867
80.7947-0.84110.57462.82521.15331.5285-0.286-0.2104-0.23920.0753-0.00330.3591-0.2524-0.43920.22190.93650.2025-0.02931.3387-0.17441.0494
92.9075-1.07181.42080.75710.0332.2011-0.3186-0.1229-0.74420.59720.1670.0954-0.1569-0.27830.07161.8430.3301-0.49880.9466-0.08141.0413
100.82410.397-0.51493.5896-1.05442.68020.5247-0.19810.65831.8826-0.07871.15060.09780.1868-0.36592.14420.0020.17091.62670.17511.8958
112.2962-1.98010.05354.6677-0.07671.6794-0.2097-0.255-0.10941.14160.2448-0.03180.18250.2369-0.06751.73240.3382-0.22591.278-0.01131.057
122.7367-0.8147-1.8466-0.0148-2.3787-6.09720.5421-0.31150.17452.0983-0.0712-0.1622-1.68360.3284-0.28733.7005-0.11580.23621.71780.05630.8842
Refinement TLS groupSelection details: chain C and resid 110:214

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