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- PDB-3hi1: Structure of HIV-1 gp120 (core with V3) in Complex with CD4-Bindi... -

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Basic information

Entry
Database: PDB / ID: 3hi1
TitleStructure of HIV-1 gp120 (core with V3) in Complex with CD4-Binding-Site Antibody F105
Components
  • F105 Heavy Chain
  • F105 Light Chain
  • Glycoprotein 120
KeywordsSTRUCTURAL PROTEIN/Immune System / HIV / GP120 / CD4 BINDING SITE ANTIBODY / F105 / IMMUNE EVASION / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Transmembrane / Viral immunoevasion / Virion / STRUCTURAL PROTEIN-Immune System COMPLEX
Function / homology
Function and homology information


Dectin-2 family / immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / 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 / extracellular region / membrane / plasma 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 ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Envelope glycoprotein gp160 / IGK@ protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKwon, Y.D. / Chen, L. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. ...Kwon, Y.D. / Chen, L. / Zhou, T. / Wu, X. / O'Dell, S. / Cavacini, L. / Hessell, A.J. / Pancera, M. / Tang, M. / Xu, L. / Yang, Z. / Zhang, M.-Y. / Arthos, J. / Burton, D.R. / Dimitrov, D. / 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
DepositionMay 18, 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 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jul 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_dif / 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_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 6, 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: Glycoprotein 120
L: F105 Light Chain
H: F105 Heavy Chain
J: Glycoprotein 120
A: F105 Light Chain
B: F105 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,57833
Polymers166,6056
Non-polymers5,97327
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22590 Å2
ΔGint-1 kcal/mol
Surface area66980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)412.403, 412.403, 83.206
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21J
12H
22B
13L
23A

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRVALVALGA90 - 2551 - 93
211THRTHRVALVALJD90 - 2551 - 93
121SERSERILEILEGA256 - 29494 - 132
221SERSERILEILEJD256 - 29494 - 132
131ASNASNLEULEUGA332 - 390169 - 227
231ASNASNLEULEUJD332 - 390169 - 227
141ILEILEGLUGLUGA449 - 492278 - 321
241ILEILEGLUGLUJD449 - 492278 - 321
112GLNGLNSERSERHC1 - 1131 - 123
212GLNGLNSERSERBF1 - 1131 - 123
122ALAALASERSERHC114 - 215124 - 225
222ALAALASERSERBF114 - 215124 - 225
113GLUGLUTHRTHRLB1 - 1091 - 110
213GLUGLUTHRTHRAE1 - 1091 - 110
123VALVALCYSCYSLB110 - 214111 - 215
223VALVALCYSCYSAE110 - 214111 - 215

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glycoprotein 120 / gp120 / SU


Mass: 35962.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: YU-2 / Gene: env / Plasmid: PSHUTTLE-CMV / Cell (production host): KIDNEY EMBRYONIC CELL LINE 293 / Production host: ADENOVIRUS / Strain (production host): AD5 / References: UniProt: P35961
#2: Antibody F105 Light Chain


Mass: 23495.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PRODUCED BY FUSION OF ANTIBODY-PRODUCING EPSTEIN BARR VIURS-TRANSFORMED CELLS WITH THE HMMA2.11TG/O CELL LINE
Source: (natural) Homo sapiens (human) / References: UniProt: Q6PIL8*PLUS
#3: Antibody F105 Heavy Chain


Mass: 23844.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PRODUCED BY FUSION OF ANTIBODY-PRODUCING EPSTEIN BARR VIURS-TRANSFORMED CELLS WITH THE HMMA2.11TG/O CELL LINE
Source: (natural) Homo sapiens (human)
#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.: 27
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 4.08 Å3/Da / Density % sol: 69.89 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 16% PEG 6000, 8% 2-PROPANOL, 0.2M AMMONIUM SULFATE, 0.1M HEPES, PH 7.5, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 48590 / Redundancy: 4.4 % / Rmerge(I) obs: 0.123 / Rsym value: 0.085 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.21 / Rsym value: 0.413

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BBD, 1BBJ

1bbd

1bbj


Resolution: 2.9→43.48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 39.865 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2247 5 %RANDOM
Rwork0.202 ---
obs0.204 42563 75.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11214 0 378 78 11670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.98816179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08551448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95824.619472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.623151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8511552
X-RAY DIFFRACTIONr_chiral_restr0.0670.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028738
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.35339
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.58314
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5696
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.37127342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.445311780
X-RAY DIFFRACTIONr_scbond_it0.7125030
X-RAY DIFFRACTIONr_scangle_it1.21334399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1G1835tight positional0.020.05
2H1680tight positional0.030.05
3L1651tight positional0.030.05
1G1835tight thermal0.190.5
2H1680tight thermal0.060.5
3L1651tight thermal0.040.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 24 -
Rwork0.386 550 -
obs--13.17 %
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)
13.4047-1.42410.97493.14190.41091.480.1289-0.16250.021-0.08530.0378-0.4345-0.30940.6019-0.1667-0.5734-0.130.0659-0.20650.0258-0.873257.25127.313-38.547
24.01041.60181.55752.3046-0.58061.47370.2177-0.55070.15260.517-0.1257-0.3541-0.35050.3974-0.092-0.4243-0.26520.06380.4614-0.306-0.355779.15528.189-31.572
31.5716-3.0255-1.01427.17037.912727.04950.56480.3710.2197-0.3207-0.2017-0.2825-1.0771-2.0154-0.3631-0.7853-0.0441-0.0333-0.27390.0429-0.84248.89928.574-41.644
41.40373.0659-3.03046.9676-8.685622.29690.3397-0.41380.50540.8351-0.181-0.1776-1.23073.1143-0.1587-0.5192-0.4131-0.03820.6401-0.3991-0.249987.42930.021-28.475
55.9338-1.2422-0.32063.2057-0.84925.85910.5081-0.41170.59460.4312-0.0651-0.187-0.98150.4383-0.443-0.3617-0.18180.2028-0.56940.0168-0.650348.39843.802-24.897
63.78542.0502-0.13723.03410.03194.86640.5526-0.31760.3063-0.1884-0.3168-0.0809-0.93870.0921-0.2357-0.3533-0.36230.2362-0.0111-0.3127-0.056686.75545.046-45.292
72.31832.5081-0.36363.1091-1.01921.184-0.10660.02920.1684-0.13640.127-0.1324-0.1520.277-0.0204-0.54680.028-0.0064-0.46640.0018-0.829736.39517.406-13.361
80.2823-0.0131-0.19523.63962.47555.0218-0.1327-0.08760.12830.36320.1910.3032-0.49420.1576-0.0583-0.51110.1006-0.0063-0.510.0171-0.754919.60521.28814.083
95.4992-1.1475-3.68843.44030.65125.7641-0.5141-1.1172-0.9532-0.0843-0.4004-0.23910.40570.77890.9145-0.5254-0.1070.28760.12410.18150.196599.79118.823-56.704
104.21420.5375-1.024.11-5.058313.0706-0.5401-0.0033-1.00150.1739-0.1655-0.2962-1.06750.51860.7056-0.2743-0.19680.2685-0.2571-0.1550.1971117.36122.98-83.482
111.57830.3062-0.74841.1344-0.58847.6763-0.0362-0.1033-0.19810.0661-0.0894-0.1648-0.27391.00240.1256-0.7299-0.0592-0.0888-0.2117-0.0058-0.712352.33419.1781.692
126.49862.11490.77922.530.23912.7122-0.0271-0.32890.08440.5070.09480.11420.17990.0081-0.0677-0.45790.05370.0367-0.5574-0.0009-1.011823.91611.95925.946
132.7637-0.9653-3.09620.50941.802712.9083-0.23620.8068-0.8039-0.1661-0.660.11410.1421-1.5990.8962-0.6379-0.15880.12740.2826-0.380.101684.2820.794-72.09
1410.4774-4.2184-2.32861.81740.09166.5312-0.58760.4144-1.2384-0.3935-0.25870.10150.3002-0.26590.8462-0.3828-0.31650.4553-0.1523-0.4410.4289113.26513.999-95.848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G90 - 255
2X-RAY DIFFRACTION2J90 - 255
3X-RAY DIFFRACTION3G475 - 492
4X-RAY DIFFRACTION4J475 - 492
5X-RAY DIFFRACTION5G256 - 474
6X-RAY DIFFRACTION6J256 - 474
7X-RAY DIFFRACTION7H1 - 113
8X-RAY DIFFRACTION8H114 - 215
9X-RAY DIFFRACTION9B1 - 113
10X-RAY DIFFRACTION10B114 - 215
11X-RAY DIFFRACTION11L1 - 109
12X-RAY DIFFRACTION12L110 - 214
13X-RAY DIFFRACTION13A1 - 109
14X-RAY DIFFRACTION14A110 - 214

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