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- PDB-6db7: Crystal structure of anti-HIV-1 V3 Fab 1334 in complex with a HIV... -

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Basic information

Entry
Database: PDB / ID: 6db7
TitleCrystal structure of anti-HIV-1 V3 Fab 1334 in complex with a HIV-1 gp120 V3 peptide from MN strain
Components
  • HIV-1 gp120 V3 peptide from MN strain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / gp120 / V3 / mAb
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glylcoprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.213 Å
AuthorsChan, K.-W. / Kong, X.-P.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082676 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI087191 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112546 United States
CitationJournal: J. Virol. / Year: 2018
Title: Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection.
Authors: Chan, K.W. / Pan, R. / Costa, M. / Gorny, M.K. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain
P: HIV-1 gp120 V3 peptide from MN strain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain
Q: HIV-1 gp120 V3 peptide from MN strain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,72718
Polymers102,6226
Non-polymers1,10512
Water6,756375
1
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain
P: HIV-1 gp120 V3 peptide from MN strain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8649
Polymers51,3113
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-26 kcal/mol
Surface area21020 Å2
MethodPISA
2
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain
Q: HIV-1 gp120 V3 peptide from MN strain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8649
Polymers51,3113
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-29 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.802, 69.630, 97.191
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab heavy chain


Mass: 25594.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 1334 Fab light chain


Mass: 23005.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 V3 peptide from MN strain


Mass: 2711.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A9Q0A0, UniProt: P05877*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Citrate pH 4.5, 2.0 M (NH4)2SO4, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.213→29.17 Å / Num. obs: 46644 / % possible obs: 99.29 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 2.213→2.293 Å / Rmerge(I) obs: 0.844 / Num. measured obs: 10799

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
XDSdata scaling
PHASERphasing
RefinementResolution: 2.213→29.168 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2602 1998 4.29 %
Rwork0.2133 --
obs0.2154 46622 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.213→29.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 72 375 7374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027175
X-RAY DIFFRACTIONf_angle_d0.5459770
X-RAY DIFFRACTIONf_dihedral_angle_d14.934281
X-RAY DIFFRACTIONf_chiral_restr0.0431077
X-RAY DIFFRACTIONf_plane_restr0.0051248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2135-2.26880.37011340.3123003X-RAY DIFFRACTION95
2.2688-2.33010.38511430.30413175X-RAY DIFFRACTION100
2.3301-2.39870.3431420.28413193X-RAY DIFFRACTION100
2.3987-2.47610.36131420.28413174X-RAY DIFFRACTION100
2.4761-2.56450.32251430.26643191X-RAY DIFFRACTION100
2.5645-2.66710.31531430.25073188X-RAY DIFFRACTION100
2.6671-2.78840.28121430.25523192X-RAY DIFFRACTION100
2.7884-2.93530.2911430.24973181X-RAY DIFFRACTION100
2.9353-3.1190.34091430.23533178X-RAY DIFFRACTION100
3.119-3.35950.25511440.22093226X-RAY DIFFRACTION100
3.3595-3.6970.24011420.19643200X-RAY DIFFRACTION100
3.697-4.23060.23441440.17983197X-RAY DIFFRACTION99
4.2306-5.32480.1941430.16013226X-RAY DIFFRACTION100
5.3248-29.17020.22241490.19783300X-RAY DIFFRACTION100

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