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- PDB-6db5: Crystal structure of anti-HIV-1 V3 Fab TA6 in complex with a HIV-... -

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Basic information

Entry
Database: PDB / ID: 6db5
TitleCrystal structure of anti-HIV-1 V3 Fab TA6 in complex with a HIV-1 gp120 V3 peptide from NY5 strain
Components
  • HIV-1 gp120 V3 peptide from NY5 strain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / gp120 / V3 / mAb
Function / homology
Function and homology information


Dectin-2 family / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Truncated surface protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.599 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab heavy chain
L: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab light chain
P: HIV-1 gp120 V3 peptide from NY5 strain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab heavy chain
M: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab light chain
Q: HIV-1 gp120 V3 peptide from NY5 strain


Theoretical massNumber of molelcules
Total (without water)99,9416
Polymers99,9416
Non-polymers00
Water5,549308
1
H: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab heavy chain
L: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab light chain
P: HIV-1 gp120 V3 peptide from NY5 strain


Theoretical massNumber of molelcules
Total (without water)49,9713
Polymers49,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab heavy chain
M: Human monoclonal anti-HIV-1 gp120 V3 antibody TA6 Fab light chain
Q: HIV-1 gp120 V3 peptide from NY5 strain


Theoretical massNumber of molelcules
Total (without water)49,9713
Polymers49,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.616, 67.361, 103.038
Angle α, β, γ (deg.)90.00, 100.25, 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 TA6 Fab heavy chain


Mass: 24837.857 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 TA6 Fab light chain


Mass: 22940.334 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 NY5 strain


Mass: 2192.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P12490*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Citrate pH 5.6, 1.5 M (NH4)2SO4, 5% Glycerol, and 15% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91979 Å / Relative weight: 1
ReflectionResolution: 2.599→29.79 Å / Num. obs: 32650 / % possible obs: 99.11 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.2
Reflection shellResolution: 2.599→2.692 Å / Rmerge(I) obs: 0.696 / Num. measured obs: 2265

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PHASERphasing
XDSdata scaling
Cootmodel building
RefinementResolution: 2.599→29.79 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.82
RfactorNum. reflection% reflection
Rfree0.2827 1998 6.12 %
Rwork0.227 --
obs0.2304 32630 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.599→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 0 308 7112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026976
X-RAY DIFFRACTIONf_angle_d0.4799506
X-RAY DIFFRACTIONf_dihedral_angle_d10.4564168
X-RAY DIFFRACTIONf_chiral_restr0.0421070
X-RAY DIFFRACTIONf_plane_restr0.0041204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5992-2.66420.29651330.28382042X-RAY DIFFRACTION94
2.6642-2.73620.34441430.29092183X-RAY DIFFRACTION100
2.7362-2.81660.38181430.29432201X-RAY DIFFRACTION100
2.8166-2.90750.40681420.28252167X-RAY DIFFRACTION100
2.9075-3.01130.33541430.27792192X-RAY DIFFRACTION100
3.0113-3.13170.35151440.272202X-RAY DIFFRACTION99
3.1317-3.27410.29491400.25722165X-RAY DIFFRACTION99
3.2741-3.44650.30051440.23362199X-RAY DIFFRACTION100
3.4465-3.66210.28561420.22392181X-RAY DIFFRACTION99
3.6621-3.94420.28331430.21152199X-RAY DIFFRACTION99
3.9442-4.34010.22181440.18882199X-RAY DIFFRACTION100
4.3401-4.96560.21181430.17942209X-RAY DIFFRACTION100
4.9656-6.24660.2721450.20772198X-RAY DIFFRACTION99
6.2466-29.79240.26911490.21412295X-RAY DIFFRACTION100

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