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- PDB-5v6l: Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in comp... -

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Basic information

Entry
Database: PDB / ID: 5v6l
TitleCrystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A37 in complex with V3 peptide JR-FL
Components
  • Envelope glycoprotein, v3 region
  • Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
  • Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / V3 / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / positive regulation of cell growth / clathrin-dependent endocytosis of virus by host cell / 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 / 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 glycoprotein gp160 / Glycoprotein 120
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.549 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074286 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: J. Virol. / Year: 2018
Title: Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120.
Authors: Pan, R. / Qin, Y. / Banasik, M. / Lees, W. / Shepherd, A.J. / Cho, M.W. / Kong, X.P.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: 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 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
H: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
P: Envelope glycoprotein, v3 region
M: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
I: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
Q: Envelope glycoprotein, v3 region


Theoretical massNumber of molelcules
Total (without water)96,5616
Polymers96,5616
Non-polymers00
Water4,089227
1
L: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
H: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
P: Envelope glycoprotein, v3 region


Theoretical massNumber of molelcules
Total (without water)48,2813
Polymers48,2813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-38 kcal/mol
Surface area19370 Å2
MethodPISA
2
M: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
I: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37
Q: Envelope glycoprotein, v3 region


Theoretical massNumber of molelcules
Total (without water)48,2813
Polymers48,2813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-41 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.234, 173.904, 70.912
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37


Mass: 22839.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V3 mAb 10A37


Mass: 22934.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein, v3 region


Mass: 2506.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q85825, UniProt: P20871*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 18% polyethylene glycol 4000, 8.5% Isopropanol, 0.1 M HEPES pH 7.5, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.549→44 Å / Num. obs: 33285 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rsym value: 0.1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.298→2.44 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6977 / CC1/2: 0.92 / Rsym value: 0.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
PHENIXmodel building
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JO1

4jo1


Resolution: 2.549→44 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 3278 5.03 %
Rwork0.2061 --
obs0.2084 65233 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.549→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6622 0 0 227 6849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086782
X-RAY DIFFRACTIONf_angle_d1.0499288
X-RAY DIFFRACTIONf_dihedral_angle_d15.93994
X-RAY DIFFRACTIONf_chiral_restr0.0581098
X-RAY DIFFRACTIONf_plane_restr0.0071182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5492-2.58720.39041330.30792528X-RAY DIFFRACTION96
2.5872-2.62760.33361400.2922732X-RAY DIFFRACTION97
2.6276-2.67070.34721420.28432656X-RAY DIFFRACTION98
2.6707-2.71680.3831450.30072737X-RAY DIFFRACTION98
2.7168-2.76610.30921400.28792597X-RAY DIFFRACTION98
2.7661-2.81930.32611420.27942698X-RAY DIFFRACTION98
2.8193-2.87690.29171440.27562737X-RAY DIFFRACTION98
2.8769-2.93940.31861410.26552646X-RAY DIFFRACTION98
2.9394-3.00780.32951380.24982669X-RAY DIFFRACTION98
3.0078-3.0830.2881470.24422769X-RAY DIFFRACTION98
3.083-3.16630.26141400.24992623X-RAY DIFFRACTION98
3.1663-3.25950.29271430.24032715X-RAY DIFFRACTION98
3.2595-3.36460.29571400.21822699X-RAY DIFFRACTION98
3.3646-3.48480.25011420.21142676X-RAY DIFFRACTION99
3.4848-3.62430.23821500.20272756X-RAY DIFFRACTION98
3.6243-3.78920.26171420.1972681X-RAY DIFFRACTION99
3.7892-3.98880.2441440.19662731X-RAY DIFFRACTION99
3.9888-4.23860.19941430.17842724X-RAY DIFFRACTION99
4.2386-4.56550.2051400.15472658X-RAY DIFFRACTION99
4.5655-5.02440.2071480.14632752X-RAY DIFFRACTION99
5.0244-5.75020.1981440.16462713X-RAY DIFFRACTION99
5.7502-7.23960.22551450.18722753X-RAY DIFFRACTION100
7.2396-44.61160.20881450.15562705X-RAY DIFFRACTION99

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