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- PDB-4jo3: Crystal structure of rabbit mAb R20 Fab in complex with V3 C-term... -

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Basic information

Entry
Database: PDB / ID: 4jo3
TitleCrystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus B gp120
Components
  • gp120
  • monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
  • monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Ig / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / 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 ...membrane fusion involved in viral entry into host cell / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / 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 / symbiont entry into host cell / 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 / Envelope glycoprotein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2013
Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans.
Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
P: gp120
M: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4238
Polymers96,2316
Non-polymers1922
Water6,648369
1
L: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
P: gp120


Theoretical massNumber of molelcules
Total (without water)48,1153
Polymers48,1153
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-37 kcal/mol
Surface area18640 Å2
MethodPISA
2
M: monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3085
Polymers48,1153
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-54 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.223, 118.977, 134.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R20 light chain


Mass: 22596.881 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R20 heavy chain


Mass: 23888.824 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide gp120


Mass: 1629.794 Da / Num. of mol.: 2
Fragment: third variable region (V3) C-terminus (UNP residues 48-62)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / References: UniProt: Q9YY05, UniProt: P35961*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M ammonium sulfate, 1.7% PEG400, 85 mM sodium cacodylate, pH 6.5, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→38.05 Å / Num. all: 35182 / Num. obs: 34658 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.155 / Rsym value: 0.159 / Net I/σ(I): 11.11
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1674 / Rsym value: 0.664 / % possible all: 95.4

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Processing

Software
NameVersionClassification
Blu-Icelikedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.05 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1747 5.04 %RANDOM
Rwork0.1845 ---
obs0.1871 34658 97.61 %-
all-35182 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.61 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1528 Å20 Å2-0 Å2
2--10.3622 Å20 Å2
3----7.2095 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 10 369 7039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096826
X-RAY DIFFRACTIONf_angle_d1.1889326
X-RAY DIFFRACTIONf_dihedral_angle_d15.1372346
X-RAY DIFFRACTIONf_chiral_restr0.0731110
X-RAY DIFFRACTIONf_plane_restr0.0051186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.32351400.27762629X-RAY DIFFRACTION95
2.6765-2.76290.35181300.27472641X-RAY DIFFRACTION95
2.7629-2.86160.33111430.23022606X-RAY DIFFRACTION95
2.8616-2.97610.28981320.23762671X-RAY DIFFRACTION96
2.9761-3.11150.30011260.20482686X-RAY DIFFRACTION96
3.1115-3.27550.24861540.20432680X-RAY DIFFRACTION97
3.2755-3.48060.25311640.19442724X-RAY DIFFRACTION99
3.4806-3.74910.22261450.1782813X-RAY DIFFRACTION100
3.7491-4.1260.21641490.16462796X-RAY DIFFRACTION100
4.126-4.72210.17661360.13142846X-RAY DIFFRACTION100
4.7221-5.94570.19811530.1482854X-RAY DIFFRACTION100
5.9457-38.05390.20081750.18412965X-RAY DIFFRACTION99

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