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- PDB-3mly: Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR2... -

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Basic information

Entry
Database: PDB / ID: 3mly
TitleCrystal structure of anti-HIV-1 V3 Fab 3074 in complex with a UR29 V3 peptide
Components
  • HIV-1 gp120 third variable region (V3) crown
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
KeywordsIMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKong, X.-P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Conserved structural elements in the V3 crown of HIV-1 gp120.
Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionApr 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)99,4536
Polymers99,4536
Non-polymers00
Water15,835879
1
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,7263
Polymers49,7263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-32 kcal/mol
Surface area20440 Å2
MethodPISA
2
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,7263
Polymers49,7263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-29 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.948, 128.787, 60.096
Angle α, β, γ (deg.)90.000, 92.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab light chain


Mass: 22662.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 3074 Fab heavy chain


Mass: 24468.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 third variable region (V3) crown


Mass: 2596.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN.

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M NH4 citrate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2008
Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→500 Å / Num. obs: 96835 / % possible obs: 96.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
1.7-1.760.23591
1.76-1.830.18493
1.83-1.910.14194.9
1.91-2.020.11395.9
2.02-2.140.09697.7
2.14-2.310.08698.3
2.31-2.540.07999.2
2.54-2.910.07399.6
2.91-3.660.068100
3.66-500.06699.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.511 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.85 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 4843 5.01 %
Rwork0.1807 --
obs0.1824 96742 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.396 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0805 Å20 Å2-0.2702 Å2
2--0.0197 Å2-0 Å2
3---1.0608 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 0 879 7711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067013
X-RAY DIFFRACTIONf_angle_d1.1389548
X-RAY DIFFRACTIONf_dihedral_angle_d12.0382497
X-RAY DIFFRACTIONf_chiral_restr0.0741076
X-RAY DIFFRACTIONf_plane_restr0.0051225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75980.234620.17968562X-RAY DIFFRACTION90
1.7598-1.83030.21674280.18198783X-RAY DIFFRACTION93
1.8303-1.91350.22464870.17988949X-RAY DIFFRACTION95
1.9135-2.01440.22144910.17359110X-RAY DIFFRACTION96
2.0144-2.14060.21484790.1759272X-RAY DIFFRACTION98
2.1406-2.30580.23294910.18529323X-RAY DIFFRACTION98
2.3058-2.53780.24084750.19839382X-RAY DIFFRACTION99
2.5378-2.90470.22475180.19859429X-RAY DIFFRACTION100
2.9047-3.65870.19514980.17589518X-RAY DIFFRACTION100
3.6587-30.51610.18715140.15689571X-RAY DIFFRACTION100
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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