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- PDB-3mlt: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1... -

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Basic information

Entry
Database: PDB / ID: 3mlt
TitleCrystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 V3 peptide
Components
  • HIV-1 gp120 third variable region (V3) crown
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
KeywordsIMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion 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
Envelope glycoprotein gp120
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 1.3Nov 6, 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 2557 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown
A: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
B: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
C: HIV-1 gp120 third variable region (V3) crown
D: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
E: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
G: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)195,01710
Polymers195,01710
Non-polymers00
Water5,909328
1
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,9863
Polymers49,9863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-64 kcal/mol
Surface area39030 Å2
2
A: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
B: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
C: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,9863
Polymers49,9863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-64 kcal/mol
Surface area38790 Å2
3
D: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
E: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5232
Polymers47,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5232
Polymers47,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.683, 142.927, 85.013
Angle α, β, γ (deg.)90.000, 95.000, 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 2557 Fab light chain


Mass: 23331.873 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody
Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain


Mass: 24191.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 third variable region (V3) crown


Mass: 2462.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: Q9WNX3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Na formate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2007
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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 62552 / % possible obs: 99.9 % / Rmerge(I) obs: 0.047 / Χ2: 0.335 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.49-2.590.31162270.166100
2.59-2.690.22862480.174100
2.69-2.820.1862490.188100
2.82-2.960.12262150.207100
2.96-3.150.08862820.243100
3.15-3.390.06162260.307100
3.39-3.730.04562530.405100
3.73-4.270.03462870.491100
4.27-5.380.02762720.584100
5.38-500.02562930.59298.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→35.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.082 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.863 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3177 5.1 %RANDOM
Rwork0.202 ---
obs0.206 62523 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.51 Å2 / Biso mean: 44.123 Å2 / Biso min: 11.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.49→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13294 0 0 328 13622
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 212 -
Rwork0.279 4053 -
all-4265 -
obs--92.32 %

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