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- PDB-3mlv: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an NO... -

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Basic information

Entry
Database: PDB / ID: 3mlv
TitleCrystal structure of anti-HIV-1 V3 Fab 2557 in complex with an NOF 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


host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
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
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
N: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)99,5396
Polymers99,5396
Non-polymers00
Water7,819434
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)49,7703
Polymers49,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-28 kcal/mol
Surface area20480 Å2
MethodPISA
2
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
N: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,7703
Polymers49,7703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-26 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.554, 42.745, 116.063
Angle α, β, γ (deg.)87.91, 85.22, 85.97
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain


Mass: 23357.996 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 2557 Fab heavy chain


Mass: 24191.055 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: 2220.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: Q79790
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2007
Details: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. User choice of either mirror depending on the desired energy
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 25853 / % possible obs: 90.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
2.48-2.590.36690.2
2.59-2.690.27987.8
2.69-2.820.24190.2
2.82-2.960.20988.9
2.96-3.150.1687.4
3.15-3.390.12987
3.39-3.730.10888.4
3.73-4.270.09590.8
4.27-5.380.08295.8
5.38-500.08399

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→35.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.39 / σ(F): 1.96 / Phase error: 47.07 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.3419 1319 5.15 %
Rwork0.2331 --
obs0.2387 25624 88.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.651 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1322 Å20.4564 Å20.0586 Å2
2--0.3857 Å2-0.1257 Å2
3----0.5179 Å2
Refinement stepCycle: LAST / Resolution: 2.48→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 0 434 7268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087019
X-RAY DIFFRACTIONf_angle_d1.2289551
X-RAY DIFFRACTIONf_dihedral_angle_d15.6552509
X-RAY DIFFRACTIONf_chiral_restr0.0781080
X-RAY DIFFRACTIONf_plane_restr0.0051209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.57930.42431350.2672492X-RAY DIFFRACTION82
2.5793-2.69660.35461370.24862698X-RAY DIFFRACTION88
2.6966-2.83870.3971230.24732746X-RAY DIFFRACTION88
2.8387-3.01650.41071530.24782644X-RAY DIFFRACTION89
3.0165-3.24920.32021620.22962626X-RAY DIFFRACTION87
3.2492-3.57590.34471250.22032657X-RAY DIFFRACTION87
3.5759-4.09270.35971540.21652706X-RAY DIFFRACTION90
4.0927-5.15390.28531550.20422874X-RAY DIFFRACTION94
5.1539-35.54370.29241750.22582862X-RAY DIFFRACTION95

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