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- PDB-3mlr: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5... -

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Basic information

Entry
Database: PDB / ID: 3mlr
TitleCrystal structure of anti-HIV-1 V3 Fab 2557 in complex with a NY5 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


Dectin-2 family / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / 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
Truncated surface protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 20, 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

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


Theoretical massNumber of molelcules
Total (without water)49,7153
Polymers49,7153
Non-polymers00
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-29 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.414, 43.076, 58.212
Angle α, β, γ (deg.)87.860, 85.500, 85.820
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: 23331.873 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 third variable region (V3) crown


Mass: 2192.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus type 1 / Strain: NEW YORK-5 ISOLATE / References: UniProt: P12490
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M NH4 acetate, 0.1 M Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→500 Å / Num. obs: 37562 / % possible obs: 97.6 % / Rmerge(I) obs: 0.053 / Χ2: 1.357 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.13137011.56996.3
1.86-1.940.137351.47896.4
1.94-2.030.08437121.44996.6
2.03-2.130.07237281.42197.3
2.13-2.270.06637371.37897.2
2.27-2.440.0637641.34797.7
2.44-2.690.05737951.34398.1
2.69-3.080.04937781.21798.4
3.08-3.880.04438041.08298.9
3.88-500.03938081.29399.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.216 3681 9.7 %
Rwork0.181 --
obs-36720 96.7 %
Solvent computationBsol: 33.854 Å2
Displacement parametersBiso max: 58.51 Å2 / Biso mean: 14.122 Å2 / Biso min: 2.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.837 Å20.102 Å20.107 Å2
2---0.087 Å2-0.204 Å2
3---0.924 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 479 3927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.421
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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