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- PDB-3mlw: Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3mlw
TitleCrystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an MN V3 peptide
Components
  • HIV-1 gp120 third variable region (V3) crown
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D 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 / 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 / virion attachment to 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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
PHOSPHATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 M:B_MN (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Nov 20, 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 / _pdbx_entry_details.has_protein_modification / _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

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Assembly

Deposited unit
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,21212
Polymers100,6426
Non-polymers5706
Water2,900161
1
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6066
Polymers50,3213
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-46 kcal/mol
Surface area20830 Å2
MethodPISA
2
M: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab light chain
I: Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab heavy chain
Q: HIV-1 gp120 third variable region (V3) crown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6066
Polymers50,3213
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-44 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.924, 82.312, 149.830
Angle α, β, γ (deg.)90.000, 110.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 1006-15D Fab light chain


Mass: 23035.328 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 1006-15D Fab heavy chain


Mass: 24574.516 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: 2711.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HIV-1 M:B_MN (virus) / References: UniProt: P05877
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, K dihydrogen phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29061 / % possible obs: 94 % / Rmerge(I) obs: 0.156 / Χ2: 0.825 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.80.36322000.4371.2
2.8-2.910.34624620.43880
2.91-3.040.31327610.50290.3
3.04-3.20.28930280.60298.4
3.2-3.40.24130820.702100
3.4-3.660.19530600.923100
3.66-4.030.17131041.148100
4.03-4.620.14230891.291100
4.62-5.810.12831181.003100
5.81-500.09531570.71699.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0091refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.27 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.659 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1473 5.1 %RANDOM
Rwork0.214 ---
obs0.218 29059 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 112.98 Å2 / Biso mean: 48.043 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 0 30 161 7170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227189
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9549796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89423.846273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.466151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1921532
X-RAY DIFFRACTIONr_chiral_restr0.0860.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215420
X-RAY DIFFRACTIONr_mcbond_it0.4881.54576
X-RAY DIFFRACTIONr_mcangle_it0.91427406
X-RAY DIFFRACTIONr_scbond_it1.02432613
X-RAY DIFFRACTIONr_scangle_it1.8254.52390
LS refinement shellResolution: 2.7→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 82 -
Rwork0.244 1380 -
all-1462 -
obs--64.6 %

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