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

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Basic information

Entry
Database: PDB / ID: 3mls
TitleCrystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a HIV-1 gp120 V3 mimotope
Components
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
  • Rationally designed V3 mimotope
KeywordsIMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction / mimotope
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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: Rationally designed V3 mimotope
M: 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
Q: Rationally designed V3 mimotope
N: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
J: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
R: Rationally designed V3 mimotope
O: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
K: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
S: Rationally designed V3 mimotope


Theoretical massNumber of molelcules
Total (without water)198,42912
Polymers198,42912
Non-polymers00
Water12,773709
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: Rationally designed V3 mimotope


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-29 kcal/mol
Surface area21140 Å2
MethodPISA
2
M: 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
Q: Rationally designed V3 mimotope


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-34 kcal/mol
Surface area21020 Å2
MethodPISA
3
N: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
J: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
R: Rationally designed V3 mimotope


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-32 kcal/mol
Surface area21160 Å2
MethodPISA
4
O: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
K: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
S: Rationally designed V3 mimotope


Theoretical massNumber of molelcules
Total (without water)49,6073
Polymers49,6073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-31 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.746, 43.051, 274.341
Angle α, β, γ (deg.)90.000, 94.200, 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 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
Rationally designed V3 mimotope


Mass: 2084.402 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG4K, 8.5% 2-Propanol, 85mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9809 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2009
Details: Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 2.5→500 Å / Num. obs: 63477 / % possible obs: 90.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.078 / Χ2: 1.25 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.543.80.31824451.37170.7
2.54-2.5940.31128481.33383.4
2.59-2.644.20.27229271.30184.6
2.64-2.694.20.25629191.34684.1
2.69-2.754.20.23628871.38184.6
2.75-2.824.20.20829741.34385.2
2.82-2.894.10.16829891.34886
2.89-2.964.20.1529761.32787.2
2.96-3.054.10.13131021.32388.9
3.05-3.154.20.11630501.36488.2
3.15-3.264.10.09532051.27691.8
3.26-3.394.10.08332631.28894.1
3.39-3.554.10.07133741.23996.5
3.55-3.734.10.06433371.1897.6
3.73-3.974.10.0635361.19998.7
3.97-4.274.20.05434691.16699.2
4.27-4.74.30.04934801.10299.3
4.7-5.384.30.0535381.06399.4
5.38-6.784.20.05635121.15699
6.78-5040.04736461.08397.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.274 6131 8.8 %
Rwork0.216 --
obs-60726 87.3 %
Solvent computationBsol: 40.21 Å2
Displacement parametersBiso max: 82.26 Å2 / Biso mean: 28.021 Å2 / Biso min: 1.93 Å2
Baniso -1Baniso -2Baniso -3
1--7.239 Å20 Å21.44 Å2
2--0.928 Å20 Å2
3---6.311 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13937 0 0 709 14646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.391
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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