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- PDB-3lex: 2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F1... -

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Basic information

Entry
Database: PDB / ID: 3lex
Title2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41
Components
  • 11f10 Antibody Heavy Chain
  • 11f10 Antibody Light Chain
  • Envelope glycoprotein gp41
KeywordsIMMUNE SYSTEM / HIV-1 / GP-41 / MONOCLONAL ANTIBODY / 2F5 / SCAFFOLD / EPITOPE / TRANSPLANT / GRAFT / RE-ELCITATION / Envelope protein / VACCINE DESIGN
Function / homology
Function and homology information


viral envelope / structural molecule activity / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsOfek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elicitation of structure-specific antibodies by epitope scaffolds.
Authors: Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 11f10 Antibody Heavy Chain
L: 11f10 Antibody Light Chain
P: Envelope glycoprotein gp41
A: 11f10 Antibody Heavy Chain
B: 11f10 Antibody Light Chain
C: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)98,3346
Polymers98,3346
Non-polymers00
Water11,313628
1
H: 11f10 Antibody Heavy Chain
L: 11f10 Antibody Light Chain
P: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,1673
Polymers49,1673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area18830 Å2
MethodPISA
2
A: 11f10 Antibody Heavy Chain
B: 11f10 Antibody Light Chain
C: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,1673
Polymers49,1673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-31 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.543, 70.962, 78.265
Angle α, β, γ (deg.)90.08, 90.02, 90.29
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 11f10 Antibody Heavy Chain


Mass: 23916.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#2: Antibody 11f10 Antibody Light Chain


Mass: 24264.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#3: Protein/peptide Envelope glycoprotein gp41


Mass: 986.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: HIV-1 gp41 peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9IJQ0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 4000, 0.08 M CH3COONA, 0.04 M, TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2009
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→25.9 Å / Num. obs: 49925 / % possible obs: 94.6 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 19.46 Å2 / Rsym value: 0.038 / Net I/σ(I): 33
Reflection shellResolution: 1.97→2.04 Å / Mean I/σ(I) obs: 12.9 / Rsym value: 0.092 / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LEY

3ley


Resolution: 1.97→25.9 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.16 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1992 4.03 %
Rwork0.165 --
obs0.166 49480 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.85 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1-11.486 Å21.457 Å2-2.512 Å2
2---10.321 Å20.631 Å2
3----1.165 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6783 0 0 628 7411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096967
X-RAY DIFFRACTIONf_angle_d0.8929496
X-RAY DIFFRACTIONf_dihedral_angle_d14.1742419
X-RAY DIFFRACTIONf_chiral_restr0.061074
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.965-2.0140.2491260.1853168X-RAY DIFFRACTION86
2.014-2.0690.2351430.1733431X-RAY DIFFRACTION94
2.069-2.1290.2251450.1763416X-RAY DIFFRACTION94
2.129-2.1980.2471420.1663434X-RAY DIFFRACTION95
2.198-2.2770.2521350.1833429X-RAY DIFFRACTION95
2.277-2.3680.2251460.1813473X-RAY DIFFRACTION95
2.368-2.4750.2381470.1843486X-RAY DIFFRACTION95
2.475-2.6060.2561450.1773433X-RAY DIFFRACTION95
2.606-2.7690.2071400.183414X-RAY DIFFRACTION94
2.769-2.9820.2221470.1733413X-RAY DIFFRACTION95
2.982-3.2820.191400.1623399X-RAY DIFFRACTION93
3.282-3.7560.1651390.1453362X-RAY DIFFRACTION92
3.756-4.7270.1471450.1343327X-RAY DIFFRACTION92
4.727-25.9030.1541520.1673303X-RAY DIFFRACTION91

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