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- PDB-3egs: Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 ... -

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Basic information

Entry
Database: PDB / ID: 3egs
TitleCrystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671 soaked in ammonium sulfate
Components
  • 2F5 Fab' heavy chain
  • 2F5 Fab' light chain
  • gp41 scrFP-MPER construct
KeywordsIMMUNE SYSTEM / 2F5 / gp41 / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsJulien, J.-P. / Bryson, S. / de la Torre, B.G. / Andreu, D. / Nieva, J.L. / Pai, E.F.
CitationJournal: J.Phys.Chem.B / Year: 2009
Title: Structural constraints imposed by the conserved fusion peptide on the HIV-1 gp41 epitope recognized by the broadly neutralizing antibody 2F5.
Authors: de la Arada, I. / Julien, J.P. / de la Torre, B.G. / Huarte, N. / Andreu, D. / Pai, E.F. / Arrondo, J.L. / Nieva, J.L.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2F5 Fab' light chain
B: 2F5 Fab' heavy chain
C: gp41 scrFP-MPER construct


Theoretical massNumber of molelcules
Total (without water)52,1723
Polymers52,1723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-24 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 75.900, 93.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 2F5 Fab' light chain


Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody 2F5 Fab' heavy chain


Mass: 24985.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide gp41 scrFP-MPER construct


Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized by Fmoc chemistry. The sequence of the peptide is naturally found in the human immunodeficiency virus.
Nonpolymer detailsACA IN THE PEPTIDE SEQUENCE STANDS FOR 6-AMINO-HEXANOIC ACID LINKER.

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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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Growth: 0.1 M sodium acetate, pH 5.6, 16-20% 2-propanol, 16-20% PEG 4K. Soak: 0.1 M sodium acetate, pH 5.6, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2008 / Details: Micromax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.6→17 Å / Num. all: 5537 / Num. obs: 5386 / % possible obs: 95.5 % / Redundancy: 3.8 % / Rsym value: 0.28 / Net I/σ(I): 4.7
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 418 / Rsym value: 0.462 / % possible all: 99.5

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0L

3d0l


Resolution: 3.6→16.73 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1744119.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 240 5 %RANDOM
Rwork0.235 ---
obs0.235 4828 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 1.55999 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---4.84 Å20 Å2
3---4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.6→16.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 0 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d29.1
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 42 5.4 %
Rwork0.277 737 -
obs-737 86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.paramgol.top
X-RAY DIFFRACTION3water.paramwater.top

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