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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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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.
Has protein modificationY
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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