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

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Basic information

Entry
Database: PDB / ID: 3drt
TitleCrystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671
Components
  • 2F5 Fab' heavy chain
  • 2F5 Fab' light chain
  • scrHyb3K construct
KeywordsIMMUNE SYSTEM / HIV-1 / gp41 / 2F5 / nmAb
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 8, 2017Group: Other
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: 2F5 Fab' light chain
B: 2F5 Fab' heavy chain
C: scrHyb3K construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2644
Polymers52,1723
Non-polymers921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-27 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.200, 76.400, 93.600
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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma cells
#2: Antibody 2F5 Fab' heavy chain


Mass: 24985.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma cells
#3: Protein/peptide scrHyb3K 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.
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystals were grown in reservoir solution containing 0.1 M Na citrate pH 5.6, 16% 2-propanol, 16% PEG 4K, 0.01% Tween-20, 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: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.3→17 Å / Num. all: 7263 / Num. obs: 6826 / % possible obs: 94 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.265
Reflection shellResolution: 3.3→3.51 Å / Redundancy: 8.15 % / Rmerge(I) obs: 0.497 / % possible all: 89.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0L

3d0l


Resolution: 3.3→16.81 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 508628.56 / 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
Rfree0.229 346 5.1 %RANDOM
Rwork0.203 ---
obs0.203 6826 94 %-
all-7263 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.7845 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---0.62 Å20 Å2
3----0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3.3→16.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 6 0 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 52 4.9 %
Rwork0.24 1011 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.paramgol.top

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