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- PDB-3d0l: Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 ... -

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Basic information

Entry
Database: PDB / ID: 3d0l
TitleCrystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 FP-MPER Hyb3K construct 514GIGALFLGFLGAAGS528KK-Ahx-655KNEQELLELDKWASLWN671
Components
  • 2F5 heavy chain
  • 2F5 light chain
  • Hyb3k peptide construct
KeywordsIMMUNE SYSTEM / HIV / antibody / neutralization / epitope / 2F5 / gp41
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBryson, S. / Julien, J.P. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.
Authors: Julien, J.P. / Bryson, S. / Nieva, J.L. / Pai, E.F.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 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 1.3Nov 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 heavy chain
B: 2F5 light chain
C: Hyb3k peptide construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7736
Polymers52,4893
Non-polymers2843
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-51 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.300, 76.700, 94.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Hyb3k peptide construct


Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in the human immunodeficiency virus.

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Antibody , 2 types, 2 molecules AB

#1: Antibody 2F5 heavy chain


Mass: 23420.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody 2F5 light chain


Mass: 25245.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6GMX6*PLUS

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Non-polymers , 3 types, 181 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsACA IN THE PEPTIDE SEQUENCE STANDS FOR 6-AMINO-HEXANOIC ACID LINKER. YCM IN THE SEQUENCE OF CHAIN A ...ACA IN THE PEPTIDE SEQUENCE STANDS FOR 6-AMINO-HEXANOIC ACID LINKER. YCM IN THE SEQUENCE OF CHAIN A STANDS FOR S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE.

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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: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: A reservoir solution of 1.4-1.8 M ammonium sulphate and 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 16911 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.35→2.5 Å / Num. unique all: 2029

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F5B

2f5b


Resolution: 2.35→48.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1135021.22 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 832 4.9 %RANDOM
Rwork0.211 ---
obs0.211 16911 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.886 Å2 / ksol: 0.374791 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--0.7 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.35→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 16 178 3559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d28.6
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 112 5.2 %
Rwork0.289 2029 -
obs--66.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.paramgol.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4so4.paramso4.top

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