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- PDB-3o6m: Anti-Tat HIV 11H6H1 Fab' complexed with a 9-mer Tat peptide -

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Basic information

Entry
Database: PDB / ID: 3o6m
TitleAnti-Tat HIV 11H6H1 Fab' complexed with a 9-mer Tat peptide
Components
  • 11H6H1 Fab' heavy chain
  • 11H6H1 Fab' light chain
  • Protein Tat 9-mer peptide
KeywordsIMMUNE SYSTEM / antigen-binding site / U-shaped groove / Tat HIV
Function / homology
Function and homology information


positive regulation of viral transcription / host cell nucleolus / RNA-binding transcription regulator activity / molecular adaptor activity / RNA binding
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSerriere, J. / Gouet, P. / Guillon, C.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Fab'-induced folding of antigenic N-terminal peptides from intrinsically disordered HIV-1 Tat revealed by X-ray crystallography.
Authors: Serriere, J. / Dugua, J.M. / Bossus, M. / Verrier, B. / Haser, R. / Gouet, P. / Guillon, C.
#1: Journal: Proteins / Year: 2010
Title: UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate
Authors: Foucault, M. / Mayol, K. / Receveur-Brechot, V. / Bussat, M.C. / Klinguer-Hamour, C. / Verrier, B. / Beck, A. / Haser, R. / Gouet, P. / Guillon, C.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 11H6H1 Fab' light chain
H: 11H6H1 Fab' heavy chain
C: Protein Tat 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)48,9073
Polymers48,9073
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-29 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.840, 69.720, 62.160
Angle α, β, γ (deg.)90.00, 109.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 11H6H1 Fab' light chain


Mass: 24219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody 11H6H1 Fab' heavy chain


Mass: 23553.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Protein/peptide Protein Tat 9-mer peptide


Mass: 1134.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized' / References: UniProt: Q98XH7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 289 K / Method: soaking / pH: 6.5
Details: 0.05M CaCl2, 0.1M Bis-Tris pH 6.5, 30% (v/v) polyethylene glycol 550 monomethyl ether, Soaking of Fab' crystals with 5mM Tat-peptide for 15 min, soaking, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19524 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.79
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.79 / Num. unique all: 298 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLB

1mlb


Resolution: 2.4→19.97 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.87 / SU B: 9.094 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29031 1002 5.1 %RANDOM
Rwork0.21055 ---
all0.2146 18518 --
obs0.2146 18518 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 0 101 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9564763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2725440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27223.778135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.4415557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6281516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212626
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.52206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78123583
X-RAY DIFFRACTIONr_scbond_it2.66131290
X-RAY DIFFRACTIONr_scangle_it4.1544.51180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 67 -
Rwork0.28 1340 -
obs--100 %

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