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- PDB-1elr: Crystal structure of the TPR2A domain of HOP in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 1elr
TitleCrystal structure of the TPR2A domain of HOP in complex with the HSP90 peptide MEEVD
Components
  • HSP90-PEPTIDE MEEVD
  • TPR2A-DOMAIN OF HOP
KeywordsCHAPERONE / Hop / Tpr-Domain / Peptide-Complex / Helical Repeat / Hsp90 / Protein Binding
Function / homology
Function and homology information


dynein axonemal particle / protein folding chaperone complex / cellular response to interleukin-7 / RND1 GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Hsp90 protein binding / Golgi apparatus / protein-containing complex / RNA binding / nucleus / cytosol
Similarity search - Function
STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain ...STI1/HOP, DP domain / STI1/HOP, DP domain / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Stress-induced-phosphoprotein 1 / DSCR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsScheufler, C. / Brinker, A. / Hartl, F.U. / Moarefi, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine.
Authors: Scheufler, C. / Brinker, A. / Bourenkov, G. / Pegoraro, S. / Moroder, L. / Bartunik, H. / Hartl, F.U. / Moarefi, I.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPR2A-DOMAIN OF HOP
B: HSP90-PEPTIDE MEEVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2313
Polymers16,1722
Non-polymers591
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.280, 48.270, 38.060
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-90-

HOH

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Components

#1: Protein TPR2A-DOMAIN OF HOP


Mass: 15524.575 Da / Num. of mol.: 1 / Fragment: MIDDLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPRO EX HTA / Production host: Escherichia coli (E. coli) / References: UniProt: P31948
#2: Protein/peptide HSP90-PEPTIDE MEEVD


Mass: 647.695 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PENTAPEPTIDE / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q9H2A1*PLUS
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG MME 2000, TRIS, Nickel chloride, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein-peptide complex1drop
250 mMTris1drop
32 mMDDT1drop
4100 mMTris1reservoir
520 %(w/v)PEG2000MME1reservoir
65 mM1reservoirNiCl2
710 %(w/v)xylitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9402
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9402 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 22.8
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.068 / % possible all: 91.7
Reflection shell
*PLUS
% possible obs: 91.7 % / Mean I/σ(I) obs: 9

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
MLPHAREphasing
CNS1refinement
XDSdata scaling
RefinementResolution: 1.9→9.93 Å / Rfactor Rfree error: 0.007 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1003 9.8 %RANDOM
Rwork0.181 ---
obs0.181 10220 97.5 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.21 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20.46 Å2
2--3.43 Å20 Å2
3----5.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→9.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 1 151 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 160 9.9 %
Rwork0.222 1453 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAION.TOPM
X-RAY DIFFRACTION3ION.PARAMCAPPING.TOP
X-RAY DIFFRACTION4CAPPING.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.222

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