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- PDB-1elw: Crystal structure of the TPR1 domain of HOP in complex with a HSC... -

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Basic information

Entry
Database: PDB / ID: 1elw
TitleCrystal structure of the TPR1 domain of HOP in complex with a HSC70 peptide
Components
  • HSC70-PEPTIDE
  • TPR1-DOMAIN OF HOP
KeywordsCHAPERONE / Hop / Tpr-Domain / Peptide-Complex / Helical Repeat / Hsc70 / Hsp70 / Protein Binding
Function / homology
Function and homology information


dynein axonemal particle / cellular response to interleukin-7 / protein folding chaperone complex / 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 domain / Tetratricopeptide repeat ...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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPR1-DOMAIN OF HOP
B: TPR1-DOMAIN OF HOP
C: HSC70-PEPTIDE
D: HSC70-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,33512
Polymers28,6124
Non-polymers7238
Water4,414245
1
A: TPR1-DOMAIN OF HOP
C: HSC70-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6686
Polymers14,3062
Non-polymers3624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-13 kcal/mol
Surface area6770 Å2
MethodPISA
2
B: TPR1-DOMAIN OF HOP
D: HSC70-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6686
Polymers14,3062
Non-polymers3624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.470, 75.470, 42.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein TPR1-DOMAIN OF HOP


Mass: 13446.996 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 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 HSC70-PEPTIDE


Mass: 858.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
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: 45 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Details: used to microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein-peptide complex1drop
215 mMHEPES1drop
3100 mMTris1reservoir
424 %(w/v)PEG2000 MME1reservoir
510 mM1reservoirNiCl2
615 %(w/v)xylitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.949
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 32.5
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.305 / Num. unique all: 0 / % possible all: 75.2
Reflection shell
*PLUS
% possible obs: 75.2 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 1.6→18.87 Å / Rfactor Rfree error: 0.004 / 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
Rfree0.215 3100 10.1 %RANDOM
Rwork0.18 ---
obs0.18 30804 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.36 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---1.65 Å20 Å2
3---3.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→18.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 36 245 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 433 10 %
Rwork0.244 3879 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARATRS.TOP
X-RAY DIFFRACTION3ION.PARION.TOP
X-RAY DIFFRACTION4TRS.PARWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
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: 0.264 / % reflection Rfree: 10 % / Rfactor Rwork: 0.244

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