[English] 日本語
Yorodumi
- PDB-1elr: Crystal structure of the TPR2A domain of HOP in complex with the ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more