[English] 日本語
Yorodumi
- PDB-1yuw: crystal structure of bovine hsc70(aa1-554)E213A/D214A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yuw
Titlecrystal structure of bovine hsc70(aa1-554)E213A/D214A mutant
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / postsynaptic cytosol / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / terminal bouton / mRNA processing / melanosome / protein-macromolecule adaptor activity / protein refolding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, J. / Lafer, E.M. / Prasad, K. / Sousa, R.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural basis of interdomain communication in the Hsc70 chaperone
Authors: Jiang, J. / Prasad, K. / Lafer, E.M. / Sousa, R.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)60,9791
Polymers60,9791
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.694, 50.140, 87.156
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8 / Intracellular vitamin D binding protein 1 / Hsc70


Mass: 60978.867 Da / Num. of mol.: 1 / Mutation: E213A, D214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Plasmid: pREST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 8
Details: PEG8000,trimethyl amine oxide, pH 8.0, microbatch, temperature 289K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 14, 2004 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17513 / Num. obs: 16521 / % possible obs: 94.3 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.459 / % possible all: 97.1

-
Phasing

Phasing MRRfactor: 0.506 / Cor.coef. Fo:Fc: 0.331
Highest resolutionLowest resolution
Rotation4 Å34.63 Å
Translation4 Å34.63 Å

-
Processing

Software
NameClassificationNB
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1640 9.4 %RANDOM
Rwork0.22 ---
obs-16521 --
Displacement parametersBiso mean: 24.662 Å2
Baniso -1Baniso -2Baniso -3
1--7.672 Å20 Å22.765 Å2
2--0.767 Å20 Å2
3---6.904 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 0 121 4403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.57
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection
Rfree0.297 1640
Rwork0.22 -
obs-1715

+
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://pdbjlvh1.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