|Entry||Database: PDB / ID: 1atr|
|Title||THREONINE 204 OF THE CHAPERONE PROTEIN HSC70 INFLUENCES THE STRUCTURE OF THE ACTIVE SITE BUT IS NOT ESSENTIAL FOR ATP HYDROLYSIS|
|Components||HEAT-SHOCK COGNATE 70 KD PROTEIN|
|Function / homology|
Function and homology information
synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / postsynaptic cytosol ...synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / postsynaptic cytosol / chaperone cofactor-dependent protein refolding / non-chaperonin molecular chaperone ATPase / protein folding chaperone / autophagosome / cellular response to unfolded protein / spliceosomal complex / heat shock protein binding / RNA splicing / vesicle-mediated transport / terminal bouton / melanosome / mRNA processing / unfolded protein binding / ribonucleoprotein complex / protein refolding / lysosome / : / negative regulation of transcription, DNA-templated / dendrite / nucleolus / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock protein 70, conserved site / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Defensin A-like ...Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock protein 70, conserved site / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Defensin A-like / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock cognate 71 kDa protein
Similarity search - Component
|Biological species||Bos taurus (cattle)|
|Method||X-RAY DIFFRACTION / Resolution: 2.34 Å|
|Authors||O'Brien, M.C. / Mckay, D.B.|
Journal: J.Biol.Chem. / Year: 1993
Title: Threonine 204 of the chaperone protein Hsc70 influences the structure of the active site, but is not essential for ATP hydrolysis.
Authors: O'Brien, M.C. / McKay, D.B.
|Structure viewer||Molecule: |
Downloads & links
A: HEAT-SHOCK COGNATE 70 KD PROTEIN
|#1: Protein|| |
Mass: 42511.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P19120, adenosinetriphosphatase
|#2: Chemical|| ChemComp-MG / |
|#3: Chemical|| ChemComp-PO4 / |
|#4: Chemical|| ChemComp-ADP / |
|#5: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 2.6 Å3/Da / Density % sol: 52.77 %|
*PLUSpH: 9 / Method: other
|Components of the solutions|
|Radiation||Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
*PLUSHighest resolution: 2.1 Å / Num. all: 14417 / Num. obs: 16797 / Rmerge(I) obs: 0.031
|Refinement||Highest resolution: 2.34 Å / |
|Refinement step||Cycle: LAST / Highest resolution: 2.34 Å|
|Refine LS restraints|
*PLUSName: X-PLOR / Classification: refinement
*PLUSHighest resolution: 2.34 Å / Num. reflection obs: 16797 / Rfactor obs: 0.218
|Refine LS restraints|
*PLUSType: x_angle_d / Dev ideal: 1.43
-Aug 12, 2020. Covid-19 info
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
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+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
+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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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