[English] 日本語
Yorodumi
- PDB-1ba0: HEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL 1NGE 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ba0
TitleHEAT-SHOCK COGNATE 70KD PROTEIN 44KD ATPASE N-TERMINAL 1NGE 3
ComponentsHEAT-SHOCK COGNATE 70KD PROTEIN
KeywordsHYDROLASE / ACTING ON ACID ANHYDRIDES / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated protein transport involved in chaperone-mediated autophagy / slow axonal transport / chaperone-mediated autophagy translocation complex disassembly / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding ...synaptic vesicle uncoating / clathrin-uncoating ATPase activity / chaperone-mediated protein transport involved in chaperone-mediated autophagy / slow axonal transport / chaperone-mediated autophagy translocation complex disassembly / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / axo-dendritic transport / postsynaptic cytosol / chaperone cofactor-dependent protein refolding / autophagosome / cellular response to unfolded protein / spliceosomal complex / response to unfolded protein / protein folding chaperone / heat shock protein binding / RNA splicing / vesicle-mediated transport / terminal bouton / mRNA processing / melanosome / unfolded protein binding / ribonucleoprotein complex / protein refolding / lysosome / ATPase activity / axon / negative regulation of transcription, DNA-templated / dendrite / nucleolus / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70, conserved site / Heat shock protein 70 family / Defensin A-like - #30 / Defensin A-like / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70, conserved site / Heat shock protein 70 family / Defensin A-like - #30 / Defensin A-like / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Heat shock cognate 71 kDa protein
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWilbanks, S.M. / Mckay, D.B.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural replacement of active site monovalent cations by the epsilon-amino group of lysine in the ATPase fragment of bovine Hsc70.
Authors: Wilbanks, S.M. / McKay, D.B.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Structural Basis of the 70-Kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity. II. Structure of the Active Site with Adp or ATP Bound to Wild Type and Mutant ATPase Fragment
Authors: Flaherty, K.M. / Wilbanks, S.M. / Deluca-Flaherty, C. / Mckay, D.B.
#2: Journal: Nature / Year: 1990
Title: Three-Dimensional Structure of the ATPase Fragment of a 70K Heat-Shock Cognate Protein
Authors: Flaherty, K.M. / Deluca-Flaherty, C. / Mckay, D.B.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 21, 1998-
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEAT-SHOCK COGNATE 70KD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1687
Polymers42,5271
Non-polymers6406
Water7,620423
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)143.300, 63.800, 46.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein HEAT-SHOCK COGNATE 70KD PROTEIN


Mass: 42527.129 Da / Num. of mol.: 1 / Fragment: 44KD ATPASE N-TERMINAL FRAGMENT / Mutation: D206K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 (DE3) / Cellular location: CYTOSOL / Organ: BRAIN / Plasmid: BL21 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P19120, adenosinetriphosphatase

-
Non-polymers , 6 types, 429 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growpH: 9
Details: 20% PEG-8000 1.0M NACL 50MM CHES, PH 9 1MM MGATP, pH 9.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %ethylene glycol1reservoir
220 %PEG80001reservoir
31.0 M1reservoirNaCl
440 mMCHES1reservoir
51reservoirNaOH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 34106 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 1 / Rsym value: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 12 / Rsym value: 0.133 / % possible all: 69.7
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 102051 / Rmerge(I) obs: 0.056

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HPM
Resolution: 1.9→8 Å / Rfactor Rfree error: 0.6 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3357 9.8 %RANDOM
Rwork0.2161 ---
Obs0.2161 34106 88.2 %-
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 27 9 423 3367
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.94 Å / Rfactor Rfree error: 0.6 / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.312 212
Rwork0.297 1867
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29809 / Rfactor Rfree: 0.2751
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: 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

Related info.:Yorodumi Speices / Aug 12, 2020. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
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

Read more

-
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.

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