[English] 日本語
Yorodumi
- PDB-1qqm: D199S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qqm
TitleD199S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN
ComponentsD199S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN
KeywordsHYDROLASE / HYDROLASE (ACTING ON ACID ANHYDRIDES) / MOLECULAR CHAPERONE / ATPASE
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 / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy ...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 / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / : / Prp19 complex / heat shock protein binding / protein folding chaperone / RNA splicing / spliceosomal complex / ATP-dependent protein folding chaperone / mRNA processing / melanosome / presynapse / protein refolding / protein-macromolecule adaptor activity / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Defensin A-like - #30 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein ...Defensin A-like - #30 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJohnson, E.R. / Mckay, D.B.
Citation
Journal: Biochemistry / Year: 1999
Title: Mapping the role of active site residues for transducing an ATP-induced conformational change in the bovine 70-kDa heat shock cognate protein.
Authors: Johnson, E.R. / McKay, D.B.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Structural Basis of the 70-Kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity
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.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: 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
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Feb 14, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D199S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9587
Polymers41,3021
Non-polymers6566
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.455, 64.211, 46.488
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 D199S MUTANT OF BOVINE 70 KILODALTON HEAT SHOCK PROTEIN


Mass: 41301.535 Da / Num. of mol.: 1 / Fragment: HSC70 ATPASE FRAGMENT / Mutation: D199S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19120

-
Non-polymers , 6 types, 446 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ADP / ADENOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: POLYETHYLENE GLYCOL 8000, POTASSIUM CHLORIDE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG800011
21 M11KCl
350 mMCHES/KOH11
41 mMATP12
55 mM12MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 30759 / Num. obs: 30759 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2 % / Rmerge(I) obs: 0.089 / % possible all: 92.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 86567
Reflection shell
*PLUS
% possible obs: 92.1 % / Num. unique obs: 5255 / Num. measured obs: 10470 / Mean I/σ(I) obs: 8.7

-
Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 475628.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: ENGH & HUBER, HENDRICKSON W.A. AND KONNERT J.H.
Details: BIJVOET PAIRS WERE TREATED SEPARATELY IN REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.234 907 3 %
Rwork0.193 --
obs0.193 30331 87.4 %
all-30759 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.86 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--5.01 Å20 Å2
3----2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 36 440 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.741.5
X-RAY DIFFRACTIONc_mcangle_it1.242
X-RAY DIFFRACTIONc_scbond_it1.282
X-RAY DIFFRACTIONc_scangle_it1.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 155 3.1 %
Rwork0.258 4890 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
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: 0.291 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.258 / Rfactor obs: 0.258

+
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