[English] 日本語
Yorodumi
- PDB-4rwu: J-domain of Sis1 protein, Hsp40 co-chaperone from Saccharomyces c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rwu
TitleJ-domain of Sis1 protein, Hsp40 co-chaperone from Saccharomyces cerevisiae
ComponentsProtein SIS1
KeywordsCHAPERONE / hsp40 / J-domain / cochaperone / structural genomics / APC90055.5 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / : / cellular response to starvation / translational initiation / unfolded protein binding ...detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / : / cellular response to starvation / translational initiation / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / cytosolic small ribosomal subunit / nucleolus / DNA binding / nucleus / cytosol
Similarity search - Function
: / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...: / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOsipiuk, J. / Zhou, M. / Gu, M. / Sahi, C. / Craig, E.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1.
Authors: Yu, H.Y. / Ziegelhoffer, T. / Osipiuk, J. / Ciesielski, S.J. / Baranowski, M. / Zhou, M. / Joachimiak, A. / Craig, E.A.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionDec 17, 2014ID: 2O37
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SIS1


Theoretical massNumber of molelcules
Total (without water)9,9181
Polymers9,9181
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.645, 43.564, 65.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein SIS1


Mass: 9918.003 Da / Num. of mol.: 1 / Fragment: J-domain (UNP residues 1-89)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288C / Gene: N2879, SIS1, YNL007C / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25294
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→26.2 Å / Num. all: 23934 / Num. obs: 23934 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.048 / Χ2: 0.975 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.25-1.273.10.4132.047490.71159.3
1.27-1.293.60.4078480.79568
1.29-1.324.30.3749180.79270.2
1.32-1.354.60.3659910.80379
1.35-1.384.90.33811010.8386.8
1.38-1.415.40.32611700.79291.5
1.41-1.445.60.29212030.85295.4
1.44-1.485.90.24312610.86299.1
1.48-1.536.20.20712720.88999.5
1.53-1.576.60.17813000.902100
1.57-1.6370.16212770.955100
1.63-1.770.14112700.943100
1.7-1.7770.11812971.008100
1.77-1.8770.09512961.056100
1.87-1.9870.0813001.215100
1.98-2.1470.06112901.304100
2.14-2.356.90.05112951.216100
2.35-2.696.70.03613250.996100
2.69-3.396.80.02413460.891100
3.39-406.60.01914250.93999.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DMX

2dmx


Resolution: 1.25→26.2 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.324 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1494 1228 5.1 %RANDOM
Rwork0.122 ---
obs0.1234 23883 92.53 %-
all-23883 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.92 Å2 / Biso mean: 15.937 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20 Å2
2---0.47 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms643 0 0 146 789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02806
X-RAY DIFFRACTIONr_bond_other_d0.0010.02814
X-RAY DIFFRACTIONr_angle_refined_deg1.5332.0171106
X-RAY DIFFRACTIONr_angle_other_deg0.82631933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7075117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27625.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58415180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.712155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02167
X-RAY DIFFRACTIONr_mcbond_it1.4181.165369
X-RAY DIFFRACTIONr_mcbond_other1.3281.152366
X-RAY DIFFRACTIONr_mcangle_it1.6871.748469
X-RAY DIFFRACTIONr_rigid_bond_restr2.70931620
X-RAY DIFFRACTIONr_sphericity_free32.43530
X-RAY DIFFRACTIONr_sphericity_bonded9.57751703
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 71 -
Rwork0.207 1078 -
all-1149 -
obs-1149 60.89 %

+
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