[English] 日本語
Yorodumi
- PDB-2y4t: Crystal structure of the human co-chaperone P58(IPK) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y4t
TitleCrystal structure of the human co-chaperone P58(IPK)
ComponentsDNAJ HOMOLOG SUBFAMILY C MEMBER 3
KeywordsCHAPERONE / ENDOPLASMIC RETICULUM / PROTEIN FOLDING / TETRATRICOPEPTIDEREPEAT / J DOMAIN / UNFOLDED PROTEIN RESPONSE
Function / homology
Function and homology information


positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / negative regulation of translation in response to endoplasmic reticulum stress / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / Viral mRNA Translation / response to unfolded protein ...positive regulation of translation initiation in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / negative regulation of translation in response to endoplasmic reticulum stress / protein folding in endoplasmic reticulum / XBP1(S) activates chaperone genes / misfolded protein binding / cellular response to cold / protein kinase inhibitor activity / Viral mRNA Translation / response to unfolded protein / proteolysis involved in protein catabolic process / Post-translational protein phosphorylation / PKR-mediated signaling / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / azurophil granule lumen / extracellular vesicle / protein-folding chaperone binding / defense response to virus / endoplasmic reticulum lumen / Neutrophil degranulation / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
: / DnaJ domain / DnaJ domain / Tetratricopeptide repeat / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Tetratricopeptide repeat / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeat ...: / DnaJ domain / DnaJ domain / Tetratricopeptide repeat / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Tetratricopeptide repeat / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily C member 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSvard, M. / Biterova, E.I. / Bourhis, J.-M. / Guy, J.E.
CitationJournal: Plos One / Year: 2011
Title: The Crystal Structure of the Human Co-Chaperone P58Ipk
Authors: Svard, M. / Biterova, E.I. / Bourhis, J.-M. / Guy, J.E.
History
DepositionJan 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3
B: DNAJ HOMOLOG SUBFAMILY C MEMBER 3
C: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)155,8413
Polymers155,8413
Non-polymers00
Water45025
1
A: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNAJ HOMOLOG SUBFAMILY C MEMBER 3


Theoretical massNumber of molelcules
Total (without water)51,9471
Polymers51,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)212.250, 212.250, 283.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.4497, 0.8931, 0.01416), (0.8931, -0.4498, 0.008273), (0.01376, 0.008923, -0.9999)-1.346, 3.614, -89.41
2given(0.4432, 0.8964, 0.01124), (0.8963, -0.4433, 0.01285), (0.01651, 0.004378, -0.9999)-1.443, 4.663, -180.6
3given(1, 0.007427, -0.003283), (-0.007413, 1, 0.004333), (0.003315, -0.004308, 1)-0.501, -0.269, 91.2

-
Components

#1: Protein DNAJ HOMOLOG SUBFAMILY C MEMBER 3 / INTERFERON-INDUCED\ / DOUBLE-STRANDED RNA-ACTIVATED PROTEIN KINASE INHIBITOR / PROTEIN KINASE ...INTERFERON-INDUCED\ / DOUBLE-STRANDED RNA-ACTIVATED PROTEIN KINASE INHIBITOR / PROTEIN KINASE INHIBITOR OF 58 KDA / PROTEIN KINASE INHIBITOR P58 / P58IPK


Mass: 51946.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 35-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P58IPK_6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q13217
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 0.1 M HEPES, PH 8.2, 1.4 M SUCCINIC ACID, 1% (W/V) PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 44987 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 79.2

-
Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 39.464 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.211 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE REGIONS THAT CORRESPOND TO AMINO ACIDS 400-406, 451-452 OF CHAIN B AND 400-409, 449- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE REGIONS THAT CORRESPOND TO AMINO ACIDS 400-406, 451-452 OF CHAIN B AND 400-409, 449-450 OF CHAIN C ARE LOCALIZED TO VERY FLEXIBLE LOOPS, CONTAIN VERY WEAK ELECTRON DENSITY AND HAVE BEEN MODELED BASED ON THE POSITION OF RESPECTIVE AMINO ACIDS OF BETTER ORDERED CHAIN A. IN CHAINS B AND C, THE LOOP BETWEEN HELICES I AND II OF THE J DOMAIN (AMINO ACID RESIDUES 402-408) AND THE LOOP IN THE J DOMAIN (RESIDUES 425-428) HAVE VERY WEAK DENSITY AND ARE MODELED BASED ON THEIR POSITION IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.29058 2416 5.1 %RANDOM
Rwork0.24338 ---
obs0.24582 44987 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.121 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10234 0 0 25 10259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210390
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.97513934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.67451262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33625.141531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.699152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011569
X-RAY DIFFRACTIONr_chiral_restr0.0740.21505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027751
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 144 -
Rwork0.326 2511 -
obs--74.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42220.1733-0.02990.2975-0.03210.2407-0.01670.06550.1265-0.0788-0.02330.1837-0.0488-0.14660.040.0749-0.0057-0.060.1878-0.04910.130581.1791-49.378724.0866
20.5292-0.22420.08210.7409-0.12780.27570.0262-0.0997-0.13480.1887-0.05190.25210.0341-0.11690.02580.0944-0.00320.06570.2641-0.05090.112281.2235-73.3271-20.705
30.46210.1346-0.0650.3753-0.10350.36920.00430.06690.1649-0.0978-0.0180.2469-0.0602-0.19050.01380.1297-0.0335-0.0730.2297-0.05420.199281.1394-49.5399-67.1397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 455
2X-RAY DIFFRACTION2B35 - 455
3X-RAY DIFFRACTION3C34 - 455

+
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