[English] 日本語
Yorodumi
- PDB-6psi: Structural Basis for Client Recognition and Activity of Hsp40 Cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6psi
TitleStructural Basis for Client Recognition and Activity of Hsp40 Chaperones
Components
  • Alkaline phosphatase
  • Chaperone protein DnaJ 2
KeywordsCHAPERONE / Client Recognition
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / protein dephosphorylation / unfolded protein binding / outer membrane-bounded periplasmic space / protein refolding ...oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / protein dephosphorylation / unfolded protein binding / outer membrane-bounded periplasmic space / protein refolding / DNA replication / periplasmic space / magnesium ion binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Nt-dnaJ domain signature. / DnaJ domain, conserved site ...HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Alkaline phosphatase / Alkaline phosphatase / Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsJiang, Y. / Rossi, P. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM122462-04 United States
CitationJournal: Science / Year: 2019
Title: Structural basis for client recognition and activity of Hsp40 chaperones.
Authors: Jiang, Y. / Rossi, P. / Kalodimos, C.G.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein DnaJ 2
B: Alkaline phosphatase
C: Chaperone protein DnaJ 2


Theoretical massNumber of molelcules
Total (without water)111,5393
Polymers111,5393
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18620 Å2
ΔGint-80 kcal/mol
Surface area54050 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Chaperone protein DnaJ 2


Mass: 31023.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: dnaJ2, TTHA1489 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56237
#2: Protein Alkaline phosphatase / Bacterial alkaline phosphatase


Mass: 49492.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: phoA, ACU57_12080, AUQ13_18595, BANRA_02023, BANRA_03586, BET08_14335, BHF46_20915, BUE81_15475, C4J69_09555, C5N07_12695, CA593_01230, D0X26_07375, D3821_12940, DNQ41_05820, EAI52_02910, ...Gene: phoA, ACU57_12080, AUQ13_18595, BANRA_02023, BANRA_03586, BET08_14335, BHF46_20915, BUE81_15475, C4J69_09555, C5N07_12695, CA593_01230, D0X26_07375, D3821_12940, DNQ41_05820, EAI52_02910, EC3234A_4c00530, EC3426_01222, ECTO6_03716, ED648_16735, EEP23_01005, EL75_3367, EL79_3462, EL80_3416, NCTC13462_01945, NCTC9037_03964, NCTC9062_04458, RK56_026750, SAMEA3753300_00450, UN91_18770
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A086VD57, UniProt: P00634*PLUS, alkaline phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HMQC
141isotropic13D 1H-13C NOESY
151isotropic13D 1H-15N NOESY
1121isotropic13D HN(CA)CB
1111isotropic13D HNCO
1101isotropic13D CCH-SOFAST HMQC-NOESY-HMQC
191isotropic13D NCH-SOFAST HMQC-NOESY-HMQC
181isotropic13D HCH-sofastNOESY-HMQC
171isotropic13D HNH-sofastNOESY-HMQC
161isotropic13D CNH-SOFAST HMQC-NOESY-HMQC

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N; U-80% 2H] PhoA_DnaJ, 75 mM potassium chloride, 20 mM potassium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O
Details: Highly deuterated selectively ILVMAT methyl labeled
Label: NCD_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPhoA_DnaJ[U-100% 13C; U-100% 15N; U-80% 2H]1
75 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.04 %sodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 25 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpinBruker Biospincollection
PSVSBhattacharya and Montelioneprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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