[English] 日本語
Yorodumi
- PDB-6d6s: Solution structure of Trigger Factor dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d6s
TitleSolution structure of Trigger Factor dimer
ComponentsTrigger factor
KeywordsCHAPERONE / protein folding / molecular chaperone / oligomerization
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat / cell cycle / cell division / identical protein binding / membrane / cytosol
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsSaio, T. / Kawagoe, S. / Ishimori, K. / Kalodimos, C.G.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM122462 United States
Japan Science and TechnologyPRESTO Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI (17H05657) Japan
CitationJournal: Elife / Year: 2018
Title: Oligomerization of a molecular chaperone modulates its activity.
Authors: Saio, T. / Kawagoe, S. / Ishimori, K. / Kalodimos, C.G.
History
DepositionApr 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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: Trigger factor
B: Trigger factor


Theoretical massNumber of molelcules
Total (without water)99,3922
Polymers99,3922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6430 Å2
ΔGint-23 kcal/mol
Surface area46550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 800target function
RepresentativeModel #1target function

-
Components

#1: Protein Trigger factor / TF / PPIase


Mass: 49696.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tig, b0436, JW0426 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A850, peptidylprolyl isomerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
121isotropic43D (1H)-13C HMQC-NOESY-1H-13C HMQC
231isotropic43D (1H)-13C HMQC-NOESY-1H-13C HMQC
341isotropic43D (1H)-13C HMQC-NOESY-1H-13C HMQC
452isotropic13D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQC
462isotropic113C-edited SOFAST-NOESY-HMQC
473isotropic53D (1H)-13C HMQC-NOESY-1H-13C HMQC
483isotropic13D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQC
493isotropic113C-edited SOFAST-NOESY-HMQC
1106isotropic23D (1H)-13C HMQC-NOESY-1H-13C HMQC
1116isotropic23D (1H)-15N HMQC-NOESY-1H-13C HMQC
1126isotropic23D (1H)-13C HMQC-NOESY-1H-15N HMQC
4136isotropic413C-edited NOESY-HMQC
1146isotropic415N-edited NOESY-HSQC
1155isotropic413C-edited NOESY-HSQC
1165isotropic115N-edited NOESY-HSQC
1174isotropic13D (1H)-13C HMQC-NOESY-1H-13C HMQC
1184isotropic313C-edited NOESY-HSQC
1191isotropic42D 1H-13C HMQC
2221isotropic42D 1H-13C HMQC
3231isotropic42D 1H-13C HMQC
4241isotropic42D 1H-13C HSQC aromatic
1201isotropic12D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.2 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] TF, 93% H2O/7% D2OILVMAYF-TF93% H2O/7% D2O
solution20.6 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3] Trigger Factor, 0.6 mM [Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] TF, 100% D2OIMA_LVYF-TF100% D2O
solution30.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] RBD, 0.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3] PPD-SBD, 100% D2OR-PS100% D2O
solution40.3 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] RBD, 93% H2O/7% D2ORBD93% H2O/7% D2O
solution50.8 mM [U-99% 13C; U-99% 15N] PPD, 93% H2O/7% D2OPPD93% H2O/7% D2O
solution60.5 mM [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N] SBD, 93% H2O/7% D2OSBD93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.2 mMTF[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N]1
0.6 mMTrigger Factor[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3]2
0.6 mMTF[Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N]2
0.3 mMRBD[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N]3
0.3 mMPPD-SBD[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3]3
0.3 mMRBD[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N]4
0.8 mMPPD[U-99% 13C; U-99% 15N]5
0.5 mMSBD[U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N]6
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM295K7.0 1 atm295 K
2100 mM283K7.0 1 atm283 K
3100 mM308K7.0 1 atm308 K
4100 mMD2O7.0 pD1 atm295 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III6003
Varian UNITYVarianUNITY8004
Varian UNITYVarianUNITY6005

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
OliviaMasashi Yokochichemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 800 / 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://pdbjlvh1.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