[English] 日本語
Yorodumi
- PDB-8heq: Solution structure of the periplasmic domain of the anti-sigma fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8heq
TitleSolution structure of the periplasmic domain of the anti-sigma factor RsgI2 from Clostridium thermocellum
Components(Anti-sigma-I factor RsgI2) x 2
KeywordsSIGNALING PROTEIN / ANTI-SIGMA FACTOR / TRANSCRIPTION
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily
Similarity search - Domain/homology
Anti-sigma-I factor RsgI2
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2023
Title: Essential autoproteolysis of bacterial anti-sigma factor RsgI for transmembrane signal transduction.
Authors: Chen, C. / Dong, S. / Yu, Z. / Qiao, Y. / Li, J. / Ding, X. / Li, R. / Lin, J. / Bayer, E.A. / Liu, Y.J. / Cui, Q. / Feng, Y.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-sigma-I factor RsgI2
B: Anti-sigma-I factor RsgI2


Theoretical massNumber of molelcules
Total (without water)18,7662
Polymers18,7662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area8130 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Anti-sigma-I factor RsgI2


Mass: 1216.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI2, Cthe_0267 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DC27
#2: Protein Anti-sigma-I factor RsgI2


Mass: 17549.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: rsgI2, Cthe_0267 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DC27

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D HBHA(CO)NH
191isotropic13D HBHANH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D (H)CCH-COSY
1121isotropic13D CCH-TOCSY
1131isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-15N NOESY

-
Sample preparation

DetailsType: solution
Contents: 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM [U-100% 13C; U-100% 15N] RsgI2PD, 0.02 % w/v DSS, 90% H2O/10% D2O
Label: nmr / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
1 mMRsgI2PD[U-100% 13C; U-100% 15N]1
0.02 % w/vDSSnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: condition1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJJohnson, One Moon Scientificchemical shift assignment
NMRViewJJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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