[English] 日本語
Yorodumi
- PDB-6fw4: Protein-protein interactions and conformational changes : Importa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fw4
TitleProtein-protein interactions and conformational changes : Importance of the hydrophobic cavity of TolA C-terminal domain
ComponentsTolA protein
KeywordsPROTEIN BINDING / complex / induced fit / conformation / vibrio / cholerae / pressure / viral / phage / interaction / TolA / pIII / G3P / cavitie / protein
Function / homology
Function and homology information


bacteriocin transport / toxin transmembrane transporter activity / membrane => GO:0016020 / membrane
Similarity search - Function
TolA C-terminal / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TolA protein / TolA protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / distance geometry / molecular dynamics
AuthorsNavarro, R. / van Heijenoort, C. / Bornet, O. / Houot, L. / Lloubes, R. / Guerlesquin, F. / Nouailler, M.
CitationJournal: To Be Published
Title: Induced fit conformational changes of Vibrio cholerae TolAIII domain during the complex formation with the viral PIIIN1 domain: Structural and High-pressure NMR studies.
Authors: Navarro, R. / van Heijenoort, C. / Bornet, O. / Houot, L. / Lloubes, R. / Guerlesquin, F. / Nouailler, M.
History
DepositionMar 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: database_2 / pdbx_database_related
Item: _database_2.database_code / _pdbx_database_related.db_id
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TolA protein


Theoretical massNumber of molelcules
Total (without water)11,0101
Polymers11,0101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6610 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein TolA protein


Mass: 11009.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013140_01933 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6WQ38, UniProt: Q9KR10*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-15N HSQC
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H COSY
172isotropic12D 1H-13C CBCACO
1102isotropic13D HNCO
192isotropic13D HN(CA)CB
182isotropic13D CBCA(CO)NH
1112isotropic13D (H)CCH-TOCSY
2122isotropic32D 1H-15N HSQC
2132isotropic22D 1H-15N HSQC
1142isotropic33D 1H-15N NOESY
1152isotropic33D 1H-15N TOCSY
1162isotropic33D (H)CCH-TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM TolAIII, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] TolAIII, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTolAIIInatural abundance1
0.5 mMTolAIII[U-13C; U-15N]2
Sample conditions

Ionic strength: 0.5 M / Ionic strength err: 0.05 / pH: 6.9 / PH err: 0.1 / Temperature: 300 K / Temperature err: 5

Conditions-IDLabelPressure (kPa)Pressure err
1conditions_11 bar
2HP_conditions2500 bar10

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001IMM platform
Bruker AVANCE IIIBrukerAVANCE III9502TGIR Gif sur Yvette
Bruker AVANCE IIIBrukerAVANCE III8003TGIR Gif sur Yvette

-
Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
distance geometry6
molecular dynamics5
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