[English] 日本語
Yorodumi
- PDB-8pek: Structure of the dimeric, periplasmic domain of ExbD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pek
TitleStructure of the dimeric, periplasmic domain of ExbD
ComponentsBiopolymer transport protein ExbD
KeywordsTRANSPORT PROTEIN / ton / tonb-binding / exbb-integrated / periplasmic / exbb-exbd / dimer
Function / homologyTonB system transport protein ExbD type-1 / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / transmembrane transporter activity / protein transport / membrane => GO:0016020 / plasma membrane / Biopolymer transport protein ExbD
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZinke, M. / Bardiaux, B. / Izadi-Pruneyre, N.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0039 France
Agence Nationale de la Recherche (ANR)ANR-16-CONV-0005 France
Citation
Journal: Nat Commun / Year: 2024
Title: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake.
Authors: Zinke, M. / Lejeune, M. / Mechaly, A. / Bardiaux, B. / Boneca, I.G. / Delepelaire, P. / Izadi-Pruneyre, N.
#1: Journal: Biorxiv / Year: 2023
Title: Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake.
Authors: Zinke, M. / Lejeune, M. / Mechaly, A. / Bardiaux, B. / Boneca, I.G. / Delepelaire, P. / Izadi-Pruneyre, N.
History
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Biopolymer transport protein ExbD
B: Biopolymer transport protein ExbD


Theoretical massNumber of molelcules
Total (without water)21,7412
Polymers21,7412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4120 Å2
ΔGint-30 kcal/mol
Surface area8760 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #7medoid

-
Components

#1: Protein Biopolymer transport protein ExbD


Mass: 10870.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria)
Gene: exbD, AN695_0216350, AR325_24260, BVG93_18405, BVG97_18665, C3R40_07870, CHR63_10945, DMW43_16865, FOT62_00910, HMI62_22190, HP475_23720
Plasmid: pet30(a)+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Escherichia coli / References: UniProt: V5YUQ0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CO)CA
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HN(CA)CB
161isotropic13D HN(COCA)CB
171isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic12D (HB)CB(CGCD)HD
1101isotropic12D (HB)CB(CGCDCE)HE
1111isotropic12D 1H-15N TROSY
1121isotropic12D 1H-15N HSQC
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aromatic
1152isotropic13D 1H-13C NOESY aliphatic
1163isotropic13D HNCO hydrogen bond detection
1174isotropic23D DOUBLY-FILTERED 1H-13C NOESY
1184isotropic23D DOUBLY-FILTERED 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution150 mM sodium phosphate, 50 mM sodium chloride, 1.5 mM [U-100% 13C; U-100% 15N] periplasmic domain of ExbD from Serratia marcescens, 90% H2O/10% D2O15N13C_ExbD_Sm90% H2O/10% D2O
solution250 mM sodium phosphate, 50 mM sodium chloride, 1.5 mM [U-100% 13C; U-100% 15N] periplasmic domain of ExbD from Serratia marcescens, 100% D2O15N13C_ExbD_Sm_in_D2O100% D2O
solution350 mM sodium phosphate, 50 mM sodium chloride, 2 mM [U-100% 13C; U-100% 15N; U-95% 2H] periplasmic domain of ExbD from Serratia marcescens, 90% H2O/10% D2O2H15N13C_ExbD_Sm90% H2O/10% D2O
solution450 mM sodium phosphate, 50 mM sodium chloride, 2 mM [U-100% 13C; U-100% 15N; U-95% 2H; natural abundance] periplasmic domain of ExbD from Serratia marcescens, 90% H2O/10% D2O15N13C_ExbD_Sm_mixed90% H2O/10% D2Omixed sample of natural abundance ExbD_Sm and 15N13C ExbD_Sm to acquire intermolecular NOEs
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1.5 mMperiplasmic domain of ExbD from Serratia marcescens[U-100% 13C; U-100% 15N]1
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1.5 mMperiplasmic domain of ExbD from Serratia marcescens[U-100% 13C; U-100% 15N]2
50 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
2 mMperiplasmic domain of ExbD from Serratia marcescens[U-100% 13C; U-100% 15N; U-95% 2H]3
50 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
2 mMperiplasmic domain of ExbD from Serratia marcescens[U-100% 13C; U-100% 15N; U-95% 2H; natural abundance]4
Sample conditionsIonic strength: 0.3 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 293.15 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE III HDBrukerAVANCE III HD6002

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis Assign3.1Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GWchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2.3.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.5Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue EDpeak picking
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
TALOS-N4.12Shen and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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