[English] 日本語
Yorodumi
- PDB-8glk: The Type 9 Secretion System dGldL peak II, NucA substrate bound c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8glk
TitleThe Type 9 Secretion System dGldL peak II, NucA substrate bound complex
Components
  • Endonuclease I
  • Peptidyl-prolyl cis-trans isomerase
  • Protein involved in gliding motility SprA
  • Type IX secretion system protein PorV domain-containing protein
KeywordsMEMBRANE PROTEIN / T9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - NucA Complex
Function / homology
Function and homology information


: / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / endonuclease activity
Similarity search - Function
Endonuclease I / Endonuclease I / Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / Peptidyl-prolyl cis-trans isomerase FKBP2/11 / Lamin tail domain ...Endonuclease I / Endonuclease I / Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / Peptidyl-prolyl cis-trans isomerase FKBP2/11 / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / His-Me finger 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Endonuclease I / Type IX secretion system protein PorV domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United Kingdom, European Union, United States, 6items
OrganizationGrant numberCountry
Wellcome Trust219477/Z/19/Z United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
European Research Council (ERC)833713European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007474/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S021264/1 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Microbiol / Year: 2024
Title: The Type 9 Secretion System caught in the act of transport
Authors: Lauber, F. / Deme, J.C. / Liu, X. / Kjaer, A. / Miller, H.L. / Alcock, F. / Lea, S.M. / Berks, B.C.
History
DepositionMar 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Endonuclease I
A: Protein involved in gliding motility SprA
B: Peptidyl-prolyl cis-trans isomerase
F: Type IX secretion system protein PorV domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,1115
Polymers342,1054
Non-polymers1,0051
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Endonuclease I


Mass: 8454.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FAQ0
#2: Protein Protein involved in gliding motility SprA


Mass: 270221.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5G5I4
#3: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 19219.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5F9W9
#4: Protein Type IX secretion system protein PorV domain-containing protein


Mass: 44210.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJM7
#5: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Type 9 Secretion System NucA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 62.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57573 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222384
ELECTRON MICROSCOPYf_angle_d0.51330390
ELECTRON MICROSCOPYf_dihedral_angle_d5.2263047
ELECTRON MICROSCOPYf_chiral_restr0.0453303
ELECTRON MICROSCOPYf_plane_restr0.0044024

+
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