[English] 日本語
Yorodumi
- EMDB-6675: CryoEM structure of type II secretion system secretin GspD in E.c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6675
TitleCryoEM structure of type II secretion system secretin GspD in E.coli K12
Map dataK12_GspD post-processing map 3.04
Sample
  • Complex: Full length T2SS secretin GspD complex
    • Complex: Putative type II secretion system protein D
      • Protein or peptide: Putative type II secretion system protein D
KeywordsSecretin family / C15 symmetry / T2SS / PROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain ...Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Putative secretin GspD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYan Z / Yin M
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structural insights into the secretin translocation channel in the type II secretion system.
Authors: Zhaofeng Yan / Meng Yin / Dandan Xu / Yongqun Zhu / Xueming Li /
Abstract: The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. ...The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel. The secretin domain constitutes a novel double β-barrel channel, with at least 60 β-strands in each barrel, and is stabilized by S domains. The outer membrane channel is sealed by β-strand-enriched gates. On the basis of the partially open state captured, we proposed a detailed gate-opening mechanism. Our structures provide a structural basis for understanding the secretin superfamily and the mechanism of substrate translocation in T2SS.
History
DepositionNov 23, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseDec 28, 2016-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5wq7
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6675.png

Downloads & links

-
Map

FileDownload / File: emd_6675.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationK12_GspD post-processing map 3.04
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 380 pix.
= 501.6 Å		1.32 Å/pix.
x 380 pix.
= 501.6 Å		1.32 Å/pix.
x 380 pix.
= 501.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.16052145 - 0.29636604
Average (Standard dev.)0.00016180739 (±0.004977131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 501.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z501.600501.600501.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.1610.2960.000

-
Supplemental data

-
Additional map: K12 GspD unpost-processing map

Fileemd_6675_additional.map
AnnotationK12_GspD unpost-processing map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Full length T2SS secretin GspD complex

EntireName: Full length T2SS secretin GspD complex
Components
  • Complex: Full length T2SS secretin GspD complex
    • Complex: Putative type II secretion system protein D
      • Protein or peptide: Putative type II secretion system protein D

-
Supramolecule #1: Full length T2SS secretin GspD complex

SupramoleculeName: Full length T2SS secretin GspD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 1 MDa

-
Supramolecule #2: Putative type II secretion system protein D

SupramoleculeName: Putative type II secretion system protein D / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

-
Macromolecule #1: Putative type II secretion system protein D

MacromoleculeName: Putative type II secretion system protein D / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 68.410789 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: ENEQYGANFN NADIRQFVEI VGQHLGKTIL IDPSVQGTIS VRSNDTFSQQ EYYQFFLSIL DLYGYSVITL DNGFLKVVRS ANVKTSPGM IADSSRPGVG DELVTRIVPL ENVPARDLAP LLRQMMDAGS VGNVVHYEPS NVLILTGRAS TINKLIEVIK R VDVIGTEK ...String:
ENEQYGANFN NADIRQFVEI VGQHLGKTIL IDPSVQGTIS VRSNDTFSQQ EYYQFFLSIL DLYGYSVITL DNGFLKVVRS ANVKTSPGM IADSSRPGVG DELVTRIVPL ENVPARDLAP LLRQMMDAGS VGNVVHYEPS NVLILTGRAS TINKLIEVIK R VDVIGTEK QQIIHLEYAS AEDLAEILNQ LISESHGKSQ MPALLSAKIV ADKRTNSLII SGPEKARQRI TSLLKSLDVE ES EEGNTRV YYLKYAKATN LVEVLTGVSE KLKDEKGNAR KPSSSGAMDN VAITADEQTN SLVITADQSV QEKLATVIAR LDI RRAQVL VEAIIVEVQD GNGLNLGVQW ANKNVGAQQF TNTGLPIFNA AQGVADYKKN GGITSANPAW DMFSAYNGMA AGFF NGDWG VLLTALASNN KNDILATPSI VTLDNKLASF NVGQDVPVLS GSQTTSGDNV FNTVERKTVG TKLKVTPQVN EGDAV LLEI EQEVSSVDSS SNSTLGPTFN TRTIQNAVLV KTGETVVLGG LLDDFSKEQV SKVPLLGDIP LVGQLFRYTS TERAKR NLM VFIRPTIIRD DDVYRSLSKE KYTRYRQEQQ QRIDGKSKAL VGSEDLPVLD ENTFNSHAPA PSSR

UniProtKB: Putative secretin GspD

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30659
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-5wq7:
CryoEM structure of type II secretion system secretin GspD in E.coli K12

+
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