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- EMDB-6678: CryoEM structure of type II secretion system cap deletion secreti... -

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Basic information

Entry
Database: EMDB / ID: EMD-6678
TitleCryoEM structure of type II secretion system cap deletion secretin GspD in Vibrio choleraeType II secretion system
Map dataVC_GspD_DelCap post-processing map
Sample
  • Complex: T2SS secretin GspD cap deletion
    • Complex: T2SS secretin GspD cap deletion
      • Protein or peptide: T2SS secretin GspD cap deletion
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/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsYan ZF / Yin M / Li XM
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-
UpdateFeb 22, 2017-
Current statusFeb 22, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6678.png

Downloads & links

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Map

FileDownload / File: emd_6678.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVC_GspD_DelCap post-processing map
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.06133565 - 0.09999309
Average (Standard dev.)0.00021615539 (±0.0027166458)
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-0.0610.1000.000

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Supplemental data

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Additional map: VC GspD DelCap unpost-processing map

Fileemd_6678_additional.map
AnnotationVC_GspD_DelCap unpost-processing map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T2SS secretin GspD cap deletion

EntireName: T2SS secretin GspD cap deletion
Components
  • Complex: T2SS secretin GspD cap deletion
    • Complex: T2SS secretin GspD cap deletion
      • Protein or peptide: T2SS secretin GspD cap deletion

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Supramolecule #1: T2SS secretin GspD cap deletion

SupramoleculeName: T2SS secretin GspD cap deletion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

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Supramolecule #2: T2SS secretin GspD cap deletion

SupramoleculeName: T2SS secretin GspD cap deletion / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

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Macromolecule #1: T2SS secretin GspD cap deletion

MacromoleculeName: T2SS secretin GspD cap deletion / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MKYWLKKSSW LLAGSLLSTP LAMANEFSAS FKGTDIQEFI NIVGRNLEKT IIVDPSVRGK VDVRSFDTLN EEQYYSFFLS VLEVYGFAV VEMDNGVLKV IKSKDAKTSA IPVLSGEERA NGDEVITQVV AVKNVSVREL SPLLRQLIDN AGAGNVVHYD P ANIILITG ...String:
MKYWLKKSSW LLAGSLLSTP LAMANEFSAS FKGTDIQEFI NIVGRNLEKT IIVDPSVRGK VDVRSFDTLN EEQYYSFFLS VLEVYGFAV VEMDNGVLKV IKSKDAKTSA IPVLSGEERA NGDEVITQVV AVKNVSVREL SPLLRQLIDN AGAGNVVHYD P ANIILITG RAAVVNRLAE IIRRVDQAGD KEIEVVELNN ASAAEMVRIV EALNKTTDAQ NTPEFLKPKF VADERTNSIL IS GDPKVRE RLKRLIKQLD VEMAAKGNNR VVYLKYAKAE DLVEVLKGVS ENLQAEKGTG QPTTSKRNEV MIAAHADTNS LVL TAPQDI MNAMLEVIGQ LDIRRAQVLI EALIVEMAEG DGINLGVQWG SLESGSVIQY GNTGASIGNV MIGLEEAKKG DYTK LASAL SSIQGAAVSI AMGDWTALIN AVSNDSSSNI LSSPSITVMD NGEASFIVGE EVPVITGSTA GSNNDNPFQT VDRKE VGIK LKVVPQINEG NSVQLNIEQE VSNVLGANGA VDVRFAKRQL NTSVMVQDGQ MLVLGGLIDE RALESESKVP LLGDIP LLG QLFRSTSSQV EKKNLMVFIK PTIIRDGVTA DGITQRKYNY IRAEQLFRAE KGLRLLDDAS VPVLPKFGDD RRHSPEI QA FIEQMEAKQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DARK FIELD
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Relion / Number images used: 3957

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