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Yorodumi- EMDB-6678: CryoEM structure of type II secretion system cap deletion secreti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6678 | |||||||||
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Title | CryoEM structure of type II secretion system cap deletion secretin GspD in Vibrio cholerae | |||||||||
Map data | VC_GspD_DelCap post-processing map | |||||||||
Sample |
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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 | |||||||||
Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 Å | |||||||||
Authors | Yan ZF / Yin M / Li XM | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6678.map.gz | 14 MB | EMDB map data format | |
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Header (meta data) | emd-6678-v30.xml emd-6678.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_6678.png | 95.8 KB | ||
Others | emd_6678_additional.map.gz | 165.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6678 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6678 | HTTPS FTP |
-Validation report
Summary document | emd_6678_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_6678_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_6678_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6678 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6678 | HTTPS FTP |
-Related structure data
Related structure data | 6675C 6676C 6677C 5wq7C 5wq8C 5wq9C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6678.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | VC_GspD_DelCap post-processing map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: VC GspD DelCap unpost-processing map
File | emd_6678_additional.map | ||||||||||||
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Annotation | VC_GspD_DelCap unpost-processing map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T2SS secretin GspD cap deletion
Entire | Name: T2SS secretin GspD cap deletion |
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Components |
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-Supramolecule #1: T2SS secretin GspD cap deletion
Supramolecule | Name: T2SS secretin GspD cap deletion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) |
-Supramolecule #2: T2SS secretin GspD cap deletion
Supramolecule | Name: 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
Macromolecule | Name: T2SS secretin GspD cap deletion / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: OTHER |