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- PDB-6ixh: Type VI secretion system membrane core complex -

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Basic information

Entry
Database: PDB / ID: 6ixh
TitleType VI secretion system membrane core complex
Components
  • Type VI Secretion System TssJType VI secretion system
  • Type VI Secretion System TssMType VI secretion system
KeywordsMEMBRANE PROTEIN / Type VI secretion system membrane core complex
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Type VI secretion system, lipoprotein SciN / IcmF-related / Intracellular multiplication and human macrophage-killing / Type VI secretion system IcmF, C-terminal / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion protein IcmF C2-like domain / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...Type VI secretion system, lipoprotein SciN / IcmF-related / Intracellular multiplication and human macrophage-killing / Type VI secretion system IcmF, C-terminal / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion protein IcmF C2-like domain / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type VI secretion system lipoprotein TssJ / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsYin, M. / Yan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722015 and 31570730 China
CitationJournal: Cell Res / Year: 2019
Title: Architecture of type VI secretion system membrane core complex.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li /
History
DepositionDec 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Type VI Secretion System TssJ
B: Type VI Secretion System TssJ
C: Type VI Secretion System TssJ
D: Type VI Secretion System TssJ
E: Type VI Secretion System TssJ
F: Type VI Secretion System TssJ
G: Type VI Secretion System TssJ
H: Type VI Secretion System TssJ
I: Type VI Secretion System TssJ
J: Type VI Secretion System TssJ
K: Type VI Secretion System TssJ
L: Type VI Secretion System TssJ
M: Type VI Secretion System TssJ
N: Type VI Secretion System TssJ
O: Type VI Secretion System TssJ
P: Type VI Secretion System TssM
Q: Type VI Secretion System TssM
R: Type VI Secretion System TssM
S: Type VI Secretion System TssM
T: Type VI Secretion System TssM
U: Type VI Secretion System TssM
V: Type VI Secretion System TssM
W: Type VI Secretion System TssM
X: Type VI Secretion System TssM
Y: Type VI Secretion System TssM


Theoretical massNumber of molelcules
Total (without water)1,560,19725
Polymers1,560,19725
Non-polymers00
Water0
1


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

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Components

#1: Protein
Type VI Secretion System TssJ / Type VI secretion system


Mass: 19271.090 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: EC55989_3320 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7LFS8
#2: Protein
Type VI Secretion System TssM / Type VI secretion system


Mass: 127113.070 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: EC55989_3325 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7LFU0

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Type VI Secretion System membrane core complex TssJLMType VI secretion system
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli 55989 (bacteria) / Strain: 55989
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44069 / Symmetry type: POINT

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