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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 / homologyIcmF-related / 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 C-terminal / Intracellular multiplication and human macrophage-killing / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / integral component of membrane / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsYin, M. / Yan, Z.
CitationJournal: Cell Res. / Year: 2019
Title: Architecture of type VI secretion system membrane core complex.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2018 / Release: Jan 23, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 23, 2019Structure modelrepositoryInitial release
1.1Jan 30, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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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
Polyers1,560,19725
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 19271.090 Da / Num. of mol.: 15
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/peptide
Type VI Secretion System TssM / Type VI secretion system


Mass: 127113.070 Da / Num. of mol.: 10
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 / 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: 1,2 / 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
MicroscopyMicroscope model: 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 / Number of particles: 44069 / Symmetry type: POINT

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