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- PDB-5urx: Structure of the contracted type VI secretion system sheath in My... -

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Basic information

Entry
Database: PDB / ID: 5urx
TitleStructure of the contracted type VI secretion system sheath in Myxococcus xanthus
DescriptorTssB, TssC
KeywordsPROTEIN TRANSPORT / T6SS / type IV secretion / protein machine / secretion system / sheath / contractile
Specimen sourceMyxococcus xanthus / bacteria / ミクソコッカス・キサンタス
MethodElectron microscopy (28 Å resolution / Cell / Subtomogram averaging)
AuthorsChang, Y.-W. / Rettberg, L.A. / Jensen, G.J.
CitationEMBO Rep., 2017, 18, 1090-1099

EMBO Rep., 2017, 18, 1090-1099 Yorodumi Papers
In vivo structures of an intact type VI secretion system revealed by electron cryotomography.
Yi-Wei Chang / Lee A Rettberg / Davi R Ortega / Grant J Jensen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 13, 2017 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1May 24, 2017Structure modelDatabase references
1.2Jul 12, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
1A: TssB
1B: TssC
1C: TssB
1D: TssC
1E: TssB
1F: TssC
1G: TssB
1H: TssC
1I: TssB
1J: TssC
1K: TssB
1L: TssC
2A: TssB
2B: TssC
2C: TssB
2D: TssC
2E: TssB
2F: TssC
2G: TssB
2H: TssC
2I: TssB
2J: TssC
2K: TssB
2L: TssC
3A: TssB
3B: TssC
3C: TssB
3D: TssC
3E: TssB
3F: TssC
3G: TssB
3H: TssC
3I: TssB
3J: TssC
3K: TssB
3L: TssC


Theoretical massNumber of molelcules
Total (without water)1,335,69236
Polyers1,335,69236
Non-polymers00
Water0
#1


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

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Components

#1: Polypeptide(L)
TssB


Mass: 18016.617 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
References: UniProt: Q1D305
#2: Polypeptide(L)
TssC


Mass: 56188.469 Da / Num. of mol.: 18
Source: (natural) Myxococcus xanthus / bacteria / ミクソコッカス・キサンタス
References: UniProt: Q1D304

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / Reconstruction method: SUBTOMOGRAM AVERAGING

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Sample preparation

ComponentName: Type VI secretion system / Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Source (natural)Organism: Myxococcus xanthus DK 1622
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategoryImaging IDImage processing ID
2UCSFTomoIMAGE ACQUISITION1
4IMODCTF CORRECTION1
11PEETFINAL EULER ASSIGNMENT1
12PEETCLASSIFICATION1
13Tomo3dRECONSTRUCTION1
CTF correctionType: NONE
3D reconstructionResolution: 28 Å / Resolution method: OTHER / Number of particles: 407 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 24 / Number of volumes extracted: 407

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