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- PDB-5mxn: Atomic model of the VipA/VipB/Hcp, the type six secretion system ... -

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Entry
Database: PDB / ID: 5mxn
TitleAtomic model of the VipA/VipB/Hcp, the type six secretion system non-contractile sheath-tube of Vibrio cholerae from cryo-EM
DescriptorPROTEIN
KeywordsTRANSPORT PROTEIN / Type IV secretion system / protein export / transport protein
Specimen sourceVibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
MethodElectron microscopy (3.7 Å resolution / Helical array / Helical)
AuthorsWang, J. / Brackmann, M. / Castano-Diez, D. / Kudryashev, M. / Goldie, K. / Maier, T. / Stahlberg, H. / Basler, M.
CitationNat Microbiol, 2017, 2, 1507-1512

Nat Microbiol, 2017, 2, 1507-1512 Yorodumi Papers
Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 23, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Nov 8, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
1: Haemolysin co-regulated protein
A: Type VI secretion protein
a: Type VI secretion protein
2: Haemolysin co-regulated protein
B: Type VI secretion protein
b: Type VI secretion protein
3: Haemolysin co-regulated protein
C: Type VI secretion protein
c: Type VI secretion protein
4: Haemolysin co-regulated protein
D: Type VI secretion protein
d: Type VI secretion protein
5: Haemolysin co-regulated protein
E: Type VI secretion protein
e: Type VI secretion protein
6: Haemolysin co-regulated protein
F: Type VI secretion protein
f: Type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)539,42618
Polyers539,42618
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)84580
ΔGint (kcal/M)-575
Surface area (Å2)229790
MethodPISA
Conformers3 models

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Components

#1: Polypeptide(L)
Haemolysin co-regulated protein / Hcp / Type VI secretion system effector / Hcp1 family protein


Mass: 18878.055 Da / Num. of mol.: 6
Source: (gene. exp.) Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
References: UniProt: P72350
#2: Polypeptide(L)
Type VI secretion protein / VipB / Type VI secretion system protein ImpC


Mass: 53514.449 Da / Num. of mol.: 6
Source: (gene. exp.) Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
References: UniProt: A0A085SGI6
#3: Polypeptide(L)
Type VI secretion protein / VipA / Type VI secretion system protein ImpB / Type VI secretion system-associated protein / Uncharacterized protein ImpB


Mass: 17511.895 Da / Num. of mol.: 6
Source: (gene. exp.) Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
References: UniProt: A0A085SRC0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: Type six secretion system tube in complex with non-contractile sheath
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Vibrio cholerae
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryFitting IDImage processing ID
7Rosetta3.7MODEL FITTING1
12RELION2RECONSTRUCTION1
13PHENIX1.11.1-2575MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 23.5 deg. / Axial rise/subunit: 37.8 Å / Axial symmetry: C6
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10000 / Number of class averages: 1 / Symmetry type: HELICAL

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