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- PDB-2y9k: Three-dimensional model of Salmonella's needle complex at subnano... -

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Entry
Database: PDB / ID: 2y9k
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
DescriptorPROTEIN INVG
KeywordsPROTEIN TRANSPORT / TYPE III SECRETION SYSTEM / OUTER MEMBRANE RING / SECRETIN FAMILY / C15 FOLD
Specimen sourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
MethodElectron microscopy (8.3 Å resolution / Particle / Single particle)
AuthorsSchraidt, O. / Marlovits, T.C.
CitationScience, 2011, 331, 1192-1195

Science, 2011, 331, 1192-1195 StrPapers
Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Oliver Schraidt / Thomas C Marlovits

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2011 / Release: Mar 23, 2011
RevisionDateData content typeGroupProviderType
1.0Mar 23, 2011Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelOther / Refinement description / Version format compliance
1.2Apr 19, 2017Structure modelOther

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Assembly

Deposited unit
A: PROTEIN INVG
B: PROTEIN INVG
C: PROTEIN INVG
D: PROTEIN INVG
E: PROTEIN INVG
F: PROTEIN INVG
G: PROTEIN INVG
H: PROTEIN INVG
I: PROTEIN INVG
J: PROTEIN INVG
K: PROTEIN INVG
L: PROTEIN INVG
M: PROTEIN INVG
N: PROTEIN INVG
O: PROTEIN INVG


Theoretical massNumber of molelcules
Total (without water)234,25415
Polyers234,25415
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
PROTEIN INVG


Mass: 15616.915 Da / Num. of mol.: 15 / Fragment: N-TERMINAL DOMAIN, RESIDUES 34-170
Source: (natural) Salmonella enterica subsp. enterica serovar typhimurium / bacteria
References: UniProt: P35672

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: NEEDLE COMPLEX / Type: COMPLEX
Buffer solutionDetails: 10mM Tris-HCl 0.5M NaCl 0.1% LDAO / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Details: ACUAL MAGNIFICATION AT CCD 112968, CAMERA PIXEL SIZE 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY USING POINT-2-POINT (DEVELOPED IN-HOUSE)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 93000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTilt angle min: 0 deg.
Image recordingFilm or detector model: GENERIC GATAN (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF ChimeraMODEL FITTING
2IMAGICRECONSTRUCTION
CTF correctionDetails: EACH CCD FRAME
SymmetryPoint symmetry: C15
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33
Details: RESOLUTION 8.3 ANGSTROM (0.5 FSC), 6.7 ANGSTROM (HALF BIT) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1871. (DEPOSITION ID: 7820).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY FITTING / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: CORRELATION
Atomic model buildingPDB-ID: 3GR5
Least-squares processHighest resolution: 8.3 Å
Refine hist #LASTHighest resolution: 8.3 Å
Number of atoms included #LASTProtein: 16485 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 16485

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