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- PDB-2y9j: THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANO... -

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Basic information

Entry
Database: PDB / ID: 2y9j
TitleTHREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION
DescriptorPROTEIN PRGH, LIPOPROTEIN PRGK
KeywordsPROTEIN TRANSPORT / TYPE III SECRETION / IR1 / INNER MEMBRANE RING / C24-FOLD
Specimen sourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
MethodElectron microscopy (6.4 Å resolution / Particle / Single particle)
AuthorsSchraidt, O. / Marlovits, T.C.
CitationScience, 2011, 331, 1192-1195

Science, 2011, 331, 1192-1195 Yorodumi Papers
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 typeGroupCategoryItemProviderType
1.0Mar 23, 2011Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Apr 19, 2017Structure modelOther
1.4Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_image_scans / em_software_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: PROTEIN PRGH
B: PROTEIN PRGH
C: PROTEIN PRGH
D: PROTEIN PRGH
E: PROTEIN PRGH
F: PROTEIN PRGH
G: PROTEIN PRGH
H: PROTEIN PRGH
I: PROTEIN PRGH
J: PROTEIN PRGH
K: PROTEIN PRGH
L: PROTEIN PRGH
M: PROTEIN PRGH
N: PROTEIN PRGH
O: PROTEIN PRGH
P: PROTEIN PRGH
Q: PROTEIN PRGH
R: PROTEIN PRGH
S: PROTEIN PRGH
T: PROTEIN PRGH
U: PROTEIN PRGH
V: PROTEIN PRGH
W: PROTEIN PRGH
X: PROTEIN PRGH
Y: LIPOPROTEIN PRGK
Z: LIPOPROTEIN PRGK
a: LIPOPROTEIN PRGK
b: LIPOPROTEIN PRGK
c: LIPOPROTEIN PRGK
d: LIPOPROTEIN PRGK
e: LIPOPROTEIN PRGK
f: LIPOPROTEIN PRGK
g: LIPOPROTEIN PRGK
h: LIPOPROTEIN PRGK
i: LIPOPROTEIN PRGK
j: LIPOPROTEIN PRGK
k: LIPOPROTEIN PRGK
l: LIPOPROTEIN PRGK
m: LIPOPROTEIN PRGK
n: LIPOPROTEIN PRGK
o: LIPOPROTEIN PRGK
p: LIPOPROTEIN PRGK
q: LIPOPROTEIN PRGK
r: LIPOPROTEIN PRGK
s: LIPOPROTEIN PRGK
t: LIPOPROTEIN PRGK
u: LIPOPROTEIN PRGK
v: LIPOPROTEIN PRGK


Theoretical massNumber of molelcules
Total (without water)980,52848
Polyers980,52848
Non-polymers00
Water28,5361584
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L) ...
PROTEIN PRGH


Mass: 21839.814 Da / Num. of mol.: 24 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 177-362
Source: (natural) Salmonella enterica subsp. enterica serovar typhimurium / bacteria
References: UniProt: P41783

Cellular component

Biological process

#2: Polypeptide(L) ...
LIPOPROTEIN PRGK / PROTEIN PRGK


Mass: 19015.523 Da / Num. of mol.: 24 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 21-190
Source: (natural) Salmonella enterica subsp. enterica serovar typhimurium / bacteria
References: UniProt: P41786

Cellular component

Biological process

#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1584 / Formula: H2O

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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: INNER MEMBRANE RING 1 / 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: MAGNIFICATION AT THE CCD 112969, CAMERA PIXEL 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY WITH 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
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1UCSF ChimeraMODEL FITTING1
2IMAGICRECONSTRUCTION1
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C24
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.4 Å / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33
Details: RESOLUTION 6.4 ANGSTROM (0.5 FSC), 4.7 ANGSTROM (HALF BIT) PRGH (3GR1) MONOMERS WERE FITTED SEPARATELY, PRGK MODEL WAS BUILT BASED ON HOMOLOGY MODEL OF ESCJ (1YJ7) AND THEN INDIVIDUALLY FITTED INTO EM MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1874. (DEPOSITION ID: 7821).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--CORRELATION / Ref protocol: OTHER / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 2Y9J
Least-squares processHighest resolution: 6.4 Å
Refine hist #LASTHighest resolution: 6.4 Å
Number of atoms included #LASTProtein: 69120 / Nucleic acid: 0 / Ligand: 0 / Solvent: 1584 / Total: 70704

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