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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 A resolution / Single particle / Vitreous ice)
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

DateDeposition: Feb 15, 2011 / Release: Mar 23, 2011 / Last modification: Apr 19, 2017

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Structure visualization

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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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

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Sample preparation

Assembly of specimenName: INNER MEMBRANE RING 1 / Aggregation state: PARTICLE
ComponentName: INNER MEMBRANE RING 1 / Type: COMPLEX
Buffer solutionDetails: 10mM Tris-HCl, 0.5M NaCl, 0.1% LDAO
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

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 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
CameraType: GATAN CCD 4KX4K
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: IMAGIC, CHIMERA
3D reconstructionMethod: PROJECTION MATCHING / Software: IMAGIC / Resolution: 6.4 A / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33 A/pix
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).
Atomic model buildingDetails: METHOD--CORRELATION / Ref protocol: OTHER / Ref space: REAL / Target criteria: CORRELATION
Atomic model buildingPDB-ID: 2Y9J
Least-squares processHighest resolution: 6.4 A
Refine hist #LASTHighest resolution: 6.4 A
Number of atoms included #LASTProtein: 69120 / Nucleic acid: 0 / Ligand: 0 / Solvent: 1584 / Total: 70704

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