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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
Components
  • LIPOPROTEIN PRGK
  • PROTEIN PRGH
KeywordsPROTEIN TRANSPORT / TYPE III SECRETION / IR1 / INNER MEMBRANE RING / C24-FOLD
Function / homology
Function and homology information


protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Protein PrgH / Lipoprotein PrgK
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsSchraidt, O. / Marlovits, T.C.
CitationJournal: Science / Year: 2011
Title: Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Authors: Oliver Schraidt / Thomas C Marlovits /
Abstract: Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core ...Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.
History
DepositionFeb 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.6May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1874
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers980,52848
Non-polymers00
Water28,5361584
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
PROTEIN PRGH


Mass: 21839.814 Da / Num. of mol.: 24 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 177-362 / Source method: isolated from a natural source
Source: (natural) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
References: UniProt: P41783
#2: Protein ...
LIPOPROTEIN PRGK / PROTEIN PRGK


Mass: 19015.523 Da / Num. of mol.: 24 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 21-190 / Source method: isolated from a natural source
Source: (natural) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
References: UniProt: P41786
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1584 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: INNER MEMBRANE RING 1 / Type: COMPLEX
Buffer solutionpH: 7.5 / Details: 10mM Tris-HCl, 0.5M NaCl, 0.1% LDAO
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
MicroscopyModel: 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
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2IMAGIC3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: C24 (24 fold cyclic)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.4 Å / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33 Å
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 ...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 buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--CORRELATION
Atomic model buildingPDB-ID: 2Y9J

Accession code: 2Y9J / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.4 Å
Refinement stepCycle: LAST / Highest resolution: 6.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms69120 0 0 1584 70704

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