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- PDB-3j6d: Model of the PrgH-PrgK periplasmic rings -

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Basic information

Entry
Database: PDB / ID: 3j6d
TitleModel of the PrgH-PrgK periplasmic rings
Components
  • Pathogenicity 1 island effector protein
  • Protein PrgH
KeywordsSTRUCTURAL PROTEIN / Bacterial secression macromolecular assemblies
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 str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
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 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 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
Remark 0THIS ENTRY 3J6D CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ...THIS ENTRY 3J6D CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-1875) DETERMINED ORIGINALLY BY AUTHORS: O.SCHRAIDT, T.C.MARLOVITS

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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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
a: Pathogenicity 1 island effector protein
b: Pathogenicity 1 island effector protein
c: Pathogenicity 1 island effector protein
d: Pathogenicity 1 island effector protein
e: Pathogenicity 1 island effector protein
f: Pathogenicity 1 island effector protein
g: Pathogenicity 1 island effector protein
h: Pathogenicity 1 island effector protein
i: Pathogenicity 1 island effector protein
j: Pathogenicity 1 island effector protein
k: Pathogenicity 1 island effector protein
l: Pathogenicity 1 island effector protein
m: Pathogenicity 1 island effector protein
n: Pathogenicity 1 island effector protein
o: Pathogenicity 1 island effector protein
p: Pathogenicity 1 island effector protein
q: Pathogenicity 1 island effector protein
r: Pathogenicity 1 island effector protein
s: Pathogenicity 1 island effector protein
t: Pathogenicity 1 island effector protein
u: Pathogenicity 1 island effector protein
v: Pathogenicity 1 island effector protein
Y: Pathogenicity 1 island effector protein
Z: Pathogenicity 1 island effector protein


Theoretical massNumber of molelcules
Total (without water)1,746,11248
Polymers1,746,11248
Non-polymers00
Water0
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: 44509.367 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: prgH, STM2874 / Production host: Escherichia coli (E. coli) / References: UniProt: P41783
#2: Protein ...
Pathogenicity 1 island effector protein / PrgK


Mass: 28245.287 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: SEETLT22_01090 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078PCJ3, UniProt: P41786*PLUS

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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: PrgH-PrgK periplasmic rings / Type: COMPLEX
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000 X
Image recordingFilm or detector model: GENERIC CCD

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Processing

EM software
IDNameCategory
1Rosettamodel fitting
2IMAGIC3D reconstruction
SymmetryPoint symmetry: C24 (24 fold cyclic)
3D reconstructionResolution: 11.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37171 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--EM-guided symmetrical modeling
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11MKY

1mky

11MKY1PDBexperimental model
24OYC

4oyc

14OYC2PDBexperimental model
34G1I

4g1i

14G1I3PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms65952 0 0 0 65952

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