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

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Basic information

Entry
Database: PDB / ID: 2y9k
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
ComponentsPROTEIN INVG
KeywordsPROTEIN TRANSPORT / TYPE III SECRETION SYSTEM / OUTER MEMBRANE RING / SECRETIN FAMILY / C15 FOLD
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
: / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 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 1.1Mar 20, 2013Group: Other / Refinement description / Version format compliance
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 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 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.5May 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-1871
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polymers234,25415
Non-polymers00
Water00
1


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

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Components

#1: Protein
PROTEIN INVG


Mass: 15616.915 Da / Num. of mol.: 15 / Fragment: N-TERMINAL DOMAIN, RESIDUES 34-170 / Source method: isolated from a natural source
Source: (natural) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
References: UniProt: P35672

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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: NEEDLE COMPLEX / 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: 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 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTilt angle min: 0 °
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
2IMAGIC3D reconstruction
CTF correctionDetails: EACH CCD FRAME
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Actual pixel size: 1.33 Å
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 buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY FITTING
Atomic model buildingPDB-ID: 3GR5

3gr5


Accession code: 3GR5 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.3 Å
Refinement stepCycle: LAST / Highest resolution: 8.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16485 0 0 0 16485

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