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Three-dimensional model of Salmonella's needle complex at subnanometer resolution

by single particle reconstruction, at 8.3 A resolution

Movie

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1871, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2y9k
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
DescriptorPROTEIN INVG
KeywordsPROTEIN TRANSPORT, TYPE III SECRETION SYSTEM, OUTER MEMBRANE RING, SECRETIN FAMILY, C15 FOLD
AuthorsSchraidt, O., Marlovits, T.C.
DateDeposition: 2011-02-15, Release: 2011-03-23
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1871, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1871

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Cite: data citing same article

Fit: target map of fitting

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleScience, Vol. 331, Issue 6021, Page 1192-5, Year 2011
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution.
AuthorsOliver Schraidt, Thomas C Marlovits
Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria.
KeywordsBacterial Proteins (chemistry), Bacterial Secretion Systems, Cryoelectron Microscopy, Crystallography, X-Ray, Image Processing, Computer-Assisted, Membrane Proteins (chemistry), Membrane Transport Proteins (chemistry), Models, Molecular, Mutation, PrgH protein, Salmonella typhimurium, PrgK protein, Salmonella typhimurium, Protein Conformation, Protein Structure, Tertiary, Salmonella typhimurium (chemistry), invG protein, Salmonella typhimurium
LinksDOI: 10.1126/science.1199358, PubMed: 21385715
Components
ID 1 : PROTEIN INVG
Image
DescriptionPROTEIN INVG
Typepolypeptide(L)
FragmentN-TERMINAL DOMAIN, RESIDUES 34-170
Formula weight15617.036 Da
Number of molecules15
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:90371
Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
LinksUniProt: P35672, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameNEEDLE COMPLEX
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsCARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsACUAL 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 gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Lens
ModeBRIGHT FIELD
MagnificationNominal: 93000 X
CsNominal: 2 mm
Nominal defocusMax: 2500 nm, Min: 1000 nm
Specimen holder
Tilt angleMin: 0 degrees
Detector
TypeCCD GATAN 4KX4K
Processing
2D projection selection
Software nameIMAGIC, CHIMERA
3D reconstruction
Actual pixel size1.33 A/pix
CTF correction methodEACH CCD FRAME
DetailsRESOLUTION 8.3 ANGSTROM (0.5 FSC), 6.7 ANGSTROM (HALF BIT) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1871. (DEPOSITION ID: 7820).
MethodPROJECTION MATCHING
Resolution8.3 A
3D fitting
MethodRIGID BODY FITTING
Refinement SpaceREAL
Target criteriaCORRELATION
3D fitting list
3D Fitting ID1
PDB entry ID3GR5
Refine
Refine idELECTRON MICROSCOPY
Ls d res high8.30 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high8.30
Total atoms16485
Protein atoms16485
Download
PDB format
Allpdb2y9k.ent.gz
pdb2y9k.ent (uncompressed file)
Header onlypdb2y9k.ent.gz
mmCIF format
mmCIF2y9k.cif.gz
XML format
All2y9k.xml.gz
No-atom2y9k-noatom.xml.gz
Ext-atom2y9k-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB