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THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION

by single particle reconstruction, at 6.4 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-1874, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
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-1874, Image by UCSF CHIMERA

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

EMDB-1874

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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 PRGH
Image
DescriptionPROTEIN PRGH
Typepolypeptide(L)
FragmentPERIPLASMIC DOMAIN, RESIDUES 177-362
Formula weight21839.992 Da
Number of molecules24
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:90371
Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
LinksUniProt: P41783, Sequence view
ID 2 : PROTEIN PRGK
Image
DescriptionLIPOPROTEIN PRGK
Typepolypeptide(L)
FragmentPERIPLASMIC DOMAIN, RESIDUES 21-190
Formula weight19015.688 Da
Number of molecules24
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:90371
Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYHPIMURIUM
LinksUniProt: P41786, Sequence view
ID 3 : water
Image
Descriptionwater
Typewater
Formula weight18.015 Da
Number of molecules1584
ID3
SourceMethod: Isolated from a natural source
Sample
Assembly
Aggregation statePARTICLE
NameINNER MEMBRANE RING 1
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsCARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsMAGNIFICATION AT THE CCD 112969, CAMERA PIXEL 15UM, 1.33 ANGSTROM PER PIXEL, DATA COLLECTED SEMI- AUTOMATICALLY WITH POINT-2-POINT (DEVELOPED IN-HOUSE)
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationNominal: 93000 X
CsNominal: 2 mm
Nominal defocusMax: 2500 nm, Min: 1000 nm
Detector
TypeGATAN CCD 4KX4K
Processing
2D projection selection
Software nameIMAGIC, CHIMERA
3D reconstruction
Actual pixel size1.33 A/pix
CTF correction methodEACH MICROGRAPH
DetailsRESOLUTION 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).
MethodPROJECTION MATCHING
Resolution6.4 A
3D fitting
MethodCORRELATION
Refinement SpaceREAL
Target criteriaCORRELATION
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high6.40 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high6.40
Solvent atoms1584
Total atoms70704
Protein atoms69120
Download
PDB format
Allpdb2y9j.ent.gz
pdb2y9j.ent (uncompressed file)
Header onlypdb2y9j.ent.gz
mmCIF format
mmCIF2y9j.cif.gz
XML format
All2y9j.xml.gz
No-atom2y9j-noatom.xml.gz
Ext-atom2y9j-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.1 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.1 MB