PDB-2y9j: THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2y9j
Title	THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION
Descriptor	PROTEIN PRGH LIPOPROTEIN PRGK
Keywords	PROTEIN TRANSPORT, TYPE III SECRETION, IR1, INNER MEMBRANE RING, C24-FOLD
Authors	Schraidt, O., Marlovits, T.C.
Date	Deposition: 2011-02-15, Release: 2011-03-23
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1874, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1874 CiteFit EMDB-1871 Cite EMDB-1875 Cite PDB-2y9k Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1874 EMDB-1329 EMDB-1330 List of similar structure data about Omokage system

Article
Citation - primary
Article	Science, Vol. 331, Issue 6021, Page 1192-5, Year 2011
Title	Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Authors	Oliver Schraidt, Thomas C Marlovits Research Institute of Molecular Pathology, Dr. Bohr Gasse 7, A-1030 Vienna, Austria.
Keywords	Bacterial 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
Links	DOI: 10.1126/science.1199358, PubMed: 21385715

Components
ID 1 : PROTEIN PRGH
Image
Description	PROTEIN PRGH
Type	polymer
Fragment	PERIPLASMIC DOMAIN, RESIDUES 177-362
Formula weight	21839.992 Da
Number of molecules	24
Source	Method: Isolated from a natural source NCBI taxonomy: ID:90371 Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
Links	UniProt: P41783, Sequence view
ID 2 : PROTEIN PRGK
Image
Description	LIPOPROTEIN PRGK
Type	polymer
Fragment	PERIPLASMIC DOMAIN, RESIDUES 21-190
Formula weight	19015.688 Da
Number of molecules	24
Source	Method: Isolated from a natural source NCBI taxonomy: ID:90371 Organism scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYHPIMURIUM
Links	UniProt: P41786, Sequence view
ID 3 : water
Image
Description	water
Type	water
Formula weight	18.015 Da
Number of molecules	1584
Source	Method: Isolated from a natural source

Electron Microscopy
Imaging
Microscope	model: OTHER
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 gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Illumination mode	LOW DOSE
Lens
Mode	BRIGHT FIELD
Magnification	nominal: 93000 X
Cs	nominal: 2 mm
Nominal defocus	max: 2500 nm, min: 1000 nm
Detector
Type	GATAN CCD 4KX4K

Processing
2D projection selection
Software name	IMAGIC, CHIMERA
3D reconstruction
Actual pixel size	1.33 A/pix
CTF correction method	EACH MICROGRAPH
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).
Method	PROJECTION MATCHING
Resolution	6.4 A
3D fitting
Method	CORRELATION
Refinement Space	REAL
Target criteria	CORRELATION
Refine
Ls d res high	6.40 A
ID	1
Refine hist
D res high	6.40
Solvent atoms	1584
Total atoms	70704
Protein atoms	69120