PDB-2wwq: E.COLI 70S RIBOSOME STALLED DURING TRANSLATION OF TNAC ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2wwq
Title	E.COLI 70S RIBOSOME STALLED DURING TRANSLATION OF TNAC LEADER PEPTIDE. THIS FILE CONTAINS THE 50S, THE P-SITE TRNA AND THE TNAC LEADER PEPTIDE (PART 2 OF 2).
Descriptor	50S RIBOSOMAL PROTEIN L28 50S RIBOSOMAL PROTEIN L29 50S RIBOSOMAL PROTEIN L30 50S RIBOSOMAL PROTEIN L32 50S RIBOSOMAL PROTEIN L33 50S RIBOSOMAL PROTEIN L1 50S RIBOSOMAL PROTEIN L34 50S RIBOSOMAL PROTEIN L35 50S RIBOSOMAL PROTEIN L36 50S RIBOSOMAL PROTEIN L4 50S RIBOSOMAL PROTEIN L5 50S RIBOSOMAL PROTEIN L6 50S RIBOSOMAL PROTEIN L9 50S RIBOSOMAL PROTEIN L11 50S RIBOSOMAL PROTEIN L13 50S RIBOSOMAL PROTEIN L14 50S RIBOSOMAL PROTEIN L15 50S RIBOSOMAL PROTEIN L16 50S RIBOSOMAL PROTEIN L17 50S RIBOSOMAL PROTEIN L18 50S RIBOSOMAL PROTEIN L19 50S RIBOSOMAL PROTEIN L20 50S RIBOSOMAL PROTEIN L21 50S RIBOSOMAL PROTEIN L22 50S RIBOSOMAL PROTEIN L23 50S RIBOSOMAL PROTEIN L24 50S RIBOSOMAL PROTEIN L25 50S RIBOSOMAL PROTEIN L27 NASCENT TNAC LEADER PEPTIDE 5
Keywords	RIBOSOME, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, TRANSLATION, ZINC-FINGER, TNAC, 70S RIBOSOME, STALLING
Authors	Seidelt, B., Innis, C.A., Wilson, D.N., Gartmann, M., Armache, J., Villa, E., Trabuco, L.G., Becker, T., Mielke, T., Schulten, K., Steitz, T.A., Beckmann, R.
Date	Deposition: 2009-10-26, Release: 2010-04-14
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: With PDB-2wwl, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1657 CiteFit PDB-2wwl CiteSplit PDB-1b75 PDB-1d6k PDB-1dfu PDB-1p85 PDB-1p86 PDB-2aw4 PDB-2awb PDB-2j28 PDB-2vhm PDB-2vhn PDB-2vrh PDB-487d Cite: data citing same article Fit: target map of fitting Split: split data constructing the same model
Similar strucutres (beta)	Diagram PDB-3j12 PDB-3j0y PDB-3bbx PDB-3j11 PDB-3j01 PDB-2xtg List of similar structure data about Omokage system

Article
Citation - primary
Article	Science, Vol. 326, Issue 5958, Page 1412-5, Year 2009
Title	Structural insight into nascent polypeptide chain-mediated translational stalling.
Authors	Birgit Seidelt, C Axel Innis, Daniel N Wilson, Marco Gartmann, Jean-Paul Armache, Elizabeth Villa, Leonardo G Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A Steitz, Roland Beckmann Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department for Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
Keywords	Binding Sites, Cryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Gene Expression Regulation, Bacterial, Image Processing, Computer-Assisted, Models, Biological, Models, Molecular, Operon, Peptidyl Transferases (metabolism, 2.3.2.12), Protein Biosynthesis, Protein Conformation, RNA-Binding Proteins (chemistry), Ribosomal Proteins (chemistry), Ribosomes (metabolism), Tryptophanase (biosynthesis, 4.1.99.1), rplV protein, E coli, tnaC protein, E coli
Links	DOI: 10.1126/science.1177662, PubMed: 19933110, PMC: PMC2920484

Components
ID 1 : 50S RIBOSOMAL PROTEIN L28
Image
Description	50S RIBOSOMAL PROTEIN L28
Type	polymer
Formula weight	8896.435 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7M2, Sequence view
ID 2 : 50S RIBOSOMAL PROTEIN L29
Image
Description	50S RIBOSOMAL PROTEIN L29
Type	polymer
Formula weight	7286.531 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7M6, Sequence view
ID 3 : 50S RIBOSOMAL PROTEIN L30
Image
Description	50S RIBOSOMAL PROTEIN L30
Type	polymer
Formula weight	6423.682 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0AG51, Sequence view
ID 4 : 50S RIBOSOMAL PROTEIN L32
Image
Description	50S RIBOSOMAL PROTEIN L32
Type	polymer
Formula weight	6332.307 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7N4, Sequence view
ID 5 : 50S RIBOSOMAL PROTEIN L33
Image
Description	50S RIBOSOMAL PROTEIN L33
Type	polymer
Formula weight	5814.909 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7N9, Sequence view
ID 6 : 50S RIBOSOMAL PROTEIN L1
Image
Description	50S RIBOSOMAL PROTEIN L1
Type	polymer
Formula weight	24765.834 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7L0, Sequence view
ID 7 : 50S RIBOSOMAL PROTEIN L34
Image
Description	50S RIBOSOMAL PROTEIN L34
Type	polymer
Formula weight	5397.506 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7P5, Sequence view
ID 8 : 50S RIBOSOMAL PROTEIN L35
Image
Description	50S RIBOSOMAL PROTEIN L35
Type	polymer
Formula weight	7181.907 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7Q1, Sequence view
ID 9 : 50S RIBOSOMAL PROTEIN L36
Image
Description	50S RIBOSOMAL PROTEIN L36
Type	polymer
Formula weight	4377.415 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7Q6, Sequence view
ID 10 : 5S RIBOSOMAL RNA
Image
Description	5S RIBOSOMAL RNA
Type	polymer
Formula weight	37848.766 Da
Number of molecules	1
Source	Method: Obtained synthetically NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	GenBank: CP001396, Sequence view
ID 11 : 23S RIBOSOMAL RNA
Image
Description	23S RIBOSOMAL RNA
Type	polymer
Formula weight	941307.500 Da
Number of molecules	1
Source	Method: Obtained synthetically NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	GenBank: CP001396, Sequence view
ID 12 : 50S RIBOSOMAL PROTEIN L2
Image
Description	50S RIBOSOMAL PROTEIN L2
Type	polymer
Formula weight	29663.471 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P60422, Sequence view
ID 13 : 50S RIBOSOMAL PROTEIN L3
Image
Description	50S RIBOSOMAL PROTEIN L3
Type	polymer
Formula weight	22277.709 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P60438, Sequence view
ID 14 : 50S RIBOSOMAL PROTEIN L4
Image
Description	50S RIBOSOMAL PROTEIN L4
Type	polymer
Formula weight	22121.723 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P60723, Sequence view
ID 15 : 50S RIBOSOMAL PROTEIN L5
Image
Description	50S RIBOSOMAL PROTEIN L5
Type	polymer
Formula weight	20202.566 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P62399, Sequence view
ID 16 : 50S RIBOSOMAL PROTEIN L6
Image
Description	50S RIBOSOMAL PROTEIN L6
Type	polymer
Formula weight	18801.766 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0AG55, Sequence view
ID 17 : 50S RIBOSOMAL PROTEIN L9
Image
Description	50S RIBOSOMAL PROTEIN L9
Type	polymer
Formula weight	15789.174 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7R1, Sequence view
ID 18 : 50S RIBOSOMAL PROTEIN L11
Image
Description	50S RIBOSOMAL PROTEIN L11
Type	polymer
Formula weight	14763.286 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7J7, Sequence view
ID 19 : 50S RIBOSOMAL PROTEIN L13
Image
Description	50S RIBOSOMAL PROTEIN L13
Type	polymer
Formula weight	16050.749 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0AA10, Sequence view
ID 20 : 50S RIBOSOMAL PROTEIN L14
Image
Description	50S RIBOSOMAL PROTEIN L14
Type	polymer
Formula weight	13352.881 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0ADY3, Sequence view
ID 21 : 50S RIBOSOMAL PROTEIN L15
Image
Description	50S RIBOSOMAL PROTEIN L15
Type	polymer
Fragment	RESIDUES 2-144
Formula weight	14877.406 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P02413, Sequence view
ID 22 : 50S RIBOSOMAL PROTEIN L16
Image
Description	50S RIBOSOMAL PROTEIN L16
Type	polymer
Formula weight	15312.394 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0ADY7, Sequence view
ID 23 : 50S RIBOSOMAL PROTEIN L17
Image
Description	50S RIBOSOMAL PROTEIN L17
Type	polymer
Formula weight	13722.047 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0AG44, Sequence view
ID 24 : 50S RIBOSOMAL PROTEIN L18
Image
Description	50S RIBOSOMAL PROTEIN L18
Type	polymer
Fragment	RESIDUES 2-117
Formula weight	12663.601 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0C018, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L19
Image
Description	50S RIBOSOMAL PROTEIN L19
Type	polymer
Formula weight	13028.207 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7K6, Sequence view
ID 26 : 50S RIBOSOMAL PROTEIN L20
Image
Description	50S RIBOSOMAL PROTEIN L20
Type	polymer
Formula weight	13396.962 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7L3, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L21
Image
Description	50S RIBOSOMAL PROTEIN L21
Type	polymer
Formula weight	11586.485 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0AG48, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L22
Image
Description	50S RIBOSOMAL PROTEIN L22
Type	polymer
Formula weight	12253.464 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P61175, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L23
Image
Description	50S RIBOSOMAL PROTEIN L23
Type	polymer
Formula weight	10546.574 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0ADZ0, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L24
Image
Description	50S RIBOSOMAL PROTEIN L24
Type	polymer
Formula weight	11078.988 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P60624, Sequence view
ID 31 : P-SITE TRNA 2
Image
Description	P-SITE TRNA 2
Type	polymer
Formula weight	24890.959 Da
Number of molecules	1
Source	Method: Obtained synthetically NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	GenBank: CP001396, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L25
Image
Description	50S RIBOSOMAL PROTEIN L25
Type	polymer
Formula weight	10713.566 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P68919, Sequence view
ID 33 : MRNA
Image
Description	MRNA
Type	polymer
Formula weight	3497.220 Da
Number of molecules	1
Source	Method: Obtained synthetically NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	Sequence view
ID 34 : 50S RIBOSOMAL PROTEIN L27
Image
Description	50S RIBOSOMAL PROTEIN L27
Type	polymer
Fragment	RESIDUES 7-85
Formula weight	8476.758 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	UniProt: P0A7L8, Sequence view
ID 35 : NASCENT TNAC LEADER PEPTIDE 5
Image
Description	NASCENT TNAC LEADER PEPTIDE 5
Type	polymer
Formula weight	1439.587 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: ESCHERICHIA COLI
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	TNAC STALLED 70S RIBOSOME WITH P-SITE TRNA.
Buffer
Name	50MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN AND 10MM DDT
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE
Sample support
Details	HOLEY CARBON
Vitrification
Details	VITRIFICATION 1 -- CRYOGEN ETHANE

Electron Microscopy
Imaging
Microscope	model: FEI TECNAI F30
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Electron dose	20 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 38900 X, nominal: 39000 X
Cs	nominal: 2.26 mm
Nominal defocus	max: 3000 nm, min: 1000 nm
Specimen holder
Temperature	95 Kelvin
Detector
Type	KODAK SO163
Image scans
Number digital images	128

Processing
2D projection selection
Number of particles	263000
Software name	SPIDER
3D reconstruction
CTF correction method	DEFOCUS GROUP VOLUMES
Method	PROJECTION MATCHING
Resolution	5.8 A
3D fitting
Method	MDFF
Refinement Protocol	FLEXIBLE FITTING
Refinement Space	REAL
Refine
Ls d res high	5.80 A
ID	1
Refine hist
D res high	5.80
Total atoms	94609
Nucleic acid atoms	66670
Protein atoms	27939