3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-2wwq

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).

by single particle reconstruction, at 5.8 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1657, Image by Jmol

#3: With PDB-2wwl, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1657 (with PDB-2wwl), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2wwq
TitleE.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).
DescriptorNASCENT TNAC LEADER PEPTIDE 5
(50S ribosomal protein ...) x 28
KeywordsRIBOSOME, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, TRANSLATION, ZINC-FINGER, TNAC, 70S RIBOSOME, STALLING
AuthorsSeidelt, 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.
DateDeposition: 2009-10-26, Release: 2010-04-14
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 simplified surface model of EM map, EMDB-1657, Image by Jmol

#3: With PDB-2wwl, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1657 (with PDB-2wwl), Image by UCSF CHIMERA

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

EMDB-1657

CiteFit

PDB-2wwl

CiteSplit

Cite: data citing same article

Fit: target map of fitting

Split: split data constructing the same model

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - primary
ArticleScience, Vol. 326, Issue 5958, Page 1412-5, Year 2009
TitleStructural insight into nascent polypeptide chain-mediated translational stalling.
AuthorsBirgit 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.
KeywordsBinding 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
LinksDOI: 10.1126/science.1177662, PubMed: 19933110, PMC: PMC2920484
Components
ID 1 : 50S RIBOSOMAL PROTEIN L28
Image
Description50S RIBOSOMAL PROTEIN L28
Typepolypeptide(L)
Formula weight8896.435 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI

LinksUniProt: P0A7M2, Sequence view
ID 2 : 50S RIBOSOMAL PROTEIN L29
Image
Description50S RIBOSOMAL PROTEIN L29
Typepolypeptide(L)
Formula weight7286.531 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7M6, Sequence view
ID 3 : 50S RIBOSOMAL PROTEIN L30
Image
Description50S RIBOSOMAL PROTEIN L30
Typepolypeptide(L)
Formula weight6423.682 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG51, Sequence view
ID 4 : 50S RIBOSOMAL PROTEIN L32
Image
Description50S RIBOSOMAL PROTEIN L32
Typepolypeptide(L)
Formula weight6332.307 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7N4, Sequence view
ID 5 : 50S RIBOSOMAL PROTEIN L33
Image
Description50S RIBOSOMAL PROTEIN L33
Typepolypeptide(L)
Formula weight5814.909 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7N9, Sequence view
ID 6 : 50S RIBOSOMAL PROTEIN L1
Image
Description50S RIBOSOMAL PROTEIN L1
Typepolypeptide(L)
Formula weight24765.834 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L0, Sequence view
ID 7 : 50S RIBOSOMAL PROTEIN L34
Image
Description50S RIBOSOMAL PROTEIN L34
Typepolypeptide(L)
Formula weight5397.506 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7P5, Sequence view
ID 8 : 50S RIBOSOMAL PROTEIN L35
Image
Description50S RIBOSOMAL PROTEIN L35
Typepolypeptide(L)
Formula weight7181.907 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7Q1, Sequence view
ID 9 : 50S RIBOSOMAL PROTEIN L36
Image
Description50S RIBOSOMAL PROTEIN L36
Typepolypeptide(L)
Formula weight4377.415 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7Q6, Sequence view
ID 10 : 5S RIBOSOMAL RNA
Image
Description5S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight37848.766 Da
Number of molecules1
ID10
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: CP001396, Sequence view
ID 11 : 23S RIBOSOMAL RNA
Image
Description23S RIBOSOMAL RNA
Typepolyribonucleotide
Formula weight941307.500 Da
Number of molecules1
ID11
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: CP001396, Sequence view
ID 12 : 50S RIBOSOMAL PROTEIN L2
Image
Description50S RIBOSOMAL PROTEIN L2
Typepolypeptide(L)
Formula weight29663.471 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60422, Sequence view
ID 13 : 50S RIBOSOMAL PROTEIN L3
Image
Description50S RIBOSOMAL PROTEIN L3
Typepolypeptide(L)
Formula weight22277.709 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60438, Sequence view
ID 14 : 50S RIBOSOMAL PROTEIN L4
Image
Description50S RIBOSOMAL PROTEIN L4
Typepolypeptide(L)
Formula weight22121.723 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60723, Sequence view
ID 15 : 50S RIBOSOMAL PROTEIN L5
Image
Description50S RIBOSOMAL PROTEIN L5
Typepolypeptide(L)
Formula weight20202.566 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P62399, Sequence view
ID 16 : 50S RIBOSOMAL PROTEIN L6
Image
Description50S RIBOSOMAL PROTEIN L6
Typepolypeptide(L)
Formula weight18801.766 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG55, Sequence view
ID 17 : 50S RIBOSOMAL PROTEIN L9
Image
Description50S RIBOSOMAL PROTEIN L9
Typepolypeptide(L)
Formula weight15789.174 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7R1, Sequence view
ID 18 : 50S RIBOSOMAL PROTEIN L11
Image
Description50S RIBOSOMAL PROTEIN L11
Typepolypeptide(L)
Formula weight14763.286 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7J7, Sequence view
ID 19 : 50S RIBOSOMAL PROTEIN L13
Image
Description50S RIBOSOMAL PROTEIN L13
Typepolypeptide(L)
Formula weight16050.749 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AA10, Sequence view
ID 20 : 50S RIBOSOMAL PROTEIN L14
Image
Description50S RIBOSOMAL PROTEIN L14
Typepolypeptide(L)
Formula weight13352.881 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADY3, Sequence view
ID 21 : 50S RIBOSOMAL PROTEIN L15
Image
Description50S RIBOSOMAL PROTEIN L15
Typepolypeptide(L)
FragmentRESIDUES 2-144
Formula weight14877.406 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P02413, Sequence view
ID 22 : 50S RIBOSOMAL PROTEIN L16
Image
Description50S RIBOSOMAL PROTEIN L16
Typepolypeptide(L)
Formula weight15312.394 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADY7, Sequence view
ID 23 : 50S RIBOSOMAL PROTEIN L17
Image
Description50S RIBOSOMAL PROTEIN L17
Typepolypeptide(L)
Formula weight13722.047 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG44, Sequence view
ID 24 : 50S RIBOSOMAL PROTEIN L18
Image
Description50S RIBOSOMAL PROTEIN L18
Typepolypeptide(L)
FragmentRESIDUES 2-117
Formula weight12663.601 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0C018, Sequence view
ID 25 : 50S RIBOSOMAL PROTEIN L19
Image
Description50S RIBOSOMAL PROTEIN L19
Typepolypeptide(L)
Formula weight13028.207 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7K6, Sequence view
ID 26 : 50S RIBOSOMAL PROTEIN L20
Image
Description50S RIBOSOMAL PROTEIN L20
Typepolypeptide(L)
Formula weight13396.962 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L3, Sequence view
ID 27 : 50S RIBOSOMAL PROTEIN L21
Image
Description50S RIBOSOMAL PROTEIN L21
Typepolypeptide(L)
Formula weight11586.485 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0AG48, Sequence view
ID 28 : 50S RIBOSOMAL PROTEIN L22
Image
Description50S RIBOSOMAL PROTEIN L22
Typepolypeptide(L)
Formula weight12253.464 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P61175, Sequence view
ID 29 : 50S RIBOSOMAL PROTEIN L23
Image
Description50S RIBOSOMAL PROTEIN L23
Typepolypeptide(L)
Formula weight10546.574 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0ADZ0, Sequence view
ID 30 : 50S RIBOSOMAL PROTEIN L24
Image
Description50S RIBOSOMAL PROTEIN L24
Typepolypeptide(L)
Formula weight11078.988 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P60624, Sequence view
ID 31 : P-SITE TRNA 2
Image
DescriptionP-SITE TRNA 2
Typepolyribonucleotide
Formula weight24890.959 Da
Number of molecules1
ID31
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksGenBank: CP001396, Sequence view
ID 32 : 50S RIBOSOMAL PROTEIN L25
Image
Description50S RIBOSOMAL PROTEIN L25
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P68919, Sequence view
ID 33 : MRNA
Image
DescriptionMRNA
Typepolyribonucleotide
Formula weight3497.220 Da
Number of molecules1
ID33
SourceMethod: Obtained synthetically
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksSequence view
ID 34 : 50S RIBOSOMAL PROTEIN L27
Image
Description50S RIBOSOMAL PROTEIN L27
Typepolypeptide(L)
FragmentRESIDUES 7-85
Formula weight8476.758 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksUniProt: P0A7L8, Sequence view
ID 35 : NASCENT TNAC LEADER PEPTIDE 5
Image
DescriptionNASCENT TNAC LEADER PEPTIDE 5
Typepolypeptide(L)
Formula weight1439.587 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: ESCHERICHIA COLI
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
NameTNAC STALLED 70S RIBOSOME WITH P-SITE TRNA.
Buffer
Name50MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN AND 10MM DDT
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 38900 X, Nominal: 39000 X
CsNominal: 2.26 mm
Nominal defocusMax: 3000 nm, Min: 1000 nm
Specimen holder
Temperature95 Kelvin
Detector
TypeKODAK SO163
Image scans
Number digital images128
Processing
2D projection selection
Number of particles263000
Software nameSPIDER
3D reconstruction
CTF correction methodDEFOCUS GROUP VOLUMES
MethodPROJECTION MATCHING
Resolution5.8 A
3D fitting
MethodMDFF
Refinement ProtocolFLEXIBLE FITTING
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high5.80 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high5.80
Total atoms94609
Nucleic acid atoms66670
Protein atoms27939
Download
PDB format
Allpdb2wwq.ent.gz
pdb2wwq.ent (uncompressed file)
Header onlypdb2wwq.ent.gz
mmCIF format
mmCIF2wwq.cif.gz
XML format
All2wwq.xml.gz
No-atom2wwq-noatom.xml.gz
Ext-atom2wwq-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.2 MB
.webm (WebM/VP8 format), 942.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.2 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.8 MB