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Structure of the 30S subunit of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143

by single particle reconstruction, at 15 A resolution

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2gyc, Made by Jmol

#4: With PDB-2akh, PDB-2aki, PDB-2gyc, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1143 (with PDB-2akh, PDB-2aki, PDB-2gyc), Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2gyb
TitleStructure of the 30S subunit of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143
Descriptor30S RIBOSOMAL SUBUNIT
KeywordsRIBOSOME, SecM, nascent chain, signal transduction, RNA world, polypeptide exit tunnel, translocation, ribosome, elongation arrest, protein-conducting channel
AuthorsMitra, K., Frank, J.
DateDeposition: 2006-05-09, Release: 2006-09-26
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, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2gyc, Made by Jmol

#4: With PDB-2akh, PDB-2aki, PDB-2gyc, Made by Jmol

#5: Superimposing with EM 3D map: EMDB-1143 (with PDB-2akh, PDB-2aki, PDB-2gyc), Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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PDB-2gyc

CiteSplit

Cite: data citing same article

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Split: split data constructing the same model

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleMol. Cell, Vol. 22, Issue 4, Page 533-43, Year 2006
TitleElongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
AuthorsKakoli Mitra, Christiane Schaffitzel, Felcy Fabiola, Michael S Chapman, Nenad Ban, Joachim Frank
Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA.
KeywordsCryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Macromolecular Substances, Models, Molecular, Nucleic Acid Conformation, Peptide Chain Elongation, Translational, Protein Conformation, RNA, Bacterial (chemistry), RNA, Ribosomal (chemistry), RNA, Ribosomal, 23S (chemistry), Ribosomes (metabolism), SecM protein, E coli, Transcription Factors (chemistry)
LinksPII: S1097-2765(06)00294-2, DOI: 10.1016/j.molcel.2006.05.003, PubMed: 16713583
Citation - 1
ArticleNature, Vol. 438, Page: 318 - 324, Year: 2005,
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome
AuthorsMitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.
Citation - 2
ArticleCell(Cambridge,Mass.), Vol. 114, Page: 123 - 134, Year: 2003,
TitleLocking and unlocking of ribosomal motions
AuthorsValle, M., Zavialov, A.V., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J.
Citation - 3
ArticleFEBS Lett., Vol. 580, Issue 14, Page 3353-60, Year 2006
TitleA model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel.
AuthorsKakoli Mitra, Joachim Frank
Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsModels, Molecular, Protein Biosynthesis, Protein Conformation, Protein Transport, Ribosomes (metabolism)
LinksPII: S0014-5793(06)00609-0, DOI: 10.1016/j.febslet.2006.05.019, PubMed: 16714018
Components
ID 1 : 16S ribosomal RNA
Image
Description16S ribosomal RNA
Typepolyribonucleotide
Formula weight482286.844 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : tRNA
Image
DescriptiontRNA
Typepolyribonucleotide
Formula weight24518.730 Da
Number of molecules3
ID2
DetailsA-site, P-site, E-site
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : 30S ribosomal subunit protein S2
Image
Description30S ribosomal subunit protein S2
Typepolypeptide(L)
Formula weight26292.264 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V0, Sequence view
ID 4 : 30S ribosomal subunit protein S3
Image
Description30S ribosomal subunit protein S3
Typepolypeptide(L)
Formula weight23078.988 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V3, Sequence view
ID 5 : 30S ribosomal subunit protein S4
Image
Description30S ribosomal subunit protein S4
Typepolypeptide(L)
Formula weight23312.113 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V8, Sequence view
ID 6 : 30S ribosomal subunit protein S5
Image
Description30S ribosomal subunit protein S5
Typepolypeptide(L)
Formula weight15618.174 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W1, Sequence view
ID 7 : 30S ribosomal subunit protein S6
Image
Description30S ribosomal subunit protein S6
Typepolypeptide(L)
Formula weight11181.960 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02358, Sequence view
ID 8 : 30S ribosomal subunit protein S7
Image
Description30S ribosomal subunit protein S7
Typepolypeptide(L)
Formula weight15384.802 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02359, Sequence view
ID 9 : 30S ribosomal subunit protein S8
Image
Description30S ribosomal subunit protein S8
Typepolypeptide(L)
Formula weight13857.312 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W7, Sequence view
ID 10 : 30S ribosomal subunit protein S9
Image
Description30S ribosomal subunit protein S9
Typepolypeptide(L)
Formula weight14440.900 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7X3, Sequence view
ID 11 : 30S ribosomal subunit protein S10
Image
Description30S ribosomal subunit protein S10
Typepolypeptide(L)
Formula weight10996.862 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R5, Sequence view
ID 12 : 30S ribosomal subunit protein S11
Image
Description30S ribosomal subunit protein S11
Typepolypeptide(L)
Formula weight12388.177 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R9, Sequence view
ID 13 : 30S ribosomal subunit protein S12
Image
Description30S ribosomal subunit protein S12
Typepolypeptide(L)
Formula weight11245.187 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S3, Sequence view
ID 14 : 30S ribosomal subunit protein S13
Image
Description30S ribosomal subunit protein S13
Typepolypeptide(L)
Formula weight12739.017 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S9, Sequence view
ID 15 : 30S ribosomal subunit protein S14
Image
Description30S ribosomal subunit protein S14
Typepolypeptide(L)
Formula weight7117.417 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG59, Sequence view
ID 16 : 30S ribosomal subunit protein S15
Image
Description30S ribosomal subunit protein S15
Typepolypeptide(L)
Formula weight9915.440 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ4, Sequence view
ID 17 : 30S ribosomal subunit protein S16
Image
Description30S ribosomal subunit protein S16
Typepolypeptide(L)
Formula weight8822.221 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T3, Sequence view
ID 18 : 30S ribosomal subunit protein S17
Image
Description30S ribosomal subunit protein S17
Typepolypeptide(L)
Formula weight9134.845 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG63, Sequence view
ID 19 : 30S ribosomal subunit protein S18
Image
Description30S ribosomal subunit protein S18
Typepolypeptide(L)
Formula weight8178.542 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T7, Sequence view
ID 20 : 30S ribosomal subunit protein S19
Image
Description30S ribosomal subunit protein S19
Typepolypeptide(L)
Formula weight9865.638 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U3, Sequence view
ID 21 : 30S ribosomal subunit protein S20
Image
Description30S ribosomal subunit protein S20
Typepolypeptide(L)
Formula weight9279.014 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U7, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000851
Name30S ribosomal protein S2
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0005840
InterPro-IDIPR:008282
Name30S ribosomal subunit protein S3
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005709
Name30S ribosomal subunit protein S4
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000851
Name30S ribosomal subunit protein S5
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000529
Name30S ribosomal subunit protein S6
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005717
Name30S ribosomal subunit protein S7
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000630
Name30S ribosomal subunit protein S8
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000754
Name30S ribosomal subunit protein S9
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005731
Name30S ribosomal subunit protein S10
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001971
Name30S ribosomal subunit protein S11
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005679
Name30S ribosomal subunit protein S12
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001892
Name30S ribosomal subunit protein S13
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001209
Name30S ribosomal subunit protein S14
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005290
Name30S ribosomal subunit protein S15
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000307
Name30S ribosomal subunit protein S16
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:000266
Name30S ribosomal subunit protein S17
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:001648
Name30S ribosomal subunit protein S18
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:005732
Name30S ribosomal subunit protein S19
Entity assembly
Assembly-ID1
Detailsstructural constituent of ribosome
GO-IDGO:0003735
InterPro-IDIPR:002583
Name30S ribosomal subunit protein S20
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration32 mg/ml
Sample support
DetailsQuantifoil holey-Carbon film grids
Vitrification
Detailsrapid-freezing in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2004-03-09
Electron gun
Electron sourcefield emission gun
Accelerating voltage300 kV
Electron dose1100 e/A**2
Illumination modeflood beam
Lens
Modebright field
MagnificationCalibrated: 39000 X, Nominal: 39000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4.3 nm, Min: 1.5 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature93 Kelvin
Detector
TypeKODAK SO163 film
Processing
2D projection selection
Software nameCNS implementation of RSRef
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
Actual pixel size3.59 A/pix
CTF correction methodCTF correction of 3D-maps by Wiener filtration
DetailsWITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP. THE RESOLUTION OF THE ATOMIC MODEL FITTED INTO EMD-1143 (11.0 ANGSTROMS AT FSC 3SIGMA, 15.0 ANGSTROMS AT FSC 0.5) IS THUS ESTIMATED TO BE BETWEEN 2-3 ANGSTROMS. REAL-SPACE REFINEMENT USING RIGID BODIES INTO EM MAP EMD-1143. RIGID BODY DEFINITION: AN AUTONOMOUS SECONDARY STRUCTURE UNIT (E.G. HELIX SEGMENT, HAIRPIN) OF THE RIBOSOMAL RNA; AN AUTONOMOUS RIBOSOMAL PROTEIN DOMAIN. THE ATOMIC MODEL USED WAS GENERATED FROM E. COLI MODELS OF X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. IN THE ABSENCE OF E. COLI MODELS, STRUCTURES WERE DERIVED DIRECTLY FROM THE X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. RESOLUTION for FSC 3SIGMA (ANGSTROMS) is 11.000, RESOLUTION for FSC 0.5 (ANGSTROMS) is 15.000.
Magnification calibrationTMV
Method3D projection matching; conjugate gradients with regularization
Nominal pixel size3.59 A/pix
Resolution15 A
3D fitting
Refinement ProtocolCNS implementation of RSRef
Refinement SpaceREAL
Software nameCNS implementation of RSRef, spider
Target criteriaMinimization of number of poor van der Waals contacts and maximation of correlation coefficient
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms54539
Nucleic acid atoms36790
Protein atoms17749
Download
PDB format
Allpdb2gyb.ent.gz
pdb2gyb.ent (uncompressed file)
Header onlypdb2gyb.ent.gz
mmCIF format
mmCIF2gyb.cif.gz
XML format
All2gyb.xml.gz
No-atom2gyb-noatom.xml.gz
Ext-atom2gyb-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), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.7 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB