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Structure 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: Deposited structure unit, Image by Jmol

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

#3: With PDB-2akh, PDB-2aki, Image by Jmol

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

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v4w
TitleStructure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143
DescriptorRibosome
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: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

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

#3: With PDB-2akh, PDB-2aki, Image by Jmol

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

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

Cite: data citing same article

Fit: target map of fitting

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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 weight482285.656 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : tRNA
Image
DescriptiontRNA
Typepolyribonucleotide
Formula weight24518.570 Da
Number of molecules3
ID2
DetailsA-site, P-site, E-site
SourceMethod: Isolated from a natural source
Src id: 1
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 weight26292.082 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
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 weight23078.785 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
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 weight23311.924 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
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 weight15618.051 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
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 weight11181.867 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
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 weight15384.665 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
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 weight13857.205 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
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 weight14440.777 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
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 weight10996.753 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
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 weight12388.068 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
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 weight11245.101 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
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 weight12738.911 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
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 weight7117.352 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9915.350 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
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 weight8822.135 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9134.767 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
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 weight8178.463 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9865.542 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9278.929 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U7, Sequence view
ID 22 : 23S ribosomal RNA
Image
Description23S ribosomal RNA
Typepolyribonucleotide
Formula weight888503.500 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 23 : 5S ribosomal RNA
Image
Description5S ribosomal RNA
Typepolyribonucleotide
Formula weight34916.805 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 24 : 50S ribosomal protein L1
Image
Description50S ribosomal protein L1
Typepolypeptide(L)
Formula weight23591.266 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L0, Sequence view
ID 25 : 50S ribosomal protein L7/L12
Image
Description50S ribosomal protein L7/L12
Typepolypeptide(L)
Formula weight12090.882 Da
Number of molecules2
ID25
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K2, Sequence view
ID 26 : 50S ribosomal protein L2
Image
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight24691.252 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 27 : 50S ribosomal protein L3
Image
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.535 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 28 : 50S ribosomal protein L4
Image
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight21806.133 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 29 : 50S ribosomal protein L5
Image
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20131.338 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 30 : 50S ribosomal protein L6
Image
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight17799.383 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 31 : 50S ribosomal protein L9
Image
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.020 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 32 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14577.000 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 33 : 50S ribosomal protein L13
Image
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight16050.606 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AA10, Sequence view
ID 34 : 50S ribosomal protein L14
Image
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13433.872 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 35 : 50S ribosomal protein L15
Image
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight14477.808 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 36 : 50S ribosomal protein L16
Image
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight14736.483 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 37 : 50S ribosomal protein L17
Image
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight12945.075 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 38 : 50S ribosomal protein L18
Image
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12273.080 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 39 : 50S ribosomal protein L19
Image
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13028.082 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 40 : 50S ribosomal protein L20
Image
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13254.673 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 41 : 50S ribosomal protein L22
Image
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight11778.791 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 42 : 50S ribosomal protein L23
Image
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight10205.000 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 43 : 50S ribosomal protein L24
Image
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight10823.561 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 44 : 50S ribosomal protein L25
Image
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.465 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 45 : 50S ribosomal protein L27
Image
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9015.344 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 46 : 50S ribosomal protein L29
Image
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7087.256 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 47 : 50S ribosomal protein L30
Image
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6223.367 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 48 : 50S ribosomal protein L32
Image
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight3317.780 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 49 : 50S ribosomal protein L33
Image
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6015.099 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Escherichia
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N9, 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
Allpdb4v4w.ent.gz
pdb4v4w.ent (uncompressed file)
Header onlypdb4v4w.ent.gz
mmCIF format
mmCIF4v4w.cif.gz
XML format
All4v4w.xml.gz
No-atom4v4w-noatom.xml.gz
Ext-atom4v4w-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 3.8 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 3.4 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB