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Structure of the 30S subunit and the tRNAs of E. coli ribosome in Pre-accommodation state

by single particle reconstruction, at 9 A resolution

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3e1a
TitleStructure of the 30S subunit and the tRNAs of E. coli ribosome in Pre-accommodation state
DescriptorRibosome
30S subunit
KeywordsRIBOSOME, ribosome, translation, accommodation, tRNA selection, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Endonuclease, Hydrolase, Nuclease, Antibiotic resistance, Repressor, Transcription, Transcription regulation, Transcription termination, Translation regulation
AuthorsDevkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C.
DateDeposition: 2008-08-03, Release: 2009-08-18
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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#1: Depositted structure unit, Image by Jmol

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PDB-3e1b

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Article
Citation - primary
ArticleTo be Published, Vol. , Page: - , Year: ,
TitleThe Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading
AuthorsDevkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C.
Components
ID 1 : A/T, P and E-site tRNAs
Image
DescriptionA/T, P and E-site tRNAs
Typepolyribonucleotide
Formula weight24518.730 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : mRNA model
Image
DescriptionmRNA model
Typepolyribonucleotide
Formula weight6078.410 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : 16S rRNA
Image
Description16S rRNA
Typepolyribonucleotide
Formula weight495928.906 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 4 : 30S ribosomal protein S2
Image
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight26781.848 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V0, Sequence view
ID 5 : 30S ribosomal protein S11
Image
Description30S ribosomal protein S11
Typepolypeptide(L)
Formula weight13871.092 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R9, Sequence view
ID 6 : 30S ribosomal protein S12
Image
Description30S ribosomal protein S12
Typepolypeptide(L)
Formula weight13768.263 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S3, Sequence view
ID 7 : 30S ribosomal protein S13
Image
Description30S ribosomal protein S13
Typepolypeptide(L)
Formula weight13128.570 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7S9, Sequence view
ID 8 : 30S ribosomal protein S14
Image
Description30S ribosomal protein S14
Typepolypeptide(L)
Formula weight11606.653 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG59, Sequence view
ID 9 : 30S ribosomal protein S15
Image
Description30S ribosomal protein S15
Typepolypeptide(L)
Formula weight10319.969 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: Q8X9M2, Sequence view
ID 10 : 30S ribosomal protein S16
Image
Description30S ribosomal protein S16
Typepolypeptide(L)
Formula weight9207.662 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T3, Sequence view
ID 11 : 30S ribosomal protein S17
Image
Description30S ribosomal protein S17
Typepolypeptide(L)
Formula weight9724.571 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG63, Sequence view
ID 12 : 30S ribosomal protein S18
Image
Description30S ribosomal protein S18
Typepolypeptide(L)
Formula weight9006.581 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7T7, Sequence view
ID 13 : 30S ribosomal protein S19
Image
Description30S ribosomal protein S19
Typepolypeptide(L)
Formula weight10455.452 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U3, Sequence view
ID 14 : 30S ribosomal protein S20
Image
Description30S ribosomal protein S20
Typepolypeptide(L)
Formula weight9708.547 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7U7, Sequence view
ID 15 : 30S ribosomal protein S3
Image
Description30S ribosomal protein S3
Typepolypeptide(L)
Formula weight26031.535 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V3, Sequence view
ID 16 : 30S ribosomal protein S21
Image
Description30S ribosomal protein S21
Typepolypeptide(L)
Formula weight8524.120 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68679, Sequence view
ID 17 : 30S ribosomal protein S4
Image
Description30S ribosomal protein S4
Typepolypeptide(L)
Formula weight23514.385 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7V8, Sequence view
ID 18 : 30S ribosomal protein S5
Image
Description30S ribosomal protein S5
Typepolypeptide(L)
Formula weight16772.539 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7W1, Sequence view
ID 19 : 30S ribosomal protein S6
Image
Description30S ribosomal protein S6
Typepolypeptide(L)
Formula weight15727.645 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02358, Sequence view
ID 20 : 30S ribosomal protein S7
Image
Description30S ribosomal protein S7
Typepolypeptide(L)
Formula weight20055.324 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02359, Sequence view
ID 21 : 30S ribosomal protein S8
Image
Description30S ribosomal protein S8
Typepolypeptide(L)
Formula weight14146.660 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: Q3YWV3, Sequence view
ID 22 : 30S ribosomal protein S9
Image
Description30S ribosomal protein S9
Typepolypeptide(L)
Formula weight14886.393 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7X3, Sequence view
ID 23 : 30S ribosomal protein S10
Image
Description30S ribosomal protein S10
Typepolypeptide(L)
Formula weight11755.708 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R5, Sequence view
Sample
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
2D projection selection
Software nameYup.scx
3D reconstruction
MethodSingle Particle
Nominal pixel size2.82 A/pix
Resolution9.0 A
3D fitting
MethodFlexible fitting
Refinement SpaceREAL
Software nameYup.scx
Target criteriacross-correlation
3D fitting list
3D Fitting ID1
PDB entry ID2I2P, 1EHZ
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms56576
Nucleic acid atoms38047
Protein atoms18529
Download
PDB format
Allpdb3e1a.ent.gz
pdb3e1a.ent (uncompressed file)
Header onlypdb3e1a.ent.gz
mmCIF format
mmCIF3e1a.cif.gz
XML format
All3e1a.xml.gz
No-atom3e1a-noatom.xml.gz
Ext-atom3e1a-extatom.xml.gz
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movie #2
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