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pdb-4v65 is replaced from PDB-3e1a

Structure of the E. coli ribosome in the Pre-accommodation state

by single particle reconstruction, at 9 A resolution

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#1: Deposited structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4v65
TitleStructure of the E. coli ribosome in the Pre-accommodation state
DescriptorRibosome
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: 2014-07-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Deposited structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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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 weight24518.570 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksSequence view
ID 2 : mRNA model
Image
DescriptionmRNA model
Typepolyribonucleotide
Formula weight6078.359 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 3 : 16S rRNA
Image
Description16S rRNA
Typepolyribonucleotide
Formula weight495927.719 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksSequence view
ID 4 : 30S ribosomal protein S2
Image
Description30S ribosomal protein S2
Typepolypeptide(L)
Formula weight26781.670 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Src id: 1
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 weight13870.975 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Src id: 1
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 weight13768.157 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Src id: 1
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 weight13128.467 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Src id: 1
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 weight11606.560 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Src id: 1
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 weight10319.882 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9207.572 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9724.491 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9006.500 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
Src id: 1
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 weight10455.355 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
Src id: 1
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 weight9708.464 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
Src id: 1
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 weight26031.316 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
Src id: 1
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 weight8524.039 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
Src id: 1
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 weight23514.199 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
Src id: 1
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 weight16772.412 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
Src id: 1
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 weight15727.512 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
Src id: 1
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 weight20055.156 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
Src id: 1
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 weight14146.557 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
Src id: 1
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 weight14886.270 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
Src id: 1
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 weight11755.597 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R5, Sequence view
ID 24 : 5S rRNA
Image
Description5S rRNA
Typepolyribonucleotide
Formula weight37848.555 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 170517292, Sequence view
ID 25 : 23S rRNA
Image
Description23S rRNA
Typepolyribonucleotide
Formula weight941306.188 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 169887498, Sequence view
ID 26 : 50S ribosomal protein L25
Image
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.465 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 27 : 50S ribosomal protein L14
Image
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13565.067 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 28 : 50S ribosomal protein L15
Image
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight15008.471 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 29 : 50S ribosomal protein L16
Image
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight15312.269 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 30 : 50S ribosomal protein L17
Image
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight14393.657 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 31 : 50S ribosomal protein L18
Image
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12794.668 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 32 : 50S ribosomal protein L19
Image
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13159.278 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 33 : 50S ribosomal protein L20
Image
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13528.024 Da
Number of molecules1
ID33
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 34 : 50S ribosomal protein L21
Image
Description50S ribosomal protein L21
Typepolypeptide(L)
Formula weight11586.374 Da
Number of molecules1
ID34
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG48, Sequence view
ID 35 : 50S ribosomal protein L22
Image
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight12253.359 Da
Number of molecules1
ID35
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 36 : 50S ribosomal protein L23
Image
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight11093.047 Da
Number of molecules1
ID36
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 37 : 50S ribosomal protein L2
Image
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight29550.166 Da
Number of molecules1
ID37
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 38 : 50S ribosomal protein L24
Image
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight11210.069 Da
Number of molecules1
ID38
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 39 : 50S ribosomal protein L27
Image
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9146.540 Da
Number of molecules1
ID39
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 40 : 50S ribosomal protein L29
Image
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7286.464 Da
Number of molecules1
ID40
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 41 : 50S ribosomal protein L30
Image
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6554.820 Da
Number of molecules1
ID41
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 42 : 50S ribosomal protein L31
Image
Description50S ribosomal protein L31
Typepolypeptide(L)
Formula weight7887.117 Da
Number of molecules1
ID42
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M9, Sequence view
ID 43 : 50S ribosomal protein L32
Image
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight6463.445 Da
Number of molecules1
ID43
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 44 : 50S ribosomal protein L33
Image
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6257.436 Da
Number of molecules1
ID44
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:624
Organism scientific: Shigella sonnei
LinksUniProt: P0A7N9, Sequence view
ID 45 : 50S ribosomal protein L34
Image
Description50S ribosomal protein L34
Typepolypeptide(L)
Formula weight5397.463 Da
Number of molecules1
ID45
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:624
Organism scientific: Shigella sonnei
LinksUniProt: P0A7P5, Sequence view
ID 46 : 50S ribosomal protein L35
Image
Description50S ribosomal protein L35
Typepolypeptide(L)
Formula weight7181.835 Da
Number of molecules1
ID46
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:624
Organism scientific: Shigella sonnei
LinksUniProt: P0A7Q1, Sequence view
ID 47 : 50S ribosomal protein L36
Image
Description50S ribosomal protein L36
Typepolypeptide(L)
Formula weight4377.390 Da
Number of molecules1
ID47
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q6, Sequence view
ID 48 : 50S ribosomal protein L3
Image
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.535 Da
Number of molecules1
ID48
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 49 : 50S ribosomal protein L1P
Image
Description50S ribosomal protein L1P
Typepolypeptide(L)
Formula weight23978.031 Da
Number of molecules1
ID49
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P35024, Sequence view
ID 50 : 50S ribosomal protein L4
Image
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight22121.566 Da
Number of molecules1
ID50
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 51 : 50S ribosomal protein L5
Image
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20202.416 Da
Number of molecules1
ID51
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 52 : 50S ribosomal protein L6
Image
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight18932.791 Da
Number of molecules1
ID52
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 53 : 50S ribosomal protein L9
Image
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.020 Da
Number of molecules1
ID53
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 54 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14894.362 Da
Number of molecules1
ID54
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 55 : 50S ribosomal protein L13
Image
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight15822.360 Da
Number of molecules1
ID55
SourceMethod: Isolated from a natural source
Src id: 1
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AA10, 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
Allpdb4v65.ent.gz
pdb4v65.ent (uncompressed file)
Header onlypdb4v65.ent.gz
mmCIF format
mmCIF4v65.cif.gz
XML format
All4v65.xml.gz
No-atom4v65-noatom.xml.gz
Ext-atom4v65-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.1 MB