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-3e1d

Structure of the 50S subunit of E. coli ribosome in Post-accommodation state

by single particle reconstruction, at 9 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: With PDB-3e1c, PDB-4v66, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3e1d
TitleStructure of the 50S subunit of E. coli ribosome in Post-accommodation state
DescriptorRibosome
30S subunit
KeywordsRIBOSOME, ribosome, translation, accommodation, tRNA selection, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, Methylation, tRNA-binding, Phosphoprotein, Antibiotic resistance, Metal-binding, Repressor, 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
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: With PDB-3e1c, PDB-4v66, Image by Jmol

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

PDB-3e1c

CiteSplit

PDB-4v66

CiteSplit

Cite: data citing same article

Split: split data constructing the same model

Similar strucutres (beta)
List of similar structure data about Omokage system
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 : 5S rRNA
Image
Description5S rRNA
Typepolyribonucleotide
Formula weight37848.766 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli

LinksGenBank: 170517292, Sequence view
ID 2 : 23S rRNA
Image
Description23S rRNA
Typepolyribonucleotide
Formula weight941307.500 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksGenBank: 169887498, Sequence view
ID 3 : 50S ribosomal protein L25
Image
Description50S ribosomal protein L25
Typepolypeptide(L)
Formula weight10713.566 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P68919, Sequence view
ID 4 : 50S ribosomal protein L14
Image
Description50S ribosomal protein L14
Typepolypeptide(L)
Formula weight13565.172 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY3, Sequence view
ID 5 : 50S ribosomal protein L15
Image
Description50S ribosomal protein L15
Typepolypeptide(L)
Formula weight15008.598 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P02413, Sequence view
ID 6 : 50S ribosomal protein L16
Image
Description50S ribosomal protein L16
Typepolypeptide(L)
Formula weight15312.394 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADY7, Sequence view
ID 7 : 50S ribosomal protein L17
Image
Description50S ribosomal protein L17
Typepolypeptide(L)
Formula weight14393.774 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG44, Sequence view
ID 8 : 50S ribosomal protein L18
Image
Description50S ribosomal protein L18
Typepolypeptide(L)
Formula weight12794.793 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0C018, Sequence view
ID 9 : 50S ribosomal protein L19
Image
Description50S ribosomal protein L19
Typepolypeptide(L)
Formula weight13159.399 Da
Number of molecules1
ID9
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7K6, Sequence view
ID 10 : 50S ribosomal protein L20
Image
Description50S ribosomal protein L20
Typepolypeptide(L)
Formula weight13528.153 Da
Number of molecules1
ID10
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L3, Sequence view
ID 11 : 50S ribosomal protein L21
Image
Description50S ribosomal protein L21
Typepolypeptide(L)
Formula weight11586.485 Da
Number of molecules1
ID11
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG48, Sequence view
ID 12 : 50S ribosomal protein L22
Image
Description50S ribosomal protein L22
Typepolypeptide(L)
Formula weight12253.464 Da
Number of molecules1
ID12
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P61175, Sequence view
ID 13 : 50S ribosomal protein L23
Image
Description50S ribosomal protein L23
Typepolypeptide(L)
Formula weight11093.154 Da
Number of molecules1
ID13
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0ADZ0, Sequence view
ID 14 : 50S ribosomal protein L2
Image
Description50S ribosomal protein L2
Typepolypeptide(L)
Formula weight29550.385 Da
Number of molecules1
ID14
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60422, Sequence view
ID 15 : 50S ribosomal protein L24
Image
Description50S ribosomal protein L24
Typepolypeptide(L)
Formula weight11210.181 Da
Number of molecules1
ID15
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60624, Sequence view
ID 16 : 50S ribosomal protein L27
Image
Description50S ribosomal protein L27
Typepolypeptide(L)
Formula weight9146.618 Da
Number of molecules1
ID16
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7L8, Sequence view
ID 17 : 50S ribosomal protein L29
Image
Description50S ribosomal protein L29
Typepolypeptide(L)
Formula weight7286.531 Da
Number of molecules1
ID17
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M6, Sequence view
ID 18 : 50S ribosomal protein L30
Image
Description50S ribosomal protein L30
Typepolypeptide(L)
Formula weight6554.875 Da
Number of molecules1
ID18
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG51, Sequence view
ID 19 : 50S ribosomal protein L31
Image
Description50S ribosomal protein L31
Typepolypeptide(L)
Formula weight7887.165 Da
Number of molecules1
ID19
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7M9, Sequence view
ID 20 : 50S ribosomal protein L32
Image
Description50S ribosomal protein L32
Typepolypeptide(L)
Formula weight6463.500 Da
Number of molecules1
ID20
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N4, Sequence view
ID 21 : 50S ribosomal protein L33
Image
Description50S ribosomal protein L33
Typepolypeptide(L)
Formula weight6257.510 Da
Number of molecules1
ID21
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7N9, Sequence view
ID 22 : 50S ribosomal protein L34
Image
Description50S ribosomal protein L34
Typepolypeptide(L)
Formula weight5397.506 Da
Number of molecules1
ID22
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7P5, Sequence view
ID 23 : 50S ribosomal protein L35
Image
Description50S ribosomal protein L35
Typepolypeptide(L)
Formula weight7181.907 Da
Number of molecules1
ID23
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q1, Sequence view
ID 24 : 50S ribosomal protein L36
Image
Description50S ribosomal protein L36
Typepolypeptide(L)
Formula weight4377.415 Da
Number of molecules1
ID24
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7Q6, Sequence view
ID 25 : 50S ribosomal protein L3
Image
Description50S ribosomal protein L3
Typepolypeptide(L)
Formula weight22277.709 Da
Number of molecules1
ID25
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60438, Sequence view
ID 26 : 50S ribosomal protein L1P
Image
Description50S ribosomal protein L1P
Typepolypeptide(L)
Formula weight23978.254 Da
Number of molecules1
ID26
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:2285
Organism scientific: Sulfolobus acidocaldarius
LinksUniProt: P35024, Sequence view
ID 27 : 50S ribosomal protein L4
Image
Description50S ribosomal protein L4
Typepolypeptide(L)
Formula weight22121.723 Da
Number of molecules1
ID27
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P60723, Sequence view
ID 28 : 50S ribosomal protein L5
Image
Description50S ribosomal protein L5
Typepolypeptide(L)
Formula weight20202.566 Da
Number of molecules1
ID28
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P62399, Sequence view
ID 29 : 50S ribosomal protein L6
Image
Description50S ribosomal protein L6
Typepolypeptide(L)
Formula weight18932.957 Da
Number of molecules1
ID29
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0AG55, Sequence view
ID 30 : 50S ribosomal protein L9
Image
Description50S ribosomal protein L9
Typepolypeptide(L)
Formula weight15789.174 Da
Number of molecules1
ID30
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7R1, Sequence view
ID 31 : 50S ribosomal protein L11
Image
Description50S ribosomal protein L11
Typepolypeptide(L)
Formula weight14894.478 Da
Number of molecules1
ID31
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:562
Organism scientific: Escherichia coli
LinksUniProt: P0A7J7, Sequence view
ID 32 : 50S ribosomal protein L13
Image
Description50S ribosomal protein L13
Typepolypeptide(L)
Formula weight15822.503 Da
Number of molecules1
ID32
SourceMethod: Isolated from a natural source
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 ID2I2V
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms92672
Nucleic acid atoms64821
Protein atoms27851
Download
PDB format
Allpdb3e1d.ent.gz
pdb3e1d.ent (uncompressed file)
Header onlypdb3e1d.ent.gz
mmCIF format
mmCIF3e1d.cif.gz
XML format
All3e1d.xml.gz
No-atom3e1d-noatom.xml.gz
Ext-atom3e1d-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.2 MB