PDB-3e1a: Structure of the 30S subunit and the tRNAs of E. coli r...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3e1a
Title	Structure of the 30S subunit and the tRNAs of E. coli ribosome in Pre-accommodation state
Descriptor	Ribosome 30S subunit
Keywords	RIBOSOME, 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
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: With PDB-3e1b, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-3e1b CiteSplit PDB-3e1c Cite PDB-3e1d Cite EMDB-1055 EMDB-1056 Cite: data citing same article Split: split data constructing the same model
Similar strucutres (beta)	Diagram PDB-3e1c PDB-3j10 PDB-3j13 PDB-2xuy PDB-3izw PDB-3j36 List of similar structure data about Omokage system

Article
Citation - primary
Article	To be Published, Vol. , Page: - , Year: ,
Title	The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading
Authors	Devkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C.

Components
ID 1 : A/T, P and E-site tRNAs
Image
Description	A/T, P and E-site tRNAs
Type	polyribonucleotide
Formula weight	24518.730 Da
Number of molecules	3
ID	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 2 : mRNA model
Image
Description	mRNA model
Type	polyribonucleotide
Formula weight	6078.410 Da
Number of molecules	1
ID	2
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 3 : 16S rRNA
Image
Description	16S rRNA
Type	polyribonucleotide
Formula weight	495928.906 Da
Number of molecules	1
ID	3
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 4 : 30S ribosomal protein S2
Image
Description	30S ribosomal protein S2
Type	polypeptide(L)
Formula weight	26781.848 Da
Number of molecules	1
ID	4
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7V0, Sequence view
ID 5 : 30S ribosomal protein S11
Image
Description	30S ribosomal protein S11
Type	polypeptide(L)
Formula weight	13871.092 Da
Number of molecules	1
ID	5
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7R9, Sequence view
ID 6 : 30S ribosomal protein S12
Image
Description	30S ribosomal protein S12
Type	polypeptide(L)
Formula weight	13768.263 Da
Number of molecules	1
ID	6
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7S3, Sequence view
ID 7 : 30S ribosomal protein S13
Image
Description	30S ribosomal protein S13
Type	polypeptide(L)
Formula weight	13128.570 Da
Number of molecules	1
ID	7
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7S9, Sequence view
ID 8 : 30S ribosomal protein S14
Image
Description	30S ribosomal protein S14
Type	polypeptide(L)
Formula weight	11606.653 Da
Number of molecules	1
ID	8
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0AG59, Sequence view
ID 9 : 30S ribosomal protein S15
Image
Description	30S ribosomal protein S15
Type	polypeptide(L)
Formula weight	10319.969 Da
Number of molecules	1
ID	9
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: Q8X9M2, Sequence view
ID 10 : 30S ribosomal protein S16
Image
Description	30S ribosomal protein S16
Type	polypeptide(L)
Formula weight	9207.662 Da
Number of molecules	1
ID	10
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7T3, Sequence view
ID 11 : 30S ribosomal protein S17
Image
Description	30S ribosomal protein S17
Type	polypeptide(L)
Formula weight	9724.571 Da
Number of molecules	1
ID	11
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0AG63, Sequence view
ID 12 : 30S ribosomal protein S18
Image
Description	30S ribosomal protein S18
Type	polypeptide(L)
Formula weight	9006.581 Da
Number of molecules	1
ID	12
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7T7, Sequence view
ID 13 : 30S ribosomal protein S19
Image
Description	30S ribosomal protein S19
Type	polypeptide(L)
Formula weight	10455.452 Da
Number of molecules	1
ID	13
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7U3, Sequence view
ID 14 : 30S ribosomal protein S20
Image
Description	30S ribosomal protein S20
Type	polypeptide(L)
Formula weight	9708.547 Da
Number of molecules	1
ID	14
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7U7, Sequence view
ID 15 : 30S ribosomal protein S3
Image
Description	30S ribosomal protein S3
Type	polypeptide(L)
Formula weight	26031.535 Da
Number of molecules	1
ID	15
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7V3, Sequence view
ID 16 : 30S ribosomal protein S21
Image
Description	30S ribosomal protein S21
Type	polypeptide(L)
Formula weight	8524.120 Da
Number of molecules	1
ID	16
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P68679, Sequence view
ID 17 : 30S ribosomal protein S4
Image
Description	30S ribosomal protein S4
Type	polypeptide(L)
Formula weight	23514.385 Da
Number of molecules	1
ID	17
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7V8, Sequence view
ID 18 : 30S ribosomal protein S5
Image
Description	30S ribosomal protein S5
Type	polypeptide(L)
Formula weight	16772.539 Da
Number of molecules	1
ID	18
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7W1, Sequence view
ID 19 : 30S ribosomal protein S6
Image
Description	30S ribosomal protein S6
Type	polypeptide(L)
Formula weight	15727.645 Da
Number of molecules	1
ID	19
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P02358, Sequence view
ID 20 : 30S ribosomal protein S7
Image
Description	30S ribosomal protein S7
Type	polypeptide(L)
Formula weight	20055.324 Da
Number of molecules	1
ID	20
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P02359, Sequence view
ID 21 : 30S ribosomal protein S8
Image
Description	30S ribosomal protein S8
Type	polypeptide(L)
Formula weight	14146.660 Da
Number of molecules	1
ID	21
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: Q3YWV3, Sequence view
ID 22 : 30S ribosomal protein S9
Image
Description	30S ribosomal protein S9
Type	polypeptide(L)
Formula weight	14886.393 Da
Number of molecules	1
ID	22
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7X3, Sequence view
ID 23 : 30S ribosomal protein S10
Image
Description	30S ribosomal protein S10
Type	polypeptide(L)
Formula weight	11755.708 Da
Number of molecules	1
ID	23
Source	Method: Isolated from a natural source NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P0A7R5, Sequence view

Sample
Experiment
Method	ELECTRON MICROSCOPY

Electron Microscopy

Processing
2D projection selection
Software name	Yup.scx
3D reconstruction
Method	Single Particle
Nominal pixel size	2.82 A/pix
Resolution	9.0 A
3D fitting
Method	Flexible fitting
Refinement Space	REAL
Software name	Yup.scx
Target criteria	cross-correlation
3D fitting list
3D fitting id	1
PDB entry ID	2I2P, 1EHZ PDB-2i2p PDB-1ehz
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	56576
Nucleic acid atoms	38047
Protein atoms	18529