PDB-1p87: Real space refined coordinates of the 30S subunit fitte...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1p87
Title	Real space refined coordinates of the 30S subunit fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome
Descriptor	30S Ribosomal Subunit
Keywords	RIBOSOME, EFG-GTP-bound state, ratchet-like movement, real-space refinement
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-1p86, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-1p86 Split PDB-1gix PDB-1giy PDB-1ibl PDB-1jj2 PDB-1lnr PDB-1m5g PDB-2vaz PDB-2wwl PDB-4a2i PDB-4adv Split: split data constructing the same model
Similar strucutres (beta)	Diagram EMDB-1770 PDB-3kc4 PDB-1p6g EMDB-1771 PDB-4adv PDB-3bbn List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell(Cambridge,Mass.), Vol. 113, Page: 789 - 801, Year: 2003,
Title	Study of the structural dynamics of the E. coli 70S ribosome using real space refinement
Authors	Gao, H., Sengupta, J., Valle, M., Korostelev, A, Eswar, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.T., Sali, A., Chapman, M.S., Frank, J.
Links	DOI: 10.1016/S0092-8674(03)00427-6
Citation - 1
Article	Cell(Cambridge,Mass.), Vol. 100, Page: 537 - 549, Year: 2000,
Title	Solution structure of the E. coli 70S ribosome at 11.5 A resolution
Authors	Gabashvili, I.S., Agrawal, R.K., Spahn, C.M.T., Grassucci, R., Svergun, D.I., Frank, J., Penczek, P.
Citation - 2
Article	Nature, Vol. 406, Page: 318 - 322, Year: 2000,
Title	A ratchet-like inter-subunit reorganization of the ribosome during translocation
Authors	Frank, J., Agrawal, R.K.

Components
ID 1 : 16S RIBOSOMAL RNA
Image
Description	16S RIBOSOMAL RNA
Type	polyribonucleotide
Formula weight	499996.344 Da
Number of molecules	1
ID	1
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	GenBank: V00348, Sequence view
ID 2 : 30S RIBOSOMAL PROTEIN S2
Image
Description	30S RIBOSOMAL PROTEIN S2
Type	polypeptide(L)
Formula weight	26650.656 Da
Number of molecules	1
ID	2
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02351, Sequence view
ID 3 : 30S RIBOSOMAL PROTEIN S3
Image
Description	30S RIBOSOMAL PROTEIN S3
Type	polypeptide(L)
Formula weight	25900.342 Da
Number of molecules	1
ID	3
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02352, Sequence view
ID 4 : 30S RIBOSOMAL PROTEIN S4
Image
Description	30S RIBOSOMAL PROTEIN S4
Type	polypeptide(L)
Formula weight	23383.191 Da
Number of molecules	1
ID	4
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02354, Sequence view
ID 5 : 30S RIBOSOMAL PROTEIN S5
Image
Description	30S RIBOSOMAL PROTEIN S5
Type	polypeptide(L)
Formula weight	17498.340 Da
Number of molecules	1
ID	5
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02356, Sequence view
ID 6 : 30S RIBOSOMAL PROTEIN S6
Image
Description	30S RIBOSOMAL PROTEIN S6
Type	polypeptide(L)
Formula weight	15727.645 Da
Number of molecules	1
ID	6
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02358, Sequence view
ID 7 : 30S RIBOSOMAL PROTEIN S7
Image
Description	30S RIBOSOMAL PROTEIN S7
Type	polypeptide(L)
Formula weight	19924.133 Da
Number of molecules	1
ID	7
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02359, Sequence view
ID 8 : 30S RIBOSOMAL PROTEIN S8
Image
Description	30S RIBOSOMAL PROTEIN S8
Type	polypeptide(L)
Formula weight	14015.469 Da
Number of molecules	1
ID	8
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02361, Sequence view
ID 9 : 30S RIBOSOMAL PROTEIN S9
Image
Description	30S RIBOSOMAL PROTEIN S9
Type	polypeptide(L)
Formula weight	14755.199 Da
Number of molecules	1
ID	9
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02363, Sequence view
ID 10 : 30S RIBOSOMAL PROTEIN S10
Image
Description	30S RIBOSOMAL PROTEIN S10
Type	polypeptide(L)
Formula weight	11755.708 Da
Number of molecules	1
ID	10
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02364, Sequence view
ID 11 : 30S RIBOSOMAL PROTEIN S11
Image
Description	30S RIBOSOMAL PROTEIN S11
Type	polypeptide(L)
Formula weight	13739.899 Da
Number of molecules	1
ID	11
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02366, Sequence view
ID 12 : 30S RIBOSOMAL PROTEIN S12
Image
Description	30S RIBOSOMAL PROTEIN S12
Type	polypeptide(L)
Formula weight	13637.070 Da
Number of molecules	1
ID	12
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02367, Sequence view
ID 13 : 30S RIBOSOMAL PROTEIN S13
Image
Description	30S RIBOSOMAL PROTEIN S13
Type	polypeptide(L)
Formula weight	12997.379 Da
Number of molecules	1
ID	13
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02369, Sequence view
ID 14 : 30S RIBOSOMAL PROTEIN S14
Image
Description	30S RIBOSOMAL PROTEIN S14
Type	polypeptide(L)
Formula weight	11475.461 Da
Number of molecules	1
ID	14
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02370, Sequence view
ID 15 : 30S RIBOSOMAL PROTEIN S15
Image
Description	30S RIBOSOMAL PROTEIN S15
Type	polypeptide(L)
Formula weight	10159.713 Da
Number of molecules	1
ID	15
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02371, Sequence view
ID 16 : 30S RIBOSOMAL PROTEIN S16
Image
Description	30S RIBOSOMAL PROTEIN S16
Type	polypeptide(L)
Formula weight	9207.662 Da
Number of molecules	1
ID	16
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02372, Sequence view
ID 17 : 30S RIBOSOMAL PROTEIN S17
Image
Description	30S RIBOSOMAL PROTEIN S17
Type	polypeptide(L)
Formula weight	9593.380 Da
Number of molecules	1
ID	17
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02373, Sequence view
ID 18 : 30S RIBOSOMAL PROTEIN S18
Image
Description	30S RIBOSOMAL PROTEIN S18
Type	polypeptide(L)
Formula weight	8874.362 Da
Number of molecules	1
ID	18
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02374, Sequence view
ID 19 : 30S RIBOSOMAL PROTEIN S19
Image
Description	30S RIBOSOMAL PROTEIN S19
Type	polypeptide(L)
Formula weight	10324.260 Da
Number of molecules	1
ID	19
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02375, Sequence view
ID 20 : 30S RIBOSOMAL PROTEIN S20
Image
Description	30S RIBOSOMAL PROTEIN S20
Type	polypeptide(L)
Formula weight	9577.354 Da
Number of molecules	1
ID	20
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli Strain: MRE 600
Links	UniProt: P02378, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	E. coli 70S ribosome bound with formyl-methionyl initiator tRNA
Buffer
Name	hepes
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.5
Sample concentration	32 mg/ml
Vitrification
Details	Rapid-freezing in liquid ethane
Experiment
Method	ELECTRON MICROSCOPY

Electron Microscopy
Imaging
Microscope	Model: FEI TECNAI F20
Date	1997-07-01
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	200 kV
Electron dose	1000 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	Calibrated: 51200 X, Nominal: 51200 X
Cs	Nominal: 2.0 mm
Nominal defocus	Max: 4340 nm, Min: 730 nm
Specimen holder
Tilt angle	Min: 0 degrees, Max: 0 degrees
Temperature	93 Kelvin
Detector
Type	KODAK SO163 FILM

Processing
2D projection selection
Software name	RSRef, TNT
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
Actual pixel size	2.93 A/pix
CTF correction method	CTF correction of 3D-maps
Details	SPIDER package
Magnification calibration	TMV
Method	Reference based alignment
Nominal pixel size	2.93 A/pix
Resolution	11.5 A
3D fitting
Method	auto
Refinement Protocol	Multi-rigid body, real-space refinement
Refinement Space	REAL
Software name	RSRef, TNT
Target criteria	cross-correlation coefficient, real space R factor
3D fitting list
3D fitting id	1
PDB entry ID	1IBL, 1FJG, 1FFK, 1JJ2, 1LNR, 1GIY PDB-1ibl PDB-1fjg PDB-1ffk PDB-1jj2 PDB-1lnr PDB-1giy
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	3622
Nucleic acid atoms	1487
Protein atoms	2135