PDB-1eg0: FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1eg0
Title	FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME
Descriptor	COMPONENTS OF 70S RIBOSOME
Keywords	RIBOSOME, 70S RIBOSOME, LOW RESOLUTION MODEL
Authors	Gabashvili, I.S., Agrawal, R.K., Spahn, C.M.T., Grassucci, R.A., Svergun, D.I., Frank, J., Penczek, P.
Date	Deposition: 2000-02-11, Release: 2000-03-06
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Sequence details	ONLY COORDINATES OF PHOSPHATE AND CA-ATOMS ARE DEPOSITED
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1003, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1003, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1003 CiteFit PDB-1jqm PDB-1jqs PDB-1jqt PDB-2xsy PDB-2xuy Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1072 EMDB-1847 EMDB-5175 EMDB-5178 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 100, Issue 5, Page 537-49, Year 2000
Title	Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
Authors	I S Gabashvili, R K Agrawal, C M Spahn, R A Grassucci, D I Svergun, J Frank, P Penczek Howard Hughes Medical Institute, Health Research, Inc., Albany, New York 11201-0509, USA.
Keywords	Bacterial Proteins (ultrastructure), Cryoelectron Microscopy, Escherichia coli (ultrastructure), GTP Phosphohydrolases (ultrastructure, 3.6.1.-), Image Processing, Computer-Assisted, Macromolecular Substances, Peptide Elongation Factor G (ultrastructure), RNA, Bacterial (ultrastructure), RNA, Ribosomal (ultrastructure), RNA, Transfer, Met (ultrastructure), Ribosomal Proteins (ultrastructure), Ribosomes (ultrastructure), Solutions, tRNA, formylmethionine-
Links	PubMed: 10721991, PII: S0092-8674(00)80690-X
Citation - 1
Article	Embo J., Vol. 17, Page: 4545 - , Year: 1998,
Title	The Crystal Structure of Ribosomal Protein S4 Reveals a Two-Domain Molecule with an Extensive RNA-Binding Surface: One Domain Shows Structural Homology to the Ets DNA-Binding Motif
Authors	Davies, C., Gerstner, R.B., Draper, D.E., Ramakrishnan, V., White, S.W.
Links	DOI: 10.1093/emboj/17.16.4545
Citation - 2
Article	Nature, Vol. 358, Page: 768 - , Year: 1992,
Title	The Structure of Ribosomal Protein S5 Reveals Sites of Interaction with 16S Rrna
Authors	Ramakrishnan, V., White, S.W.
Links	DOI: 10.1038/358768a0
Citation - 3
Article	Embo J., Vol. 13, Page: 1249 - , Year: 1994,
Title	Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus
Authors	Lindahl, M., Svensson, L.A., Liljas, A., Sedelnikova, I.A., Eliseikina, I.A., Fomenkova, N.P., Nevskaya, N., Nikonov, S.V., Garber, M.B., Muranova, T.A., Rykonova, A.I., Amons, R.
Citation - 4
Article	Structure, Vol. 5, Page: 1187 - , Year: 1997,
Title	The Structure of Ribosomal Protein S7 at 1.9 A Resolution Reveals a Beta- Hairpin Motif that Binds Double-Stranded Nucleic Acids
Authors	Wimberly, B.T., White, S.W., Ramakrishnan, V.
Links	DOI: 10.1016/S0969-2126(97)00269-4
Citation - 5
Article	J.Mol.Biol., Vol. 279, Page: 233 - , Year: 1998,
Title	Crystal Structure of Ribosomal Protein S8 from Thermus Thermophilus Reveals a High Degree of Structural Conservation of a Specific RNA Binding Site
Authors	Nevskaya, N., Tischenko, S., Nikulin, A., Al-Karadaghi, S., Liljas, A., Ehresmann, B., Ehresmann, C., Garber, M., Nikonov, S.
Links	DOI: 10.1006/jmbi.1998.1758
Citation - 6
Article	Structure, Vol. 6, Page: 429 - , Year: 1998,
Title	Conformational Variability of the N-Terminal Helix in the Structure of Ribosomal Protein S15
Authors	Clemons Jr., W.M., Davies, C.R., White, S.W., Ramakrishnan, V.
Citation - 7
Article	Biochemistry, Vol. 35, Page: 2845 - , Year: 1996,
Title	Solution Structure of Prokaryotic Ribosomal Protein S17 by High-Resolution NMR Spectroscopy
Authors	Jaishree, T., Ramakrishnan, V., White, S.W.
Links	DOI: 10.1021/bi951062i
Citation - 8
Article	Nature, Vol. 400, Page: 833 - 840, Year: 1999,
Title	Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution
Authors	Clemons Jr., W.M., May, J.L.C., Wimberly, B.T., Mccutcheon, J.P., Capel, M.S., Ramakrishnan, V.
Citation - 9
Article	Embo J., Vol. 12, Page: 4901 - , Year: 1993,
Title	Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA-Binding Protein
Authors	Golden, B.L., Davies, C., Ramakrishnan, V., White, S.W.
Citation - 10
Article	Cell(Cambridge,Mass.), Vol. 97, Page: 491 - , Year: 1999,
Title	A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
Authors	Wimberly, B.T., Guymon, R., Mccutcheon, J.P., Ramakrishnan, S.W., White, V.
Links	DOI: 10.1016/S0092-8674(00)80759-X
Citation - 11
Article	J.Mol.Biol., Vol. 292, Page: 275 - , Year: 1999,
Title	The Two Faces of the Escherichia Coli 23 S Rrna Sarcin/Ricin Domain: The Structure at 1.11 A Resolution
Authors	Correll, C.C., Wool, I.G., Munishkin, A.
Links	DOI: 10.1006/jmbi.1999.3072
Citation - 12
Article	Embo J., Vol. 15, Page: 1350 - , Year: 1996,
Title	Crystal Structure of the RNA Binding Ribosomal Prot L1 from Thermus Thermophilus
Authors	Nikonov, S., Nevskaya, N., Eliseikina, I., Briand, C., Al-Karadaghi, S., Svensson, A., Liljas, A., Aebarson, A.
Citation - 13
Article	Embo J., Vol. 17, Page: 6819 - , Year: 1998,
Title	Crystal Structure of Methionyl-Trnafmet Transformylase Complexed with the Initiator Formyl-Methionyl-Trnafmet
Authors	Schmitt, E., Panvert, M., Blanquet, S., Mechulam, Y.
Links	DOI: 10.1093/emboj/17.23.6819

Components
ID 1 : FRAGMENT OF 16S RRNA HELIX 23
Image
Description	FRAGMENT OF 16S RRNA HELIX 23
Type	polyribonucleotide
Fragment	RESIDUES 673-713
Formula weight	6426.216 Da
Number of molecules	1
ID	1
Details	MODELED AS ANALOGOUS FRAGMENT OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1QD7
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 2 : FRAGMENT OF 23S RRNA
Image
Description	FRAGMENT OF 23S RRNA
Type	polyribonucleotide
Fragment	RESIDUES 1051-1108
Formula weight	18348.066 Da
Number of molecules	1
ID	2
Details	T. MARITIMA RNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 1MMS
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 3 : HELIX 95 OF 23S RRNA
Image
Description	HELIX 95 OF 23S RRNA
Type	polyribonucleotide
Formula weight	8438.146 Da
Number of molecules	1
ID	3
Details	E.COLI RNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 480D
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 4 : FMET-TRNA
Image
Description	FORMYL-METHIONYL-TRNA
Type	polyribonucleotide
Formula weight	24526.906 Da
Number of molecules	1
ID	4
Details	E.COLI FMET-TRNA SEQUENCE AND MODEL TAKEN FROM PDB ENTRY 2FMT
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 5 : PROTEIN (S4 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S4 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	18624.512 Da
Number of molecules	1
ID	5
Details	MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1C06
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P81288, Sequence view
ID 6 : PROTEIN (S5 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S5 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	15686.451 Da
Number of molecules	1
ID	6
Details	MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1PKP
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P02357, Sequence view
ID 7 : PROTEIN (S6 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S6 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	11619.442 Da
Number of molecules	1
ID	7
Details	MODELED BY ANALOGOUS PROTEIN OF T.THERMOPHILUS TAKEN FROM PDB ENTRY 1RIS
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P23370, Sequence view
ID 8 : PROTEIN (S7 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S7 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	16758.678 Da
Number of molecules	1
ID	8
Details	MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1RSS
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P17291, Sequence view
ID 9 : PROTEIN (S8 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S8 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	15868.703 Da
Number of molecules	1
ID	9
Details	MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1AN7
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 10 : PROTEIN (S15 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S15 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	10578.502 Da
Number of molecules	1
ID	10
Details	MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1A32
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P80378, Sequence view
ID 11 : PROTEIN (S17 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S17 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	10569.444 Da
Number of molecules	1
ID	11
Details	MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRIES 1RIP AND 1QD7
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P23828, Sequence view
ID 12 : PROTEIN (S20 RIBOSOMAL PROTEIN)
Image
Description	PROTEIN (S20 RIBOSOMAL PROTEIN)
Type	polypeptide(L)
Formula weight	8528.545 Da
Number of molecules	1
ID	12
Details	MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1QD7
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	Sequence view
ID 13 : PROTEIN (RIBOSOMAL PROTEIN L1)
Image
Description	PROTEIN (RIBOSOMAL PROTEIN L1)
Type	polypeptide(L)
Formula weight	24867.895 Da
Number of molecules	1
ID	13
Details	MODELED BY ANALOGOUS PROTEIN OF T. THERMOPHILUS TAKEN FROM PDB ENTRY 1AD2
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P27150, Sequence view
ID 14 : PROTEIN (RIBOSOMAL PROTEIN L6)
Image
Description	PROTEIN (RIBOSOMAL PROTEIN L6)
Type	polypeptide(L)
Mutation	B. STEAROTHERMOPHILUS SEQUENCE AND MODEL
Formula weight	18601.621 Da
Number of molecules	1
ID	14
Details	MODELED BY ANALOGOUS PROTEIN OF T. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1RL6
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P02391, Sequence view
ID 15 : PROTEIN (RIBOSOMAL PROTEIN L11)
Image
Description	PROTEIN (RIBOSOMAL PROTEIN L11)
Type	polypeptide(L)
Formula weight	14996.956 Da
Number of molecules	1
ID	15
Details	MODELED BY ANALOGOUS PROTEIN OF T. MARITIMA TAKEN FROM PDB ENTRY 1MMS
Source	Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562 Organism scientific: Escherichia coli
Links	UniProt: P29395, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Experiment
Method	ELECTRON MICROSCOPY

Electron Microscopy
Lens
Nominal defocus	Max: 4340. nm, Min: 730. nm

Processing
Reflection
Ordinal	1
D resolution high	11.5
Single particle entity
Symmetry type	ASYMMETRIC
3D reconstruction
Resolution	11.5 A
3D fitting
Details	ALL COMPONENTS WERE FIT INTO MAP AS RIGID BODIES USING COORDINATES FROM THE REFERRED SOURCES EXCEPT FOR L1, FOR WHICH ABOUT 15-DEGREE ROTATION WAS INTRODUCED BETWEEN THE TWO DOMAINS; FITTING OF PROTEIN S17 IS RELATIVELY UNCERTAIN; CONFORMATIONAL CHANGES OF ANTICODON AND ACCEPTOR REGIONS OF TRNAFMET UPON BINDING TO THE RIBOSOME WERE NOT MODELED.
Refinement Protocol	RIGID BODY REFINEMENT
Refinement Space	RECIPROCAL
Target criteria	VECTOR R-FACTOR
Computing
Structure solution	O, SPIDER
Refine
Refine id	ELECTRON MICROSCOPY
Details	ALL COMPONENTS WERE FIT INTO MAP AS RIGID BODIES USING COORDINATES FROM THE REFERRED SOURCES EXCEPT FOR L1, FOR WHICH ABOUT 15-DEGREE ROTATION WAS INTRODUCED BETWEEN THE TWO DOMAINS; FITTING OF PROTEIN S17 IS RELATIVELY UNCERTAIN; CONFORMATIONAL CHANGES OF ANTICODON AND ACCEPTOR REGIONS OF TRNAFMET UPON BINDING TO THE RIBOSOME WERE NOT MODELED.
Ls d res high	11.5 A
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
D res high	11.5
Total atoms	1658
Nucleic acid atoms	192
Protein atoms	1466
Software
Ordinal	1
Classification	model building
Name	O
Software
Ordinal	2
Classification	model building
Name	SPIDER