ISDA

Deposition Date 2000-02-11

Release Date 2000-03-06

Last Version Date 2024-02-07

Entry Detail

PDB ID:

1EG0

Keywords:

RIBOSOME

Title:

FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

11.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S4 RIBOSOMAL PROTEIN)
Chain IDs:E (auth: A)
Chain Length:159
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P21466 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S5 RIBOSOMAL PROTEIN)
Chain IDs:F (auth: B)
Chain Length:148
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P21467 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S6 RIBOSOMAL PROTEIN)
Chain IDs:G (auth: C)
Chain Length:97
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S7 RIBOSOMAL PROTEIN)
Gene (Uniprot):rpsG
Chain IDs:H (auth: D)
Chain Length:146
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S8 RIBOSOMAL PROTEIN)
Chain IDs:I (auth: E)
Chain Length:138
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S15 RIBOSOMAL PROTEIN)
Chain IDs:J (auth: F)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S17 RIBOSOMAL PROTEIN)
Gene (Uniprot):rpsQ
Chain IDs:K (auth: G)
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P23828 Pfam ID:PF00366

Polymer Type:polypeptide(L)
Molecule:PROTEIN (S20 RIBOSOMAL PROTEIN)
Chain IDs:L (auth: H)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:FRAGMENT OF 16S RRNA HELIX 23
Chain IDs:A (auth: I)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (RIBOSOMAL PROTEIN L6)
Mutations:B. STEAROTHERMOPHILUS SEQUENCE AND MODEL
Chain IDs:N (auth: J)
Chain Length:171
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:Q5L408 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (RIBOSOMAL PROTEIN L11)
Gene (Uniprot):rplK
Chain IDs:O (auth: K)
Chain Length:140
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P29395 Pfam ID:PF03946, PF00298

Polymer Type:polyribonucleotide
Molecule:FRAGMENT OF 23S RRNA
Chain IDs:B (auth: L)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:HELIX 95 OF 23S RRNA
Chain IDs:C (auth: M)
Chain Length:26
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (RIBOSOMAL PROTEIN L1)
Chain IDs:M (auth: N)
Chain Length:229
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:Q5SLP7 Pfam ID:PF00687

Polymer Type:polyribonucleotide
Molecule:FORMYL-METHIONYL-TRNA
Chain IDs:D (auth: O)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	D	U	4-THIOURIDINE-5'-MONOPHOSPHATE
5MU	D	U	5-METHYLURIDINE 5'-MONOPHOSPHATE
H2U	D	U	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
OMC	D	C	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
PSU	D	U	PSEUDOURIDINE-5'-MONOPHOSPHATE

Ligand Molecules

Primary Citation

Solution structure of the E. coli 70S ribosome at 11.5 A resolution.

Gabashvili, I.S, Agrawal, R.K, Spahn, C.M, Grassucci, R.A, Svergun, D.I, Frank, J, Penczek, P, Davies, C, Gerstner, R.B, Draper, D.E, Ramakrishnan, V, White, S.W, Ramakrishnan, V, White, S.W, 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, Wimberly, B.T, White, S.W, Ramakrishnan, V, Nevskaya, N, Tischenko, S, Nikulin, A, Al-Karadaghi, S, Liljas, A, Ehresmann, B, Ehresmann, C, Garber, M, Nikonov, S, Clemons Jr, W.M, Davies, C.R, White, S.W, Ramakrishnan, V, Jaishree, T, Ramakrishnan, V, White, S.W, Clemons Jr, W.M, May, J.L.C, Wimberly, B.T, Mccutcheon, J.P, Capel, M.S, Ramakrishnan, V, Golden, B.L, Davies, C, Ramakrishnan, V, White, S.W, Wimberly, B.T, Guymon, R, Mccutcheon, J.P, Ramakrishnan, S.W, White, V, Correll, C.C, Wool, I.G, Munishkin, A, Nikonov, S, Nevskaya, N, Eliseikina, I, Briand, C, Al-Karadaghi, S, Svensson, A, Liljas, A, Aebarson, A, Schmitt, E, Panvert, M, Blanquet, S, Mechulam, Y.Show

Cell(Cambridge,Mass.) 100 537 549 (2000)

PMID: 10721991 DOI: 10.1016/S0092-8674(00)80690-X

Abstact

Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.

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Disease

Primary Citation of related structures