ISDA

Deposition Date 2000-08-09

Release Date 2000-09-04

Last Version Date 2024-02-07

Entry Detail

PDB ID:

1FKA

Keywords:

RIBOSOME

Title:

STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 274)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.30 Å

R-Value Free:

0.30

R-Value Work:

0.30

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:A
Chain Length:1518
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Chain IDs:B
Chain Length:111
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Chain IDs:C
Chain Length:176
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Chain IDs:E
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:151
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY9 Pfam ID:PF00410

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Chain IDs:I
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Chain IDs:J
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Chain IDs:K
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Chain IDs:L
Chain Length:103
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Chain IDs:M
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:N
Chain Length:26
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Chain IDs:P
Chain Length:73
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Chain IDs:R
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Chain IDs:S
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Chain IDs:T
Chain Length:95
Number of Molecules:1
Biological Source:Thermus thermophilus

Ligand Molecules

WO2

Primary Citation

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.

Schluenzen, F, Tocilj, A, Zarivach, R, Harms, J, Gluehmann, M, Janell, D, Bashan, A, Bartels, H, Agmon, I, Franceschi, F, Yonath, A, MARKUS, M.A, GERSTNER, R.B, DRAPER, D.E, Torchia, D.A, RAMAKRISHNAN, V, WHITE, S.W, LINDAHL, M, SVENSSON, L.A, LILJAS, A, SEDELNIKOVA, S.E, ELISEIKINA, I.A, FOMENKOVA, N.P, NEVSKAYA, N, NIKONOV, S.V, GARBER, M.B, MURANOVA, T.A, RYKONOVA, A.I, WIMBERLY, B.T, WHITE, S.W, RAMAKRISHNAN, V, NEVSKAYA, N, TISHCHENKO, S, NIKULIN, A, AL-KARADAGHI, S, LILJAS, A, EHRESMANN, B, EHRESMANN, C, GARBER, M.B, NIKONOV, S, CLEMONS, W.M, DAVIES, C, WHITE, S.W, RAMAKRISHNAN, V, AGALAROV, S.C, PRASAD, G.S, FUNKE, P.M, STOUT, C.D, WILLIAMSON, J.R, HELGSTRAND, M, RAK, A.V, ALLARD, P, DAVYDOVA, N, GARBER, M.B, HARD, T.Show

Cell(Cambridge,Mass.) 102 615 623 (2000)

PMID: 11007480 DOI: 10.1016/S0092-8674(00)00084-2

Abstact

The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle's far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation.

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Primary Citation of related structures