ISDA: 5LMR

Deposition Date 2016-08-01

Release Date 2016-10-05

Last Version Date 2025-10-01

Entry Detail

PDB ID:

5LMR

Keywords:

RIBOSOME

Title:

Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)

Biological Source:

Source Organism:

Thermus thermophilus HB8 (Taxon ID: 300852)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.45 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80371 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

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 HB8

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLP8 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P17291 Pfam ID:PF00177

Structures with similar UniProt ID

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 HB8

UniProt ID:P0DOY9 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80374 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN7 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80376 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80377 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:N
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY6 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJ76 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJH3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY7 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP2 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:P80380 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:U (auth: V)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SIH3 Pfam ID:PF17070

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-1
Gene (Uniprot):infA
Chain IDs:V (auth: W)
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHR1 Pfam ID:PF01176

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-3
Gene (Uniprot):infC
Chain IDs:W (auth: X)
Chain Length:171
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SKU2 Pfam ID:PF05198, PF00707

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:X (auth: Y)
Chain Length:42
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule:tRNAi
Chain IDs:Y (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus HB8

Ligand Molecules

Primary Citation

Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.

Hussain, T, Llacer, J.L, Wimberly, B.T, Kieft, J.S, Ramakrishnan, V.Show

Cell 167 133 144.e13 (2016)

PMID: 27662086 DOI: 10.1016/j.cell.2016.08.074

Abstact

In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.

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Primary Citation of related structures