8FR8 image
Deposition Date 2023-01-06
Release Date 2023-05-17
Last Version Date 2024-06-19
Entry Detail
PDB ID:
8FR8
Keywords:
TRANSLATION
Title:
Structure of Mycobacterium smegmatis Rsh bound to a 70S translation initiation complex
Biological Source:
Source Organism:
Mycolicibacterium smegmatis MC2 155 (Taxon ID: 246196)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.76 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8FR8 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:HA (auth: 0)
Chain Length:46
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R7K0 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:BA (auth: 1)
Chain Length:105
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG0 Pfam ID:PF17136, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:CA (auth: 2)
Chain Length:192
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R3D2 Pfam ID:PF01386, PF14693
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein eL31
Gene (Uniprot):MSMEG_1916
Chain IDs:H (auth: 3)
Chain Length:23
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QTP4
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:DA (auth: 4)
Chain Length:79
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R150 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:EA (auth: 6)
Chain Length:64
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD9 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:FA (auth: 7)
Chain Length:59
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG7 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:GA (auth: 8)
Chain Length:54
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R3I9 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:FB (auth: 9)
Chain Length:100
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R550 Pfam ID:PF00253
Polymer Type:polyribonucleotide
Molecule:23S rRNA (3119-MER)
Chain IDs:I (auth: A)
Chain Length:3119
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polyribonucleotide
Molecule:5S rRNA (118-MER)
Chain IDs:E (auth: B)
Chain Length:32
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:W (auth: C)
Chain Length:53
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QV42 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:V (auth: D)
Chain Length:82
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:I7FGD9 Pfam ID:PF00861
Polymer Type:polyribonucleotide
Molecule:fMet tRNA (77-MER)
Chain IDs:C (auth: E)
Chain Length:200
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:JA (auth: F)
Chain Length:37
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSL4 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:MA (auth: G)
Chain Length:96
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD7 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:DB (auth: H)
Chain Length:155
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R554 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP pyrophosphokinase RelA
Gene (Uniprot):relA
Chain IDs:CB (auth: I)
Chain Length:131
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:I7FCZ4 Pfam ID:PF13328, PF04607, PF02824, PF19296, PF13291
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:U (auth: J)
Chain Length:116
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSL9 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:J (auth: K)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD4 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:K (auth: L)
Chain Length:214
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD1 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:L (auth: M)
Chain Length:115
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD2 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:G (auth: N)
Chain Length:122
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD8 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:M (auth: O)
Chain Length:84
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG1 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:N (auth: P)
Chain Length:176
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG4 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:O (auth: Q)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R7F6 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:P (auth: R)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QS62 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:Q (auth: S)
Chain Length:133
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QS45 Pfam ID:PF00298, PF03946
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:R (auth: T)
Chain Length:146
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSP8 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:S (auth: U)
Chain Length:228
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSF9 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:T (auth: V)
Chain Length:20
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:I7G436 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:X (auth: W)
Chain Length:124
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QYU6 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Y (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R151 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Z (auth: Y)
Chain Length:77
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD6 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:AA (auth: Z)
Chain Length:97
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD3 Pfam ID:PF00276
Polymer Type:polyribonucleotide
Molecule:16S rRNA (1511-MER)
Chain IDs:KA (auth: a)
Chain Length:3119
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S22
Chain IDs:LA (auth: b)
Chain Length:32
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 2
Gene (Uniprot):rpmG2
Chain IDs:A (auth: c)
Chain Length:53
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R551 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:D (auth: d)
Chain Length:82
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSD5 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:NA (auth: e)
Chain Length:200
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSL7 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:OA (auth: f)
Chain Length:37
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG6 Pfam ID:PF03719, PF00333
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:PA (auth: g)
Chain Length:96
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0A2U9Q0X2 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:QA (auth: h)
Chain Length:155
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QS97 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:RA (auth: i)
Chain Length:131
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSG3 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:F (auth: j)
Chain Length:116
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSL5 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:SA (auth: k)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSP9 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:TA (auth: l)
Chain Length:214
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0A7I7K4Z0 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:UA (auth: m)
Chain Length:115
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSL6 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:VA (auth: n)
Chain Length:122
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QS96 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18 1
Gene (Uniprot):rpsR1
Chain IDs:EB (auth: o)
Chain Length:84
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R549 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:WA (auth: p)
Chain Length:176
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QVQ3 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: q)
Chain Length:113
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QV37 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: r)
Chain Length:126
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QSE0 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:ZA (auth: t)
Chain Length:146
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R102 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:AB (auth: u)
Chain Length:228
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QVB8 Pfam ID:PF00318
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:BB (auth: v)
Chain Length:20
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:IA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0QYU7 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:B (auth: y)
Chain Length:77
Number of Molecules:1
Biological Source:Mycolicibacterium smegmatis MC2 155
UniProt ID:A0R552 Pfam ID:PF00830
Ligand Molecules
NA
Primary Citation
Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation.
Proc.Natl.Acad.Sci.USA 120 e2302006120 e2302006120 (2023)
PMID: 37216503 DOI: 10.1073/pnas.2302006120

Abstact

The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12 stalk base, suggesting that the aminoacylation status of A-site tRNA is surveilled during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle.

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Protein

Chemical

Disease

Primary Citation of related structures
8FR8
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