7RR5 image
Deposition Date 2021-08-09
Release Date 2021-11-10
Last Version Date 2024-11-20
Entry Detail
PDB ID:
7RR5
Keywords:
RIBOSOME
Title:
Structure of ribosomal complex bound with Rbg1/Tma46
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Host Organism:
Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.23 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7RR5 validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 5A
Chain IDs:FC (auth: 5)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:A-tRNA
Chain IDs:CC (auth: A)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: C1)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:UA (auth: C2)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: C3)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: C4)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1
Chain IDs:IC (auth: L1)
Chain Length:210
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-B
Chain IDs:D (auth: LA)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL3 isoform 1
Chain IDs:E (auth: LB)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL4A isoform 1
Chain IDs:F (auth: LC)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL5 isoform 1
Chain IDs:G (auth: LD)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:H (auth: LE)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Chain IDs:I (auth: LF)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:J (auth: LG)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:K (auth: LH)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Polymer Type:polypeptide(L)
Molecule:RPL10 isoform 1
Chain IDs:L (auth: LI)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL11B isoform 1
Chain IDs:M (auth: LJ)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:N (auth: LL)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:O (auth: LM)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:P (auth: LN)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Chain IDs:Q (auth: LO)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Chain IDs:R (auth: LP)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-B
Chain IDs:S (auth: LQ)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:T (auth: LR)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:U (auth: LS)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX23 Pfam ID:PF01775
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Chain IDs:V (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Chain IDs:W (auth: LU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-B
Chain IDs:X (auth: LV)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL24A isoform 1
Chain IDs:Y (auth: LW)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Chain IDs:Z (auth: LX)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:AA (auth: LY)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:BA (auth: LZ)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:CA (auth: La)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL29 isoform 1
Chain IDs:DA (auth: Lb)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:EA (auth: Lc)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Chain IDs:FA (auth: Ld)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL32 isoform 1
Chain IDs:GA (auth: Le)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Chain IDs:HA (auth: Lf)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Chain IDs:IA (auth: Lg)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Chain IDs:JA (auth: Lh)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:KA (auth: Li)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Chain IDs:LA (auth: Lj)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL38 isoform 1
Chain IDs:MA (auth: Lk)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:NA (auth: Ll)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Chain IDs:OA (auth: Lm)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:PA (auth: Ln)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Chain IDs:QA (auth: Lo)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:RA (auth: Lp)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Polymer Type:polyribonucleotide
Molecule:P-tRNA
Chain IDs:DC (auth: P)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPP0 isoform 1
Chain IDs:SA (auth: P0)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPL12A isoform 1
Chain IDs:TA (auth: P2)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ribosome-interacting GTPase 1
Chain IDs:GC (auth: R)
Chain Length:410
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0
Chain IDs:VA (auth: SA)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS1A isoform 1
Chain IDs:WA (auth: SB)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS2 isoform 1
Chain IDs:XA (auth: SC)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS3 isoform 1
Chain IDs:YA (auth: SD)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Chain IDs:ZA (auth: SE)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rps5p
Gene (Uniprot):RPS5
Chain IDs:AB (auth: SF)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:A0A1L4AA68 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:BB (auth: SG)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:CB (auth: SH)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS8A isoform 1
Chain IDs:DB (auth: SI)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Chain IDs:EB (auth: SJ)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Chain IDs:FB (auth: SK)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-B
Chain IDs:GB (auth: SL)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Chain IDs:HB (auth: SM)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:IB (auth: SN)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-B
Chain IDs:JB (auth: SO)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS15 isoform 1
Chain IDs:KB (auth: SP)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Chain IDs:LB (auth: SQ)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Chain IDs:MB (auth: SR)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-B
Chain IDs:NB (auth: SS)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Chain IDs:OB (auth: ST)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS20 isoform 1
Chain IDs:PB (auth: SU)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:QB (auth: SV)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0V8 Pfam ID:PF01249
Polymer Type:polypeptide(L)
Molecule:RPS22A isoform 1
Chain IDs:RB (auth: SW)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:SB (auth: SX)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:TB (auth: SY)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS25A isoform 1
Chain IDs:UB (auth: SZ)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS26B isoform 1
Chain IDs:VB (auth: Sa)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:WB (auth: Sb)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35997 Pfam ID:PF01667
Polymer Type:polypeptide(L)
Molecule:RPS28A isoform 1
Chain IDs:XB (auth: Sc)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:RPS29A isoform 1
Chain IDs:YB (auth: Sd)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:ZB (auth: Se)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Chain IDs:AC (auth: Sf)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Chain IDs:BC (auth: Sg)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Translation machinery-associated protein 46
Chain IDs:HC (auth: T)
Chain Length:345
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:EC (auth: m)
Chain Length:16
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5CT FC LYS modified residue
Ligand Molecules
ASP
MG
ZN
Primary Citation
Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells.
Cell Rep 37 109877 109877 (2021)
PMID: 34706231 DOI: 10.1016/j.celrep.2021.109877

Abstact

Conserved developmentally regulated guanosine triphosphate (GTP)-binding proteins (Drgs) and their binding partner Drg family regulatory proteins (Dfrps) are important for embryonic development, cellular growth control, differentiation, and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog Rbg1/Tma46 facilitates translational initiation, elongation, and termination by suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, deletion of Rbg1 exacerbates the growth defect resulting from translation stalling, and Rbg1 stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoelectron microscopy (cryo-EM) structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of the Tma46 subunit binds to the 40S, establishing an interaction critical for the ribosomal association. Our results answer the fundamental question of how a paused ribosome resumes translation and show that Drg1/Dfrp1 play a critical role in ensuring orderly translation.

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Protein

Chemical

Disease

Primary Citation of related structures
7RR5
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