› 7nrc

Electron Microscopy
3.9Å resolution

Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A

Released:
DOI: 10.2210/pdb7nrc/pdb
PDB entry 7nrc coloured by chain, front view.
PDB entry 7nrc coloured by chain, side view.
PDB entry 7nrc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of Gcn1 bound to stalled and colliding 80S ribosomes.
Pochopien AA, Beckert B, Kasvandik S, Berninghausen O, Beckmann R, Tenson T, Wilson DN
OpenAccess logo Proc Natl Acad Sci U S A 118 (2021)
PMID: 33790014
Related structures: EMD-12534

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 86-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126836 (preferred)
Entry contents:
79 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (86 distinct):
Small ribosomal subunit protein uS2A Chain: SP
Molecule details ›
Chain: SP
Length: 206 amino acids
Theoretical weight: 22.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS1A Chain: SQ
Molecule details ›
Chain: SQ
Length: 232 amino acids
Theoretical weight: 26.31 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS19 Chain: SE
Molecule details ›
Chain: SE
Length: 117 amino acids
Theoretical weight: 13.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS5 Chain: SR
Molecule details ›
Chain: SR
Length: 216 amino acids
Theoretical weight: 23.08 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS3 Chain: SA
Molecule details ›
Chain: SA
Length: 222 amino acids
Theoretical weight: 24.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS4A Chain: SS
Molecule details ›
Chain: SS
Length: 258 amino acids
Theoretical weight: 29.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS7 Chain: SB
Molecule details ›
Chain: SB
Length: 206 amino acids
Theoretical weight: 22.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS6A Chain: ST
Molecule details ›
Chain: ST
Length: 228 amino acids
Theoretical weight: 26.18 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS7A Chain: SU
Molecule details ›
Chain: SU
Length: 184 amino acids
Theoretical weight: 21 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS8A Chain: SV
Molecule details ›
Chain: SV
Length: 198 amino acids
Theoretical weight: 22.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS4A Chain: SW
Molecule details ›
Chain: SW
Length: 184 amino acids
Theoretical weight: 21.08 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS10A Chain: SC
Molecule details ›
Chain: SC
Length: 92 amino acids
Theoretical weight: 11.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS17A Chain: SX
Molecule details ›
Chain: SX
Length: 142 amino acids
Theoretical weight: 16.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS12 Chain: SD
Molecule details ›
Chain: SD
Length: 121 amino acids
Theoretical weight: 13.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS15 Chain: SY
Molecule details ›
Chain: SY
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS11B Chain: SZ
Molecule details ›
Chain: SZ
Length: 127 amino acids
Theoretical weight: 13.45 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS9A Chain: SF
Molecule details ›
Chain: SF
Length: 141 amino acids
Theoretical weight: 15.66 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS17B Chain: SG
Molecule details ›
Chain: SG
Length: 125 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS13A Chain: SH
Molecule details ›
Chain: SH
Length: 145 amino acids
Theoretical weight: 16.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS19A Chain: SI
Molecule details ›
Chain: SI
Length: 143 amino acids
Theoretical weight: 15.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS10 Chain: SJ
Molecule details ›
Chain: SJ
Length: 100 amino acids
Theoretical weight: 11.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS21A Chain: Sa
Molecule details ›
Chain: Sa
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS8A Chain: Sb
Molecule details ›
Chain: Sb
Length: 129 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS12A Chain: Sc
Molecule details ›
Chain: Sc
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS24A Chain: Sd
Molecule details ›
Chain: Sd
Length: 134 amino acids
Theoretical weight: 15.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS25A Chain: SK
Molecule details ›
Chain: SK
Length: 82 amino acids
Theoretical weight: 9.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS26B Chain: Se
Molecule details ›
Chain: Se
Length: 97 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS27A Chain: Sf
Molecule details ›
Chain: Sf
Length: 81 amino acids
Theoretical weight: 8.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS14A Chain: SM
Molecule details ›
Chain: SM
Length: 53 amino acids
Theoretical weight: 6.34 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS30A Chain: Sg
Molecule details ›
Chain: Sg
Length: 57 amino acids
Theoretical weight: 6.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS31 Chain: SN
Molecule details ›
Chain: SN
Length: 73 amino acids
Theoretical weight: 8.33 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein RACK1 Chain: SO
Molecule details ›
Chain: SO
Length: 312 amino acids
Theoretical weight: 34.15 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS28A Chain: SL
Molecule details ›
Chain: SL
Length: 63 amino acids
Theoretical weight: 7.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Ribosome-interacting GTPase 2 Chain: So
Molecule details ›
Chain: So
Length: 366 amino acids
Theoretical weight: 40.54 KDa
Source organism: Saccharomyces cerevisiae S288C
GIR2 Chain: Sp
Molecule details ›
Chain: Sp
Length: 48 amino acids
Theoretical weight: 4.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL2A Chain: LD
Molecule details ›
Chain: LD
Length: 251 amino acids
Theoretical weight: 27.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL3 Chain: LE
Molecule details ›
Chain: LE
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL4A Chain: LF
Molecule details ›
Chain: LF
Length: 361 amino acids
Theoretical weight: 39.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL18 Chain: LG
Molecule details ›
Chain: LG
Length: 294 amino acids
Theoretical weight: 33.42 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL6B Chain: LH
Molecule details ›
Chain: LH
Length: 175 amino acids
Theoretical weight: 19.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL30A Chain: LI
Molecule details ›
Chain: LI
Length: 222 amino acids
Theoretical weight: 25.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL8A Chain: LJ
Molecule details ›
Chain: LJ
Length: 233 amino acids
Theoretical weight: 25.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL6A Chain: LK
Molecule details ›
Chain: LK
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL16 Chain: LL
Molecule details ›
Chain: LL
Length: 218 amino acids
Theoretical weight: 25.08 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL5B Chain: LM
Molecule details ›
Chain: LM
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL13A Chain: LN
Molecule details ›
Chain: LN
Length: 193 amino acids
Theoretical weight: 21.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL14A Chain: LO
Molecule details ›
Chain: LO
Length: 136 amino acids
Theoretical weight: 14.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL15A Chain: LP
Molecule details ›
Chain: LP
Length: 203 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL13A Chain: LQ
Molecule details ›
Chain: LQ
Length: 197 amino acids
Theoretical weight: 22.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL22A Chain: LR
Molecule details ›
Chain: LR
Length: 183 amino acids
Theoretical weight: 20.46 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL18A Chain: LS
Molecule details ›
Chain: LS
Length: 185 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL19A Chain: LT
Molecule details ›
Chain: LT
Length: 188 amino acids
Theoretical weight: 21.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL20A Chain: LU
Molecule details ›
Chain: LU
Length: 171 amino acids
Theoretical weight: 20.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL21A Chain: LV
Molecule details ›
Chain: LV
Length: 159 amino acids
Theoretical weight: 18.15 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL22A Chain: LW
Molecule details ›
Chain: LW
Length: 100 amino acids
Theoretical weight: 11.26 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL14A Chain: LX
Molecule details ›
Chain: LX
Length: 136 amino acids
Theoretical weight: 14.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL24A Chain: LY
Molecule details ›
Chain: LY
Length: 65 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL23 Chain: LZ
Molecule details ›
Chain: LZ
Length: 121 amino acids
Theoretical weight: 13.77 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL24A Chain: La
Molecule details ›
Chain: La
Length: 125 amino acids
Theoretical weight: 14.01 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL27A Chain: Lb
Molecule details ›
Chain: Lb
Length: 135 amino acids
Theoretical weight: 15.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL15 Chain: Lc
Molecule details ›
Chain: Lc
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL29 Chain: Ld
Molecule details ›
Chain: Ld
Length: 58 amino acids
Theoretical weight: 6.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL30 Chain: Le
Molecule details ›
Chain: Le
Length: 96 amino acids
Theoretical weight: 10.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL31A Chain: Lf
Molecule details ›
Chain: Lf
Length: 109 amino acids
Theoretical weight: 12.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL32 Chain: Lg
Molecule details ›
Chain: Lg
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL33A Chain: Lh
Molecule details ›
Chain: Lh
Length: 106 amino acids
Theoretical weight: 12.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL34A Chain: Li
Molecule details ›
Chain: Li
Length: 112 amino acids
Theoretical weight: 12.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein uL29A Chain: Lj
Molecule details ›
Chain: Lj
Length: 119 amino acids
Theoretical weight: 13.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL36A Chain: Lk
Molecule details ›
Chain: Lk
Length: 99 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL37A Chain: Ll
Molecule details ›
Chain: Ll
Length: 81 amino acids
Theoretical weight: 9.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL38 Chain: Lm
Molecule details ›
Chain: Lm
Length: 77 amino acids
Theoretical weight: 8.71 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL39 Chain: Ln
Molecule details ›
Chain: Ln
Length: 50 amino acids
Theoretical weight: 6.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL40A Chain: Lo
Molecule details ›
Chain: Lo
Length: 52 amino acids
Theoretical weight: 6.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS32A Chain: Lp
Molecule details ›
Chain: Lp
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL42A Chain: Lq
Molecule details ›
Chain: Lq
Length: 103 amino acids
Theoretical weight: 11.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Large ribosomal subunit protein eL43A Chain: Lr
Molecule details ›
Chain: Lr
Length: 91 amino acids
Theoretical weight: 9.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Eukaryotic translation initiation factor 5A-1 Chain: Ls
Molecule details ›
Chain: Ls
Length: 154 amino acids
Theoretical weight: 16.89 KDa
Source organism: Saccharomyces cerevisiae S288C
L1 60S ribosomal protein Chain: Lt
Molecule details ›
Chain: Lt
Length: 210 amino acids
Theoretical weight: 17.89 KDa
Source organism: Saccharomyces cerevisiae S288C
GCN1 Chain: A
Molecule details ›
Chain: A
Length: 1209 amino acids
Theoretical weight: 98.13 KDa
Source organism: Saccharomyces cerevisiae S288C
18S rRNA (1771-MER) Chain: S2
Molecule details ›
Chain: S2
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: Eukaryotic small subunit ribosomal RNA
RNA (5'-R(P*AP*UP*GP*AP*AP*A)-3') Chain: Sl
Molecule details ›
Chain: Sl
Length: 6 nucleotides
Theoretical weight: 1.92 KDa
Source organism: Saccharomyces cerevisiae S288C
tRNA (76-MER) Chain: Sm
Molecule details ›
Chain: Sm
Length: 76 nucleotides
Theoretical weight: 24.38 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: tRNA
tRNA (75-MER) Chain: Sn
Molecule details ›
Chain: Sn
Length: 75 nucleotides
Theoretical weight: 24.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: tRNA
25S rRNA (3184-MER) Chain: LA
Molecule details ›
Chain: LA
Length: 3394 nucleotides
Theoretical weight: 1096.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S rRNA (121-MER) Chain: LB
Molecule details ›
Chain: LB
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: 5S ribosomal RNA
5.8S rRNA (158-MER) Chain: LC
Molecule details ›
Chain: LC
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CT 1 x 5CT

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-12534

Quick links

Citations

12 review citations

Detecting and Rescuing Stalled Ribosomes.
Yip et al. (2021)
11 more

2 mentions without citation

An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes.
Oltion et al. (2023)
1 more