› 4v7e

Electron Microscopy
5.5Å resolution

Model of the small subunit RNA based on a 5.5 A cryo-EM map of Triticum aestivum translating 80S ribosome

Released:
DOI: 10.2210/pdb4v7e/pdb
PDB 4v7e coloured by chain and viewed from the front.
PDB 4v7e coloured by chain and viewed from the side.
PDB 4v7e coloured by chain and viewed from the top.
Source organism: Triticum aestivum
Primary publication:
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
Gogala M, Becker T, Beatrix B, Armache JP, Barrio-Garcia C, Berninghausen O, Beckmann R
Nature 506 107-10 (2014)
PMID: 24499919
Related structures: EMD-1780

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 88-mer (preferred)
Entry contents:
80 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (86 distinct):
40S ribosomal protein S24E Chain: BY
Molecule details ›
Chain: BY
Length: 138 amino acids
Theoretical weight: 15.79 KDa
Source organism: Triticum aestivum
40S ribosomal protein S8E Chain: BI
Molecule details ›
Chain: BI
Length: 220 amino acids
Theoretical weight: 24.88 KDa
Source organism: Triticum aestivum
40S ribosomal protein S10E Chain: BK
Molecule details ›
Chain: BK
Length: 183 amino acids
Theoretical weight: 20.29 KDa
Source organism: Triticum aestivum
40S ribosomal protein S12E Chain: BM
Molecule details ›
Chain: BM
Length: 171 amino acids
Theoretical weight: 18.4 KDa
Source organism: Triticum aestivum
40S ribosomal protein S31e Chain: Bf
Molecule details ›
Chain: Bf
Length: 155 amino acids
Theoretical weight: 17.72 KDa
Source organism: Triticum aestivum
40S ribosomal protein S12 Chain: BX
Molecule details ›
Chain: BX
Length: 142 amino acids
Theoretical weight: 15.7 KDa
Source organism: Triticum aestivum
WD_REPEATS_REGION domain-containing protein Chain: Bg
Molecule details ›
Chain: Bg
Length: 380 amino acids
Theoretical weight: 41.79 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8LNY6 (Residues: 1-380; Coverage: 100%)
Gene name: TaGB1
Sequence domains: WD domain, G-beta repeat
KH type-2 domain-containing protein Chain: BD
Molecule details ›
Chain: BD
Length: 208 amino acids
Theoretical weight: 23.26 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L804 (Residues: 12-219; Coverage: 92%)
Sequence domains:
40S ribosomal protein S4E Chain: BE
Molecule details ›
Chain: BE
Length: 265 amino acids
Theoretical weight: 29.92 KDa
Source organism: Triticum aestivum
40S ribosomal protein S7 Chain: BF
Molecule details ›
Chain: BF
Length: 191 amino acids
Theoretical weight: 21.25 KDa
Source organism: Triticum aestivum
40S ribosomal protein S9 Chain: BQ
Molecule details ›
Chain: BQ
Length: 149 amino acids
Theoretical weight: 16.85 KDa
Source organism: Triticum aestivum
40S ribosomal protein S10 Chain: BU
Molecule details ›
Chain: BU
Length: 128 amino acids
Theoretical weight: 14.07 KDa
Source organism: Triticum aestivum
40S ribosomal protein S11 Chain: BO
Molecule details ›
Chain: BO
Length: 151 amino acids
Theoretical weight: 16.35 KDa
Source organism: Triticum aestivum
Putative ribosomal protein S18 Chain: BS
Molecule details ›
Chain: BS
Length: 152 amino acids
Theoretical weight: 17.7 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L806 (Residues: 1-152; Coverage: 100%)
Sequence domains: Ribosomal protein S13/S18
40S ribosomal protein S15 Chain: BN
Molecule details ›
Chain: BN
Length: 151 amino acids
Theoretical weight: 17.15 KDa
Source organism: Triticum aestivum
40S ribosomal protein S17 Chain: BL
Molecule details ›
Chain: BL
Length: 160 amino acids
Theoretical weight: 18.03 KDa
Source organism: Triticum aestivum
40S ribosomal protein S19E Chain: BT
Molecule details ›
Chain: BT
Length: 146 amino acids
Theoretical weight: 16.41 KDa
Source organism: Triticum aestivum
40S ribosomal protein S19 Chain: BP
Molecule details ›
Chain: BP
Length: 154 amino acids
Theoretical weight: 17.45 KDa
Source organism: Triticum aestivum
40S ribosomal protein S25E Chain: BZ
Molecule details ›
Chain: BZ
Length: 108 amino acids
Theoretical weight: 11.94 KDa
Source organism: Triticum aestivum
S28 ribosomal protein Chain: Bc
Molecule details ›
Chain: Bc
Length: 65 amino acids
Theoretical weight: 7.48 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7X9K4 (Residues: 22-86; Coverage: 76%)
Sequence domains: Ribosomal protein S28e
40S ribosomal protein S8 Chain: BW
Molecule details ›
Chain: BW
Length: 130 amino acids
Theoretical weight: 14.83 KDa
Source organism: Triticum aestivum
40S ribosomal protein S29 Chain: Bd
Molecule details ›
Chain: Bd
Length: 56 amino acids
Theoretical weight: 6.39 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K3 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
40S ribosomal protein S27E Chain: Bb
Molecule details ›
Chain: Bb
Length: 86 amino acids
Theoretical weight: 9.54 KDa
Source organism: Triticum aestivum
40S ribosomal protein S30E Chain: Be
Molecule details ›
Chain: Be
Length: 62 amino acids
Theoretical weight: 6.95 KDa
Source organism: Triticum aestivum
40S ribosomal protein S2 Chain: BA
Molecule details ›
Chain: BA
Length: 260 amino acids
Theoretical weight: 28.72 KDa
Source organism: Triticum aestivum
40S ribosomal protein S17E Chain: BR
Molecule details ›
Chain: BR
Length: 141 amino acids
Theoretical weight: 16.46 KDa
Source organism: Triticum aestivum
40S ribosomal protein S1E Chain: BB
Molecule details ›
Chain: BB
Length: 262 amino acids
Theoretical weight: 29.78 KDa
Source organism: Triticum aestivum
40S ribosomal protein S21E Chain: BV
Molecule details ›
Chain: BV
Length: 82 amino acids
Theoretical weight: 9.27 KDa
Source organism: Triticum aestivum
40S ribosomal protein S26E Chain: Ba
Molecule details ›
Chain: Ba
Length: 133 amino acids
Theoretical weight: 15.03 KDa
Source organism: Triticum aestivum
40S ribosomal protein S4 Chain: BJ
Molecule details ›
Chain: BJ
Length: 195 amino acids
Theoretical weight: 22.63 KDa
Source organism: Triticum aestivum
40S ribosomal protein S5 Chain: BC
Molecule details ›
Chain: BC
Length: 263 amino acids
Theoretical weight: 28.86 KDa
Source organism: Triticum aestivum
40S ribosomal protein S6 Chain: BG
Molecule details ›
Chain: BG
Length: 245 amino acids
Theoretical weight: 28.11 KDa
Source organism: Triticum aestivum
40S ribosomal protein S7 Chain: BH
Molecule details ›
Chain: BH
Length: 189 amino acids
Theoretical weight: 21.9 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K2 (Residues: 4-192; Coverage: 98%)
Sequence domains: Ribosomal protein S7e
60S ribosomal protein L8E Chain: CG
Molecule details ›
Chain: CG
Length: 257 amino acids
Theoretical weight: 29.24 KDa
Source organism: Triticum aestivum
60S ribosomal protein L21 Chain: CT
Molecule details ›
Chain: CT
Length: 164 amino acids
Theoretical weight: 18.72 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: F4YWL9 (Residues: 1-164; Coverage: 100%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L27E Chain: CZ
Molecule details ›
Chain: CZ
Length: 136 amino acids
Theoretical weight: 15.51 KDa
Source organism: Triticum aestivum
Ribosomal protein Chain: Cz
Molecule details ›
Chain: Cz
Length: 216 amino acids
Theoretical weight: 24.6 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L3 (Residues: 1-216; Coverage: 100%)
Sequence domains: Ribosomal protein L1p/L10e family
60S ribosomal protein L2 Chain: CA
Molecule details ›
Chain: CA
Length: 261 amino acids
Theoretical weight: 28.31 KDa
Source organism: Triticum aestivum
Ribosomal protein L11 Chain: CJ
Molecule details ›
Chain: CJ
Length: 180 amino acids
Theoretical weight: 20.73 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L2 (Residues: 1-180; Coverage: 100%)
Sequence domains:
60S ribosomal protein L6 Chain: CH
Molecule details ›
Chain: CH
Length: 190 amino acids
Theoretical weight: 21.38 KDa
Source organism: Triticum aestivum
Ribosomal protein L17 Chain: CV
Molecule details ›
Chain: CV
Length: 140 amino acids
Theoretical weight: 15.04 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K4 (Residues: 1-140; Coverage: 100%)
Sequence domains: Ribosomal protein L14p/L23e
60S ribosomal protein L15E Chain: CN
Molecule details ›
Chain: CN
Length: 200 amino acids
Theoretical weight: 23.76 KDa
Source organism: Triticum aestivum
60S ribosomal protein L15 Chain: Ca
Molecule details ›
Chain: Ca
Length: 144 amino acids
Theoretical weight: 15.83 KDa
Source organism: Triticum aestivum
Ribosomal_L18e/L15P domain-containing protein Chain: CQ
Molecule details ›
Chain: CQ
Length: 188 amino acids
Theoretical weight: 21.38 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L0 (Residues: 1-188; Coverage: 100%)
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
60S ribosomal protein L18 Chain: CD
Molecule details ›
Chain: CD
Length: 304 amino acids
Theoretical weight: 34.72 KDa
Source organism: Triticum aestivum
Ribosomal protein L19 Chain: CR
Molecule details ›
Chain: CR
Length: 209 amino acids
Theoretical weight: 24.49 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7XY20 (Residues: 1-209; Coverage: 100%)
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L22 Chain: CP
Molecule details ›
Chain: CP
Length: 171 amino acids
Theoretical weight: 19.54 KDa
Source organism: Triticum aestivum
60S ribosomal protein L23 Chain: CX
Molecule details ›
Chain: CX
Length: 152 amino acids
Theoretical weight: 17.09 KDa
Source organism: Triticum aestivum
60S ribosomal protein L24E Chain: CW
Molecule details ›
Chain: CW
Length: 162 amino acids
Theoretical weight: 18.5 KDa
Source organism: Triticum aestivum
60S ribosomal protein L24 Chain: CY
Molecule details ›
Chain: CY
Length: 150 amino acids
Theoretical weight: 16.97 KDa
Source organism: Triticum aestivum
60S ribosomal protein L28E Chain: Cr
Molecule details ›
Chain: Cr
Length: 147 amino acids
Theoretical weight: 16.64 KDa
Source organism: Triticum aestivum
60S ribosomal protein L30 Chain: Cc
Molecule details ›
Chain: Cc
Length: 112 amino acids
Theoretical weight: 12.29 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K9 (Residues: 1-112; Coverage: 100%)
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L31E Chain: Cd
Molecule details ›
Chain: Cd
Length: 123 amino acids
Theoretical weight: 14.09 KDa
Source organism: Triticum aestivum
60S ribosomal protein L32E Chain: Ce
Molecule details ›
Chain: Ce
Length: 133 amino acids
Theoretical weight: 15.74 KDa
Source organism: Triticum aestivum
60S ribosomal protein L37E Chain: Cj
Molecule details ›
Chain: Cj
Length: 94 amino acids
Theoretical weight: 10.82 KDa
Source organism: Triticum aestivum
Ribosomal protein L39 Chain: Cl
Molecule details ›
Chain: Cl
Length: 51 amino acids
Theoretical weight: 6.53 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K7 (Residues: 1-51; Coverage: 100%)
Sequence domains: Ribosomal L39 protein
60S ribosomal protein L44E Chain: Co
Molecule details ›
Chain: Co
Length: 105 amino acids
Theoretical weight: 12.17 KDa
Source organism: Triticum aestivum
60S ribosomal protein L14E Chain: CM
Molecule details ›
Chain: CM
Length: 134 amino acids
Theoretical weight: 15.42 KDa
Source organism: Triticum aestivum
60S ribosomal protein L20 Chain: CS
Molecule details ›
Chain: CS
Length: 178 amino acids
Theoretical weight: 21.44 KDa
Source organism: Triticum aestivum
60S ribosomal protein L22E Chain: CU
Molecule details ›
Chain: CU
Length: 130 amino acids
Theoretical weight: 14.44 KDa
Source organism: Triticum aestivum
60S ribosomal protein L36 Chain: Ci
Molecule details ›
Chain: Ci
Length: 112 amino acids
Theoretical weight: 12.56 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L5 (Residues: 1-112; Coverage: 100%)
Sequence domains: Ribosomal protein L36e
60S ribosomal protein L11 Chain: CK
Molecule details ›
Chain: CK
Length: 166 amino acids
Theoretical weight: 17.78 KDa
Source organism: Triticum aestivum
Ribosomal protein P1 Chains: Cu, Cv
Molecule details ›
Chains: Cu, Cv
Length: 110 amino acids
Theoretical weight: 11.2 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K5 (Residues: 1-110; Coverage: 100%)
Sequence domains: 60s Acidic ribosomal protein
Acidic ribosomal protein P2 Chains: Cs, Ct
Molecule details ›
Chains: Cs, Ct
Length: 113 amino acids
Theoretical weight: 11.6 KDa
Source organism: Triticum aestivum
60S ribosomal protein L35 Chain: Ch
Molecule details ›
Chain: Ch
Length: 124 amino acids
Theoretical weight: 14.4 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L805 (Residues: 1-124; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Ribosomal protein L7 Chain: CF
Molecule details ›
Chain: CF
Length: 244 amino acids
Theoretical weight: 28.18 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K6 (Residues: 1-244; Coverage: 100%)
Sequence domains:
60S acidic ribosomal protein P0 Chain: Cq
Molecule details ›
Chain: Cq
Length: 319 amino acids
Theoretical weight: 34.42 KDa
Source organism: Triticum aestivum
Ribosomal protein L3-A1 Chain: CB
Molecule details ›
Chain: CB
Length: 389 amino acids
Theoretical weight: 44.72 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7X744 (Residues: 1-389; Coverage: 100%)
Gene names: RPL3, RPL3-A1, RPL3A-1
Sequence domains: Ribosomal protein L3
60S ribosomal protein L4 Chain: CC
Molecule details ›
Chain: CC
Length: 405 amino acids
Theoretical weight: 44.82 KDa
Source organism: Triticum aestivum
Ribosomal protein L13a Chain: CO
Molecule details ›
Chain: CO
Length: 206 amino acids
Theoretical weight: 23.58 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L1 (Residues: 1-206; Coverage: 100%)
Sequence domains: Ribosomal protein L13
60S ribosomal protein L37a, expressed Chain: Cp
Molecule details ›
Chain: Cp
Length: 92 amino acids
Theoretical weight: 10.27 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: D8L9P6 (Residues: 1-92; Coverage: 100%)
Gene names: TAA_ctg0616b.00240.1, TRAES_3BF073800030CFD_c1
Sequence domains: Ribosomal L37ae protein family
60S ribosomal protein L16 Chain: CI
Molecule details ›
Chain: CI
Length: 224 amino acids
Theoretical weight: 25.4 KDa
Source organism: Triticum aestivum
60S ribosomal protein L41E Chain: Cn
Molecule details ›
Chain: Cn
Length: 25 amino acids
Theoretical weight: 3.45 KDa
Source organism: Triticum aestivum
60S ribosomal protein L40E Chain: Cm
Molecule details ›
Chain: Cm
Length: 53 amino acids
Theoretical weight: 6.3 KDa
Source organism: Triticum aestivum
60S ribosomal protein L13E Chain: CL
Molecule details ›
Chain: CL
Length: 208 amino acids
Theoretical weight: 24.07 KDa
Source organism: Triticum aestivum
60S ribosomal protein L6 Chain: CE
Molecule details ›
Chain: CE
Length: 219 amino acids
Theoretical weight: 24.59 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L4 (Residues: 1-219; Coverage: 100%)
Sequence domains: Ribosomal protein L6e
60S ribosomal protein L33E Chain: Cf
Molecule details ›
Chain: Cf
Length: 111 amino acids
Theoretical weight: 12.68 KDa
Source organism: Triticum aestivum
60S ribosomal protein L38E Chain: Ck
Molecule details ›
Chain: Ck
Length: 69 amino acids
Theoretical weight: 8.05 KDa
Source organism: Triticum aestivum
60S ribosomal protein L29E Chain: Cb
Molecule details ›
Chain: Cb
Length: 60 amino acids
Theoretical weight: 7.07 KDa
Source organism: Triticum aestivum
Ribosomal protein l34 Chain: Cg
Molecule details ›
Chain: Cg
Length: 119 amino acids
Theoretical weight: 13.81 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K8 (Residues: 1-119; Coverage: 100%)
Sequence domains: Ribosomal protein L34e
18S Ribosomal RNA Chain: Ad
Molecule details ›
Chain: Ad
Length: 1810 nucleotides
Theoretical weight: 583.61 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
P-site tRNA Chain: Ae
Molecule details ›
Chain: Ae
Length: 75 nucleotides
Theoretical weight: 24.14 KDa
Sequence domains: tRNA
5'-R(*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3' Chain: Af
Molecule details ›
Chain: Af
Length: 11 nucleotides
Theoretical weight: 3.5 KDa
60S ribosomal RNA Chain: Aa
Molecule details ›
Chain: Aa
Length: 3391 nucleotides
Theoretical weight: 1097.29 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: Ac
Molecule details ›
Chain: Ac
Length: 160 nucleotides
Theoretical weight: 51.54 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chain: Ab
Molecule details ›
Chain: Ab
Length: 120 nucleotides
Theoretical weight: 38.72 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.5Å
Relevant EMDB volumes: EMD-1780

Quick links

Citations

26 review citations

Redox signaling and unfolded protein response coordinate cell fate decisions under ER stress.
Zhang et al. (2019)
25 more

1 mention without citation

Modelling the three-dimensional structure of the right-terminal domain of pospiviroids.
Steger G. (2017)