› 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 entry 4v7e coloured by chain, front view.
PDB entry 4v7e coloured by chain, side view.
PDB entry 4v7e coloured by chain, top view.
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)
PDBe Complex ID:
PDB-CPX-112911 (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
G protein beta subunit 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
30S ribosomal protein S3, chloroplastic 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%)
Gene names: CFC21_068138, CFC21_073936, CFC21_099813
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
Small ribosomal subunit protein uS14 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%)
Gene names: CFC21_051939, CFC21_057885
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 names: CFC21_068953, 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%)
Gene names: CFC21_097817, CFC21_102793, CFC21_109210
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%)
Gene names: CFC21_034625, CFC21_040490, CFC21_046497
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%)
Gene names: CFC21_006360, CFC21_011199, CFC21_085267, CFC21_090119
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
Large ribosomal subunit protein uL15/eL18 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
Large ribosomal subunit protein eL30 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%)
Gene names: CFC21_061075, CFC21_071752, CFC21_085024, CFC21_089802, CFC21_094271, CFC21_096449
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%)
Gene name: CFC21_064117
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%)
Gene names: CFC21_098223, CFC21_103245, CFC21_109590
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
Large ribosomal subunit protein uL29 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 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: CFC21_076746, 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: CFC21_098386, CFC21_109870, 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

42 review citations

Protein export through the bacterial Sec pathway.
Tsirigotaki et al. (2017)
41 more

10 mentions without citation

The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications.
Ramakrishnan et al. (2022)
9 more