› 4v3p

Electron Microscopy
34Å resolution

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

Released:
DOI: 10.2210/pdb4v3p/pdb
PDB entry 4v3p coloured by chain, front view.
PDB entry 4v3p coloured by chain, side view.
PDB entry 4v3p coloured by chain, top view.
Source organism: Triticum aestivum
Primary publication:
The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.
Myasnikov AG, Afonina ZA, Ménétret JF, Shirokov VA, Spirin AS, Klaholz BP
Nat Commun 5 5294 (2014)
PMID: 25376914
Related structures: EMD-2790

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 2001-mer (preferred)
PDBe Complex ID:
PDB-CPX-112912 (preferred)
Entry contents:
78 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (84 distinct):
G protein beta subunit Chain: Sa
Molecule details ›
Chain: Sa
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
40S ribosomal protein SA Chain: SA
Molecule details ›
Chain: SA
Length: 260 amino acids
Theoretical weight: 28.72 KDa
Source organism: Triticum aestivum
30S ribosomal protein S3, chloroplastic Chain: SB
Molecule details ›
Chain: SB
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 S4 Chain: SD
Molecule details ›
Chain: SD
Length: 200 amino acids
Theoretical weight: 22.82 KDa
Source organism: Triticum aestivum
40S ribosomal protein S2 Chain: SE
Molecule details ›
Chain: SE
Length: 263 amino acids
Theoretical weight: 28.86 KDa
Source organism: Triticum aestivum
40S ribosomal protein S5 Chain: SF
Molecule details ›
Chain: SF
Length: 191 amino acids
Theoretical weight: 21.25 KDa
Source organism: Triticum aestivum
40S ribosomal protein S16 Chain: SI
Molecule details ›
Chain: SI
Length: 126 amino acids
Theoretical weight: 14.47 KDa
Source organism: Triticum aestivum
40S ribosomal protein S20 Chain: SJ
Molecule details ›
Chain: SJ
Length: 128 amino acids
Theoretical weight: 14.07 KDa
Source organism: Triticum aestivum
40S ribosomal protein S14 Chain: SK
Molecule details ›
Chain: SK
Length: 119 amino acids
Theoretical weight: 12.86 KDa
Source organism: Triticum aestivum
40S ribosomal protein S23 Chain: SL
Molecule details ›
Chain: SL
Length: 142 amino acids
Theoretical weight: 15.7 KDa
Source organism: Triticum aestivum
40S ribosomal protein S18 Chain: SM
Molecule details ›
Chain: SM
Length: 152 amino acids
Theoretical weight: 17.7 KDa
Source organism: Triticum aestivum
40S ribosomal protein S13-1 Chain: SO
Molecule details ›
Chain: SO
Length: 121 amino acids
Theoretical weight: 13.9 KDa
Source organism: Triticum aestivum
40S ribosomal protein S17-4 Chain: SQ
Molecule details ›
Chain: SQ
Length: 141 amino acids
Theoretical weight: 16.46 KDa
Source organism: Triticum aestivum
40S ribosomal protein S11 Chain: SP
Molecule details ›
Chain: SP
Length: 85 amino acids
Theoretical weight: 9.81 KDa
Source organism: Triticum aestivum
40S ribosomal protein S19 Chain: SS
Molecule details ›
Chain: SS
Length: 146 amino acids
Theoretical weight: 16.41 KDa
Source organism: Triticum aestivum
40S ribosomal protein S15 Chain: SR
Molecule details ›
Chain: SR
Length: 91 amino acids
Theoretical weight: 10.15 KDa
Source organism: Triticum aestivum
40S ribosomal protein S25 Chain: SV
Molecule details ›
Chain: SV
Length: 100 amino acids
Theoretical weight: 11.07 KDa
Source organism: Triticum aestivum
40S WHEAT GERM RIBOSOME1 Chain: SW
Molecule details ›
Chain: SW
Length: 92 amino acids
Theoretical weight: 7.85 KDa
Source organism: Triticum aestivum
40S ribosomal protein S28 Chain: SY
Molecule details ›
Chain: SY
Length: 58 amino acids
Theoretical weight: 6.54 KDa
Source organism: Triticum aestivum
40S ribosomal protein S30 Chain: SZ
Molecule details ›
Chain: SZ
Length: 62 amino acids
Theoretical weight: 6.95 KDa
Source organism: Triticum aestivum
Unknown 40S wheat germ ribosome protein 2 Chain: Sc
Molecule details ›
Chain: Sc
Length: 25 amino acids
Theoretical weight: 2.15 KDa
Source organism: Triticum aestivum
Unknown 40S wheat germ ribosome protein 3 Chain: Sb
Molecule details ›
Chain: Sb
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Triticum aestivum
Unknown 40S wheat germ ribosome protein 3 Chain: SU
Molecule details ›
Chain: SU
Length: 98 amino acids
Theoretical weight: 11.26 KDa
Source organism: Triticum aestivum
40S ribosomal protein S27 Chain: SX
Molecule details ›
Chain: SX
Length: 50 amino acids
Theoretical weight: 5.44 KDa
Source organism: Triticum aestivum
40S ribosomal protein S9 Chain: SC
Molecule details ›
Chain: SC
Length: 195 amino acids
Theoretical weight: 22.63 KDa
Source organism: Triticum aestivum
Unknown 40S wheat germ ribosome protein 4 Chain: SG
Molecule details ›
Chain: SG
Length: 143 amino acids
Theoretical weight: 12.19 KDa
Source organism: Triticum aestivum
Ribosomal protein S15 Chain: SH
Molecule details ›
Chain: SH
Length: 130 amino acids
Theoretical weight: 14.83 KDa
Source organism: Triticum aestivum
Small ribosomal subunit protein uS14 Chain: SN
Molecule details ›
Chain: SN
Length: 48 amino acids
Theoretical weight: 5.47 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K3 (Residues: 9-56; Coverage: 86%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
40S ribosomal protein S21 Chain: ST
Molecule details ›
Chain: ST
Length: 82 amino acids
Theoretical weight: 9.27 KDa
Source organism: Triticum aestivum
Ribosomal protein Chain: LA
Molecule details ›
Chain: LA
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: LB
Molecule details ›
Chain: LB
Length: 255 amino acids
Theoretical weight: 27.69 KDa
Source organism: Triticum aestivum
Ribosomal protein L11 Chain: LE
Molecule details ›
Chain: LE
Length: 170 amino acids
Theoretical weight: 19.72 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L2 (Residues: 1-170; Coverage: 94%)
Gene names: CFC21_034625, CFC21_040490, CFC21_046497
Sequence domains:
60S ribosomal protein L9 Chain: LF
Molecule details ›
Chain: LF
Length: 190 amino acids
Theoretical weight: 21.38 KDa
Source organism: Triticum aestivum
60S ribosomal protein L7a Chain: LH
Molecule details ›
Chain: LH
Length: 201 amino acids
Theoretical weight: 22.91 KDa
Source organism: Triticum aestivum
Ribosomal protein L17 Chain: LM
Molecule details ›
Chain: LM
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
Ribosomal protein L15 Chain: LP
Molecule details ›
Chain: LP
Length: 194 amino acids
Theoretical weight: 23.12 KDa
Source organism: Triticum aestivum
60S ribosomal protein L27a-3 Chain: LO
Molecule details ›
Chain: LO
Length: 144 amino acids
Theoretical weight: 15.83 KDa
Source organism: Triticum aestivum
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: LR
Molecule details ›
Chain: LR
Length: 163 amino acids
Theoretical weight: 18.35 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L0 (Residues: 1-163; Coverage: 87%)
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
60S ribosomal protein L5 Chain: LQ
Molecule details ›
Chain: LQ
Length: 304 amino acids
Theoretical weight: 34.72 KDa
Source organism: Triticum aestivum
Ribosomal protein L19 Chain: LT
Molecule details ›
Chain: LT
Length: 189 amino acids
Theoretical weight: 22.48 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7XY20 (Residues: 1-189; Coverage: 90%)
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L21 Chain: LU
Molecule details ›
Chain: LU
Length: 164 amino acids
Theoretical weight: 18.69 KDa
Source organism: Triticum aestivum
60S ribosomal protein L17 Chain: LV
Molecule details ›
Chain: LV
Length: 171 amino acids
Theoretical weight: 19.54 KDa
Source organism: Triticum aestivum
60S ribosomal protein L23a Chain: LX
Molecule details ›
Chain: LX
Length: 122 amino acids
Theoretical weight: 14.05 KDa
Source organism: Triticum aestivum
60S ribosomal protein L24 Chain: LZ
Molecule details ›
Chain: LZ
Length: 75 amino acids
Theoretical weight: 9.05 KDa
Source organism: Triticum aestivum
60S ribosomal protein L26 Chain: LY
Molecule details ›
Chain: LY
Length: 130 amino acids
Theoretical weight: 14.97 KDa
Source organism: Triticum aestivum
60S ribosomal protein l28 Chain: Lb
Molecule details ›
Chain: Lb
Length: 73 amino acids
Theoretical weight: 8.23 KDa
Source organism: Triticum aestivum
60S ribosomal protein L29 Chain: Ld
Molecule details ›
Chain: Ld
Length: 23 amino acids
Theoretical weight: 2.83 KDa
Source organism: Triticum aestivum
Large ribosomal subunit protein eL30 Chain: Lf
Molecule details ›
Chain: Lf
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 L31 Chain: Lg
Molecule details ›
Chain: Lg
Length: 120 amino acids
Theoretical weight: 13.72 KDa
Source organism: Triticum aestivum
Ribosomal L32 Chain: Lh
Molecule details ›
Chain: Lh
Length: 133 amino acids
Theoretical weight: 15.74 KDa
Source organism: Triticum aestivum
Ribosomal protein L37 Chain: Ll
Molecule details ›
Chain: Ll
Length: 94 amino acids
Theoretical weight: 10.82 KDa
Source organism: Triticum aestivum
60S ribosomal protein L38 Chain: Ln
Molecule details ›
Chain: Ln
Length: 69 amino acids
Theoretical weight: 8.05 KDa
Source organism: Triticum aestivum
Ribosomal protein L39 Chain: Lo
Molecule details ›
Chain: Lo
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 L44 Chain: Lr
Molecule details ›
Chain: Lr
Length: 105 amino acids
Theoretical weight: 12.17 KDa
Source organism: Triticum aestivum
Unknown 60S wheat germ ribosome protein 1 Chain: Lq
Molecule details ›
Chain: Lq
Length: 25 amino acids
Theoretical weight: 3.45 KDa
Source organism: Triticum aestivum
Unknown 60S wheat germ ribosome protein 2 Chains: Lx, Ly
Molecule details ›
Chains: Lx, Ly
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: Triticum aestivum
Unknown 60S wheat germ ribosome protein 3 Chain: Lz
Molecule details ›
Chain: Lz
Length: 14 amino acids
Theoretical weight: 1.21 KDa
Source organism: Triticum aestivum
60S ribosomal protein L6 Chain: LG
Molecule details ›
Chain: LG
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
Unknown 60S wheat germ ribosome protein 5 Chain: LL
Molecule details ›
Chain: LL
Length: 182 amino acids
Theoretical weight: 15.51 KDa
Source organism: Triticum aestivum
Unknown 60S wheat germ ribosome protein 6 Chain: LN
Molecule details ›
Chain: LN
Length: 134 amino acids
Theoretical weight: 15.42 KDa
Source organism: Triticum aestivum
60S ribosomal protein L18a Chain: LS
Molecule details ›
Chain: LS
Length: 167 amino acids
Theoretical weight: 20.15 KDa
Source organism: Triticum aestivum
60S ribosomal protein L22 Chain: LW
Molecule details ›
Chain: LW
Length: 108 amino acids
Theoretical weight: 12.3 KDa
Source organism: Triticum aestivum
60S ribosomal protein L27 Chain: La
Molecule details ›
Chain: La
Length: 99 amino acids
Theoretical weight: 11.15 KDa
Source organism: Triticum aestivum
Ribosomal protein l34 Chain: Li
Molecule details ›
Chain: Li
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
ribosomal protein L35A Chain: Lj
Molecule details ›
Chain: Lj
Length: 104 amino acids
Theoretical weight: 11.86 KDa
Source organism: Triticum aestivum
60S ribosomal protein L36 Chain: Lk
Molecule details ›
Chain: Lk
Length: 77 amino acids
Theoretical weight: 8.76 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7L5 (Residues: 36-112; Coverage: 69%)
Gene name: CFC21_064117
Sequence domains: Ribosomal protein L36e
Ubiquitin-60S ribosomal protein L40-1 Chain: Lp
Molecule details ›
Chain: Lp
Length: 41 amino acids
Theoretical weight: 4.97 KDa
Source organism: Triticum aestivum
60S ribosomal protein L12 Chain: LJ
Molecule details ›
Chain: LJ
Length: 128 amino acids
Theoretical weight: 13.75 KDa
Source organism: Triticum aestivum
Ribosomal protein P1 Chains: Lt, Lu
Molecule details ›
Chains: Lt, Lu
Length: 58 amino acids
Theoretical weight: 6.16 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K5 (Residues: 6-63; Coverage: 53%)
Gene names: CFC21_098223, CFC21_103245, CFC21_109590
Sequence domains: 60s Acidic ribosomal protein
60S acidic ribosomal protein P2A Chains: Lv, Lw
Molecule details ›
Chains: Lv, Lw
Length: 59 amino acids
Theoretical weight: 6.36 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5AP46 (Residues: 1-59; Coverage: 52%)
Gene names: CAMPLR22A2D_LOCUS2926, CFC21_017295, CFC21_023699, CFC21_030030
Sequence domains: 60s Acidic ribosomal protein
Large ribosomal subunit protein uL29 Chain: Lc
Molecule details ›
Chain: Lc
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: Le
Molecule details ›
Chain: Le
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: Ls
Molecule details ›
Chain: Ls
Length: 262 amino acids
Theoretical weight: 28.41 KDa
Source organism: Triticum aestivum
Ribosomal protein L3 Chain: LC
Molecule details ›
Chain: LC
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/L1 Chain: LD
Molecule details ›
Chain: LD
Length: 372 amino acids
Theoretical weight: 41.22 KDa
Source organism: Triticum aestivum
Ribosomal protein L13a Chain: LK
Molecule details ›
Chain: LK
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: Lm
Molecule details ›
Chain: Lm
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 L10-1 Chain: LI
Molecule details ›
Chain: LI
Length: 184 amino acids
Theoretical weight: 21.29 KDa
Source organism: Triticum aestivum
40S WHEAT GERM RIBOSOME protein 4 Chain: S3
Molecule details ›
Chain: S3
Length: 11 nucleotides
Theoretical weight: 3.5 KDa
40S ribosomal RNA Chain: S2
Molecule details ›
Chain: S2
Length: 75 nucleotides
Theoretical weight: 24.14 KDa
Sequence domains: tRNA
18S Ribosomal RNA Chain: S1
Molecule details ›
Chain: S1
Length: 1743 nucleotides
Theoretical weight: 562.06 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
26S ribosomal RNA Chain: L1
Molecule details ›
Chain: L1
Length: 3352 nucleotides
Theoretical weight: 1084.82 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: L3
Molecule details ›
Chain: L3
Length: 120 nucleotides
Theoretical weight: 38.72 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: L2
Molecule details ›
Chain: L2
Length: 159 nucleotides
Theoretical weight: 51.27 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 34Å
Relevant EMDB volumes: EMD-2790

Quick links

Citations

7 review citations

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Panas et al. (2016)
6 more

1 mention without citation

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