› 4v5z

Electron Microscopy
8.7Å resolution

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

Released:
DOI: 10.2210/pdb4v5z/pdb
PDB entry 4v5z coloured by chain, front view.
PDB entry 4v5z coloured by chain, side view.
PDB entry 4v5z coloured by chain, top view.
Source organism: Canis lupus familiaris
Primary publication:
Structure of the mammalian 80S ribosome at 8.7 A resolution.
Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW
Structure 16 535-48 (2008)
PMID: 18400176
Related structures: EMD-1480

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 86-mer (preferred)
PDBe Complex ID:
PDB-CPX-216009 (preferred)
Entry contents:
50 distinct polypeptide molecules
36 distinct RNA molecules
Macromolecules (86 distinct):
40S Ribosomal protein RACK1 Chain: Aa
Molecule details ›
Chain: Aa
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein SA Chain: Ab
Molecule details ›
Chain: Ab
Length: 295 amino acids
Theoretical weight: 32.91 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S3e Chain: Ac
Molecule details ›
Chain: Ac
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S9e Chain: Ad
Molecule details ›
Chain: Ad
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S2e Chain: Ae
Molecule details ›
Chain: Ae
Length: 179 amino acids
Theoretical weight: 19.4 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S5e Chain: Ag
Molecule details ›
Chain: Ag
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S15ae Chain: Ah
Molecule details ›
Chain: Ah
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S16e Chain: Ai
Molecule details ›
Chain: Ai
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S20e Chain: Aj
Molecule details ›
Chain: Aj
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S14e Chain: Ak
Molecule details ›
Chain: Ak
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S23e Chain: Al
Molecule details ›
Chain: Al
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S18e Chain: Am
Molecule details ›
Chain: Am
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S29e Chain: An
Molecule details ›
Chain: An
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S13e Chain: Ao
Molecule details ›
Chain: Ao
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S11e Chain: Aq
Molecule details ›
Chain: Aq
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Canis lupus familiaris
40S Ribosomal protein S15e Chain: As
Molecule details ›
Chain: As
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L8 Chain: Ba
Molecule details ›
Chain: Ba
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L3 Chain: Bb
Molecule details ›
Chain: Bb
Length: 403 amino acids
Theoretical weight: 46.13 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L4 Chain: Bc
Molecule details ›
Chain: Bc
Length: 421 amino acids
Theoretical weight: 47.63 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L11 Chain: Bd
Molecule details ›
Chain: Bd
Length: 178 amino acids
Theoretical weight: 20.29 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L9 Chain: Be
Molecule details ›
Chain: Be
Length: 192 amino acids
Theoretical weight: 21.9 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L7a Chain: Bf
Molecule details ›
Chain: Bf
Length: 266 amino acids
Theoretical weight: 30.04 KDa
Source organism: Canis lupus familiaris
60S acidic ribosomal protein P0 Chain: Bg
Molecule details ›
Chain: Bg
Length: 317 amino acids
Theoretical weight: 34.31 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L10 Chain: Bh
Molecule details ›
Chain: Bh
Length: 214 amino acids
Theoretical weight: 24.63 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L12 Chain: Bi
Molecule details ›
Chain: Bi
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Canis lupus familiaris
60S ribosomal protein L13a Chain: Bj
Molecule details ›
Chain: Bj
Length: 203 amino acids
Theoretical weight: 23.6 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L23 Chain: Bk
Molecule details ›
Chain: Bk
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L27a Chain: Bl
Molecule details ›
Chain: Bl
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L15e Chain: Bm
Molecule details ›
Chain: Bm
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L5 Chain: Bn
Molecule details ›
Chain: Bn
Length: 297 amino acids
Theoretical weight: 34.51 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L18 Chain: Bo
Molecule details ›
Chain: Bo
Length: 188 amino acids
Theoretical weight: 21.7 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L19 Chain: Bp
Molecule details ›
Chain: Bp
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L19 Chain: B7
Molecule details ›
Chain: B7
Length: 13 amino acids
Theoretical weight: 1.87 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L21 Chain: Bq
Molecule details ›
Chain: Bq
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L17 Chain: Br
Molecule details ›
Chain: Br
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L23a Chain: Bs
Molecule details ›
Chain: Bs
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L26 Chain: Bt
Molecule details ›
Chain: Bt
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L24 Chain: Bu
Molecule details ›
Chain: Bu
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L35 Chain: Bv
Molecule details ›
Chain: Bv
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L35 Chain: B8
Molecule details ›
Chain: B8
Length: 10 amino acids
Theoretical weight: 1.12 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L7 Chain: Bw
Molecule details ›
Chain: Bw
Length: 270 amino acids
Theoretical weight: 31.49 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L31 Chain: Bx
Molecule details ›
Chain: Bx
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L32 Chain: By
Molecule details ›
Chain: By
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L32 Chain: B9
Molecule details ›
Chain: B9
Length: 58 amino acids
Theoretical weight: 6.59 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L37a Chain: Bz
Molecule details ›
Chain: Bz
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L37e Chain: B2
Molecule details ›
Chain: B2
Length: 97 amino acids
Theoretical weight: 11.11 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L39e Chain: B3
Molecule details ›
Chain: B3
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L44e Chain: B4
Molecule details ›
Chain: B4
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L10a Chain: B5
Molecule details ›
Chain: B5
Length: 212 amino acids
Theoretical weight: 23.38 KDa
Source organism: Canis lupus familiaris
60S Ribosomal protein L30e Chain: B6
Molecule details ›
Chain: B6
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Canis lupus familiaris
18S Ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1563 nucleotides
Theoretical weight: 504.28 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
RNA Expansion segment ES3 Chain: AB
Molecule details ›
Chain: AB
Length: 35 nucleotides
Theoretical weight: 11.18 KDa
RNA Expansion segment ES4 Chain: AC
Molecule details ›
Chain: AC
Length: 32 nucleotides
Theoretical weight: 10.2 KDa
RNA Expansion segment ES6 part I Chain: AD
Molecule details ›
Chain: AD
Length: 42 nucleotides
Theoretical weight: 13.48 KDa
RNA Expansion segment ES6 part II Chain: AE
Molecule details ›
Chain: AE
Length: 32 nucleotides
Theoretical weight: 10.26 KDa
RNA Expansion segment ES9 Chain: AF
Molecule details ›
Chain: AF
Length: 31 nucleotides
Theoretical weight: 9.92 KDa
RNA helix Chain: AG
Molecule details ›
Chain: AG
Length: 14 nucleotides
Theoretical weight: 4.54 KDa
RNA helix Chain: AH
Molecule details ›
Chain: AH
Length: 41 nucleotides
Theoretical weight: 13.34 KDa
5.8S ribosomal RNA Chain: B1
Molecule details ›
Chain: B1
Length: 123 nucleotides
Theoretical weight: 39.56 KDa
Sequence domains: 5.8S ribosomal RNA
28S ribosomal RNA Chain: B0
Molecule details ›
Chain: B0
Length: 2903 nucleotides
Theoretical weight: 940.21 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
RNA Expansion segment ES3 Chain: BA
Molecule details ›
Chain: BA
Length: 21 nucleotides
Theoretical weight: 6.69 KDa
RNA Expansion segment ES4 Chain: BB
Molecule details ›
Chain: BB
Length: 27 nucleotides
Theoretical weight: 8.62 KDa
RNA Expansion segment ES5 Chain: BC
Molecule details ›
Chain: BC
Length: 17 nucleotides
Theoretical weight: 5.5 KDa
RNA Expansion segment ES7 part I Chain: BD
Molecule details ›
Chain: BD
Length: 16 nucleotides
Theoretical weight: 5.14 KDa
RNA Expansion segment ES7 part II Chain: BE
Molecule details ›
Chain: BE
Length: 54 nucleotides
Theoretical weight: 17.44 KDa
RNA Expansion segment ES7 part III Chain: BF
Molecule details ›
Chain: BF
Length: 120 nucleotides
Theoretical weight: 38.84 KDa
RNA Expansion segment ES9 Chain: BG
Molecule details ›
Chain: BG
Length: 48 nucleotides
Theoretical weight: 15.52 KDa
RNA Expansion segment ES12 Chain: BH
Molecule details ›
Chain: BH
Length: 25 nucleotides
Theoretical weight: 8.09 KDa
RNA Expansion segment ES15 part I Chain: BI
Molecule details ›
Chain: BI
Length: 72 nucleotides
Theoretical weight: 23.29 KDa
RNA Expansion segment ES15 part II Chain: BJ
Molecule details ›
Chain: BJ
Length: 30 nucleotides
Theoretical weight: 9.64 KDa
RNA Expansion segment ES19 Chain: BK
Molecule details ›
Chain: BK
Length: 26 nucleotides
Theoretical weight: 8.3 KDa
RNA Expansion segment ES20 Chain: BL
Molecule details ›
Chain: BL
Length: 20 nucleotides
Theoretical weight: 6.47 KDa
RNA Expansion segment ES24 Chain: BM
Molecule details ›
Chain: BM
Length: 19 nucleotides
Theoretical weight: 6.07 KDa
RNA Expansion segment ES27 Chain: BN
Molecule details ›
Chain: BN
Length: 78 nucleotides
Theoretical weight: 25.06 KDa
RNA Expansion segment ES30 Chain: BO
Molecule details ›
Chain: BO
Length: 20 nucleotides
Theoretical weight: 6.41 KDa
RNA Expansion segment ES31 part I Chain: BP
Molecule details ›
Chain: BP
Length: 15 nucleotides
Theoretical weight: 4.86 KDa
RNA Expansion segment ES31 part II Chain: BQ
Molecule details ›
Chain: BQ
Length: 30 nucleotides
Theoretical weight: 9.67 KDa
RNA Expansion segment ES39 part I Chain: BR
Molecule details ›
Chain: BR
Length: 30 nucleotides
Theoretical weight: 9.62 KDa
RNA Expansion segment ES39 part II Chain: BS
Molecule details ›
Chain: BS
Length: 38 nucleotides
Theoretical weight: 12.22 KDa
RNA Expansion segment ES39 part III Chain: BT
Molecule details ›
Chain: BT
Length: 30 nucleotides
Theoretical weight: 9.64 KDa
RNA Expansion segment ES41 Chain: BU
Molecule details ›
Chain: BU
Length: 16 nucleotides
Theoretical weight: 5.03 KDa
RNA Expansion segment ES9 part2 Chain: BV
Molecule details ›
Chain: BV
Length: 22 nucleotides
Theoretical weight: 7.06 KDa
RNA Expansion segment ES10 Chain: BW
Molecule details ›
Chain: BW
Length: 16 nucleotides
Theoretical weight: 5.13 KDa
RNA helices Chain: BX
Molecule details ›
Chain: BX
Length: 113 nucleotides
Theoretical weight: 36.43 KDa
5S ribosomal RNA Chain: BY
Molecule details ›
Chain: BY
Length: 115 nucleotides
Theoretical weight: 37.08 KDa
Sequence domains: 5S ribosomal RNA
E site t-RNA Chain: BZ
Molecule details ›
Chain: BZ
Length: 72 nucleotides
Theoretical weight: 23.18 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.7Å
Relevant EMDB volumes: EMD-1480

Quick links

Citations

28 review citations

One core, two shells: bacterial and eukaryotic ribosomes.
Melnikov et al. (2012)
27 more

1 mention without citation

Through scaffold modification to 3,5-diaryl-4,5-dihydroisoxazoles: new potent and selective inhibitors of monoamine oxidase B.
Meleddu et al. (2017)