› 5uyp

Electron Microscopy
3.9Å resolution

70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc)

Released:
DOI: 10.2210/pdb5uyp/pdb
PDB entry 5uyp coloured by chain, front view.
PDB entry 5uyp coloured by chain, side view.
PDB entry 5uyp coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Ensemble cryo-EM elucidates the mechanism of translation fidelity.
Loveland AB, Demo G, Grigorieff N, Korostelev AA
Nature 546 113-117 (2017)
PMID: 28538735
Related structures: EMD-8619

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 60-mer (preferred)
PDBe Complex ID:
PDB-CPX-135516 (preferred)
Entry contents:
53 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (59 distinct):
Large ribosomal subunit protein uL2 Chain: 04
Molecule details ›
Chain: 04
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: 05
Molecule details ›
Chain: 05
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: 06
Molecule details ›
Chain: 06
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: 07
Molecule details ›
Chain: 07
Length: 177 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P62399 (Residues: 2-178; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: 08
Molecule details ›
Chain: 08
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG55 (Residues: 2-177; Coverage: 99%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: 09
Molecule details ›
Chain: 09
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chain: 10
Molecule details ›
Chain: 10
Length: 131 amino acids
Theoretical weight: 14.11 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J3 (Residues: 1-131; Coverage: 79%)
Gene names: JW3948, b3985, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: 11
Molecule details ›
Chain: 11
Length: 141 amino acids
Theoretical weight: 14.76 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J7 (Residues: 2-142; Coverage: 99%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: 12
Molecule details ›
Chain: 12
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: 13
Molecule details ›
Chain: 13
Length: 122 amino acids
Theoretical weight: 13.45 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY3 (Residues: 1-122; Coverage: 99%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: 14
Molecule details ›
Chain: 14
Length: 143 amino acids
Theoretical weight: 14.88 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02413 (Residues: 2-144; Coverage: 99%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: 15
Molecule details ›
Chain: 15
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: 16
Molecule details ›
Chain: 16
Length: 120 amino acids
Theoretical weight: 13.72 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG44 (Residues: 1-120; Coverage: 95%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: 17
Molecule details ›
Chain: 17
Length: 116 amino acids
Theoretical weight: 12.66 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0C018 (Residues: 2-117; Coverage: 99%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: 18
Molecule details ›
Chain: 18
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: 99%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: 19
Molecule details ›
Chain: 19
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: 99%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: 20
Molecule details ›
Chain: 20
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: 21
Molecule details ›
Chain: 21
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: 22
Molecule details ›
Chain: 22
Length: 93 amino acids
Theoretical weight: 10.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-93; Coverage: 93%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: 23
Molecule details ›
Chain: 23
Length: 102 amino acids
Theoretical weight: 11.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60624 (Residues: 2-103; Coverage: 98%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: 24
Molecule details ›
Chain: 24
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: 25
Molecule details ›
Chain: 25
Length: 75 amino acids
Theoretical weight: 8.17 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L8 (Residues: 11-85; Coverage: 88%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: 26
Molecule details ›
Chain: 26
Length: 77 amino acids
Theoretical weight: 8.9 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M2 (Residues: 2-78; Coverage: 99%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 27
Molecule details ›
Chain: 27
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 28
Molecule details ›
Chain: 28
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG51 (Residues: 2-59; Coverage: 98%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: 29
Molecule details ›
Chain: 29
Length: 66 amino acids
Theoretical weight: 7.52 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M9 (Residues: 1-66; Coverage: 94%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 30
Molecule details ›
Chain: 30
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 31
Molecule details ›
Chain: 31
Length: 50 amino acids
Theoretical weight: 5.81 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N9 (Residues: 4-53; Coverage: 91%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 32
Molecule details ›
Chain: 32
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 33
Molecule details ›
Chain: 33
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q1 (Residues: 2-65; Coverage: 99%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: 34
Molecule details ›
Chain: 34
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 218 amino acids
Theoretical weight: 24.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 9-226; Coverage: 91%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 157 amino acids
Theoretical weight: 16.53 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 10-166; Coverage: 94%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: F
Molecule details ›
Chain: F
Length: 100 amino acids
Theoretical weight: 11.67 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-100; Coverage: 74%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
Length: 151 amino acids
Theoretical weight: 16.86 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02359 (Residues: 2-152; Coverage: 84%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 127 amino acids
Theoretical weight: 14.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7X3 (Residues: 4-130; Coverage: 98%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: J
Molecule details ›
Chain: J
Length: 98 amino acids
Theoretical weight: 11.2 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 5-102; Coverage: 95%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
Length: 116 amino acids
Theoretical weight: 12.39 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 13-128; Coverage: 90%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: 99%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
Length: 114 amino acids
Theoretical weight: 12.63 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S9 (Residues: 2-115; Coverage: 97%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
Length: 100 amino acids
Theoretical weight: 11.48 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 2-101; Coverage: 99%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 65 amino acids
Theoretical weight: 7.61 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 10-74; Coverage: 87%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S
Molecule details ›
Chain: S
Length: 79 amino acids
Theoretical weight: 9.06 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U3 (Residues: 3-81; Coverage: 86%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 85 amino acids
Theoretical weight: 9.51 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 3-87; Coverage: 98%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: U
Molecule details ›
Chain: U
Length: 65 amino acids
Theoretical weight: 7.76 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68679 (Residues: 4-68; Coverage: 92%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein uL1 Chain: 03
Molecule details ›
Chain: 03
Length: 223 amino acids
Theoretical weight: 23.74 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L0 (Residues: 3-225; Coverage: 95%)
Gene names: JW3947, b3984, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Elongation factor Tu 1 Chain: Z
Molecule details ›
Chain: Z
Length: 392 amino acids
Theoretical weight: 43.15 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0CE47 (Residues: 2-393; Coverage: 100%)
Gene names: JW3301, b3339, tufA
Sequence domains:
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1539 nucleotides
Theoretical weight: 498.73 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: 01
Molecule details ›
Chain: 01
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 02
Molecule details ›
Chain: 02
Length: 120 nucleotides
Theoretical weight: 38.81 KDa
Sequence domains: 5S ribosomal RNA
tRNAfMet Chains: W, X
Molecule details ›
Chains: W, X
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
Messenger RNA Chain: V
Molecule details ›
Chain: V
Length: 19 nucleotides
Theoretical weight: 6.26 KDa
tRNALys Chain: Y
Molecule details ›
Chain: Y
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand FME 1 x FME
Ligand LYS 1 x LYS
Ligand GCP 1 x GCP
1 modified residue:
Ligand U8U 1 x U8U

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-8619
Expression system: Escherichia coli K-12

Quick links

Citations

22 review citations

The roles of structural dynamics in the cellular functions of RNAs.
Ganser et al. (2019)
21 more

4 mentions without citation

Translation in Prokaryotes.
Rodnina MV. (2018)
3 more