› 6h58

Electron Microscopy
7.9Å resolution

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

Released:
DOI: 10.2210/pdb6h58/pdb
PDB 6h58 coloured by chain and viewed from the front.
PDB 6h58 coloured by chain and viewed from the side.
PDB 6h58 coloured by chain and viewed from the top.
Source organism: Escherichia coli BW25113
Primary publication:
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.
Beckert B, Turk M, Czech A, Berninghausen O, Beckmann R, Ignatova Z, Plitzko JM, Wilson DN
Nat Microbiol (2018)
PMID: 30177741
Related structures: EMD-0139

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 112-mer (preferred)
Entry contents:
52 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (56 distinct):
50S ribosomal protein L32 Chains: 0, 00
Molecule details ›
Chains: 0, 00
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: 1, 11
Molecule details ›
Chains: 1, 11
Length: 50 amino acids
Theoretical weight: 5.81 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N9 (Residues: 4-53; Coverage: 91%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 2, 22
Molecule details ›
Chains: 2, 22
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chains: 3, 33
Molecule details ›
Chains: 3, 33
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q1 (Residues: 2-65; Coverage: 99%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: 4, 44
Molecule details ›
Chains: 4, 44
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
50S ribosomal protein L31 Chains: 6, 66
Molecule details ›
Chains: 6, 66
Length: 66 amino acids
Theoretical weight: 7.52 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M9 (Residues: 1-66; Coverage: 94%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L2 Chains: C, CC
Molecule details ›
Chains: C, CC
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Sequence domains:
50S ribosomal protein L3 Chains: D, DD
Molecule details ›
Chains: D, DD
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: E, EE
Molecule details ›
Chains: E, EE
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: F, FF
Molecule details ›
Chains: F, FF
Length: 177 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P62399 (Residues: 2-178; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
50S ribosomal protein L6 Chains: G, GG
Molecule details ›
Chains: G, GG
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG55 (Residues: 2-177; Coverage: 99%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: H, HH
Molecule details ›
Chains: H, HH
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
50S ribosomal protein L13 Chains: J, JJ
Molecule details ›
Chains: J, JJ
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: K, KK
Molecule details ›
Chains: K, KK
Length: 122 amino acids
Theoretical weight: 13.45 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY3 (Residues: 1-122; Coverage: 99%)
Gene names: JW3272, b3310, rplN
50S ribosomal protein L15 Chains: L, LL
Molecule details ›
Chains: L, LL
Length: 143 amino acids
Theoretical weight: 14.88 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P02413 (Residues: 2-144; Coverage: 99%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: M, MM
Molecule details ›
Chains: M, MM
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: N, NN
Molecule details ›
Chains: N, NN
Length: 120 amino acids
Theoretical weight: 13.72 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG44 (Residues: 1-120; Coverage: 95%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: O, OO
Molecule details ›
Chains: O, OO
Length: 116 amino acids
Theoretical weight: 12.66 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0C018 (Residues: 2-117; Coverage: 99%)
Gene names: JW3266, b3304, rplR
50S ribosomal protein L19 Chains: P, PP
Molecule details ›
Chains: P, PP
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: 99%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: Q, QQ
Molecule details ›
Chains: Q, QQ
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: 99%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: R, RR
Molecule details ›
Chains: R, RR
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: S, SS
Molecule details ›
Chains: S, SS
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: T, TT
Molecule details ›
Chains: T, TT
Length: 93 amino acids
Theoretical weight: 10.55 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-93; Coverage: 93%)
Gene names: JW3280, b3318, rplW
50S ribosomal protein L24 Chains: U, UU
Molecule details ›
Chains: U, UU
Length: 102 amino acids
Theoretical weight: 11.08 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60624 (Residues: 2-103; Coverage: 98%)
Gene names: JW3271, b3309, rplX
Sequence domains:
50S ribosomal protein L25 Chains: V, VV
Molecule details ›
Chains: V, VV
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
50S ribosomal protein L27 Chains: W, WW
Molecule details ›
Chains: W, WW
Length: 75 amino acids
Theoretical weight: 8.17 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L8 (Residues: 11-85; Coverage: 88%)
Gene names: JW3152, b3185, rpmA
50S ribosomal protein L28 Chains: X, XX
Molecule details ›
Chains: X, XX
Length: 77 amino acids
Theoretical weight: 8.9 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M2 (Residues: 2-78; Coverage: 99%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: Y, YY
Molecule details ›
Chains: Y, YY
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: Z, ZZ
Molecule details ›
Chains: Z, ZZ
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG51 (Residues: 2-59; Coverage: 98%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
30S ribosomal protein S2 Chains: b, bb
Molecule details ›
Chains: b, bb
Length: 226 amino acids
Theoretical weight: 25.1 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7V0 (Residues: 9-226; Coverage: 91%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: c, cc
Molecule details ›
Chains: c, cc
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: d, dd
Molecule details ›
Chains: d, dd
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: e, ee
Molecule details ›
Chains: e, ee
Length: 157 amino acids
Theoretical weight: 16.53 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7W1 (Residues: 10-166; Coverage: 94%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
30S ribosomal protein S6, non-modified isoform Chains: f, ff
Molecule details ›
Chains: f, ff
Length: 100 amino acids
Theoretical weight: 11.67 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P02358 (Residues: 1-100; Coverage: 74%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: g, gg
Molecule details ›
Chains: g, gg
Length: 161 amino acids
Theoretical weight: 18.05 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P02359 (Residues: 2-162; Coverage: 90%)
Gene names: JW3303, b3341, rpsG
30S ribosomal protein S8 Chains: h, hh
Molecule details ›
Chains: h, hh
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
30S ribosomal protein S9 Chains: i, ii
Molecule details ›
Chains: i, ii
Length: 127 amino acids
Theoretical weight: 14.55 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7X3 (Residues: 4-130; Coverage: 98%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: j, jj
Molecule details ›
Chains: j, jj
Length: 98 amino acids
Theoretical weight: 11.2 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7R5 (Residues: 5-102; Coverage: 95%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: k, kk
Molecule details ›
Chains: k, kk
Length: 116 amino acids
Theoretical weight: 12.39 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7R9 (Residues: 13-128; Coverage: 90%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: l, ll
Molecule details ›
Chains: l, ll
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: 99%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: m, mm
Molecule details ›
Chains: m, mm
Length: 114 amino acids
Theoretical weight: 12.63 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7S9 (Residues: 2-115; Coverage: 97%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 Chains: n, nn
Molecule details ›
Chains: n, nn
Length: 101 amino acids
Theoretical weight: 11.55 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG59 (Residues: 2-35, 36-101; Coverage: 99%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chains: o, oo
Molecule details ›
Chains: o, oo
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: p, pp
Molecule details ›
Chains: p, pp
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: q, qq
Molecule details ›
Chains: q, qq
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: r, rr
Molecule details ›
Chains: r, rr
Length: 65 amino acids
Theoretical weight: 7.61 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7T7 (Residues: 10-74; Coverage: 87%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: s, ss
Molecule details ›
Chains: s, ss
Length: 79 amino acids
Theoretical weight: 9.06 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7U3 (Residues: 3-81; Coverage: 86%)
Gene names: JW3278, b3316, rpsS
30S ribosomal protein S20 Chains: t, tt
Molecule details ›
Chains: t, tt
Length: 85 amino acids
Theoretical weight: 9.51 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7U7 (Residues: 3-87; Coverage: 98%)
Gene names: JW0022, b0023, rpsT
30S ribosomal protein S21 Chains: u, uu
Molecule details ›
Chains: u, uu
Length: 65 amino acids
Theoretical weight: 7.76 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P68679 (Residues: 4-68; Coverage: 92%)
Gene names: JW3037, b3065, rpsU
Ribosome modulation factor Chains: v, vv
Molecule details ›
Chains: v, vv
Length: 55 amino acids
Theoretical weight: 6.52 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AFW2 (Residues: 1-55; Coverage: 100%)
Gene names: JW0936, b0953, rmf
Sequence domains: Ribosome modulation factor
Ribosome hibernation promoting factor Chains: x, xx
Molecule details ›
Chains: x, xx
Length: 95 amino acids
Theoretical weight: 10.77 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AFX0 (Residues: 1-95; Coverage: 100%)
Gene names: JW3170, b3203, hpf, yhbH
Sequence domains: Sigma 54 modulation protein / S30EA ribosomal protein
30S ribosomal protein S1 Chains: y, yy
Molecule details ›
Chains: y, yy
Length: 557 amino acids
Theoretical weight: 61.24 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG67 (Residues: 1-557; Coverage: 100%)
Gene names: JW0894, b0911, rpsA, ssyF
Sequence domains: S1 RNA binding domain
23S ribosomal RNA Chains: A, AA
Molecule details ›
Chains: A, AA
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: B, BB
Molecule details ›
Chains: B, BB
Length: 120 nucleotides
Theoretical weight: 38.81 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: a, aa
Molecule details ›
Chains: a, aa
Length: 1539 nucleotides
Theoretical weight: 498.73 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNA Mixture Chains: w, ww
Molecule details ›
Chains: w, ww
Length: 77 nucleotides
Theoretical weight: 24.77 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.9Å
Relevant EMDB volumes: EMD-0139

Quick links

Citations

5 review citations

Challenges and opportunities in cryo-EM single-particle analysis.
Lyumkis D. (2019)
4 more