› 6fxc

Electron Microscopy
6.76Å resolution

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

Released:
DOI: 10.2210/pdb6fxc/pdb
PDB entry 6fxc coloured by chain, front view.
PDB entry 6fxc coloured by chain, side view.
PDB entry 6fxc coloured by chain, top view.
Source organisms:
Primary publication:
The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.
Matzov D, Aibara S, Basu A, Zimmerman E, Bashan A, Yap MF, Amunts A, Yonath AE
Nat Commun 8 723 (2017)
PMID: 28959035
Related structures: EMD-3637

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 104-mer (preferred)
PDBe Complex ID:
PDB-CPX-236598 (preferred)
Entry contents:
49 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (52 distinct):
Small ribosomal subunit protein uS2 Chains: Ab, Bb
Molecule details ›
Chains: Ab, Bb
Length: 226 amino acids
Theoretical weight: 25.93 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YXL2 (Residues: 1-226; Coverage: 89%)
Gene names: SAB1118, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: Ac, Bc
Molecule details ›
Chains: Ac, Bc
Length: 202 amino acids
Theoretical weight: 22.68 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYQ2 (Residues: 2-203; Coverage: 93%)
Gene names: SAB2116c, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: Ad, Bd
Molecule details ›
Chains: Ad, Bd
Length: 198 amino acids
Theoretical weight: 22.85 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YTH0 (Residues: 3-200; Coverage: 99%)
Gene names: SAB1578, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: Ae, Be
Molecule details ›
Chains: Ae, Be
Length: 156 amino acids
Theoretical weight: 16.52 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL4 (Residues: 10-165; Coverage: 94%)
Gene names: SAB2105c, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: Af, Bf
Molecule details ›
Chains: Af, Bf
Length: 95 amino acids
Theoretical weight: 11.24 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YVJ2 (Residues: 1-95; Coverage: 97%)
Gene names: SAB0316, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: Ag, Bg
Molecule details ›
Chains: Ag, Bg
Length: 152 amino acids
Theoretical weight: 17.18 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A077VHU6 (Residues: 1-152; Coverage: 97%)
Gene names: CD116_12315, ERS140147_01024, NCTC13712_00499, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: Ah, Bh
Molecule details ›
Chains: Ah, Bh
Length: 131 amino acids
Theoretical weight: 14.72 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL1 (Residues: 2-132; Coverage: 99%)
Gene names: SAB2108c, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: Ai, Bi
Molecule details ›
Chains: Ai, Bi
Length: 127 amino acids
Theoretical weight: 14.31 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A1Q4GY48 (Residues: 4-130; Coverage: 98%)
Gene names: A6760_13315, E1948_03180, EP54_02240, EQ90_01125, QU38_03565, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: Aj, Bj
Molecule details ›
Chains: Aj, Bj
Length: 97 amino acids
Theoretical weight: 11.01 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYP5 (Residues: 6-102; Coverage: 95%)
Gene names: SAB2123c, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: Ak, Bk
Molecule details ›
Chains: Ak, Bk
Length: 114 amino acids
Theoretical weight: 12.05 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYM1 (Residues: 15-128; Coverage: 88%)
Gene names: SAB2098c, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: Al, Bl
Molecule details ›
Chains: Al, Bl
Length: 135 amino acids
Theoretical weight: 15.08 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A133PZQ5 (Residues: 14-148; Coverage: 91%)
Gene names: HMPREF3211_01391, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: Am, Bm
Molecule details ›
Chains: Am, Bm
Length: 121 amino acids
Theoretical weight: 13.75 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYM0 (Residues: 1-121; Coverage: 100%)
Gene names: SAB2099c, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14B Chains: An, Bn
Molecule details ›
Chains: An, Bn
Length: 60 amino acids
Theoretical weight: 7.19 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL0 (Residues: 2-61; Coverage: 98%)
Gene names: SAB2109c, rpsN1, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: Ao, Bo
Molecule details ›
Chains: Ao, Bo
Length: 88 amino acids
Theoretical weight: 10.5 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YXP3 (Residues: 2-89; Coverage: 99%)
Gene names: SAB1135, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: Ap, Bp
Molecule details ›
Chains: Ap, Bp
Length: 89 amino acids
Theoretical weight: 9.99 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YXH8 (Residues: 2-90; Coverage: 98%)
Gene names: SAB1102, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: Aq, Bq
Molecule details ›
Chains: Aq, Bq
Length: 80 amino acids
Theoretical weight: 9.37 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYK6 (Residues: 5-84; Coverage: 92%)
Gene names: SAB2113c, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: Ar, Br
Molecule details ›
Chains: Ar, Br
Length: 54 amino acids
Theoretical weight: 6.4 KDa
Source organism: Staphylococcus aureus
Small ribosomal subunit protein uS19 Chains: As, Bs
Molecule details ›
Chains: As, Bs
Length: 80 amino acids
Theoretical weight: 9.21 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A133PYC3 (Residues: 20-99; Coverage: 74%)
Gene names: HMPREF3211_01571, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: At, Bt
Molecule details ›
Chains: At, Bt
Length: 81 amino acids
Theoretical weight: 8.78 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YT41 (Residues: 2-82; Coverage: 98%)
Gene names: SAB1458, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chains: Au, Bu
Molecule details ›
Chains: Au, Bu
Length: 52 amino acids
Theoretical weight: 6.24 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YT04 (Residues: 4-55; Coverage: 90%)
Gene names: SAB1447c, rpsU
Sequence domains: Ribosomal protein S21
Ribosome hibernation promotion factor Chains: Av, Bv
Molecule details ›
Chains: Av, Bv
Length: 190 amino acids
Theoretical weight: 22.24 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YSH7 (Residues: 1-190; Coverage: 100%)
Gene names: SAB0704, hpf
Sequence domains:
Large ribosomal subunit protein uL2 Chains: AC, BC
Molecule details ›
Chains: AC, BC
Length: 274 amino acids
Theoretical weight: 29.83 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYP9 (Residues: 2-275; Coverage: 99%)
Gene names: SAB2119c, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: AD, BD
Molecule details ›
Chains: AD, BD
Length: 215 amino acids
Theoretical weight: 23.2 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYP6 (Residues: 2-216; Coverage: 98%)
Gene names: SAB2122c, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: AE, BE
Molecule details ›
Chains: AE, BE
Length: 206 amino acids
Theoretical weight: 22.36 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYP7 (Residues: 2-207; Coverage: 100%)
Gene names: SAB2121c, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: AF, BF
Molecule details ›
Chains: AF, BF
Length: 175 amino acids
Theoretical weight: 19.73 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYK9 (Residues: 2-176; Coverage: 98%)
Gene names: SAB2110c, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: AG, BG
Molecule details ›
Chains: AG, BG
Length: 175 amino acids
Theoretical weight: 19.5 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL2 (Residues: 2-176; Coverage: 98%)
Gene names: SAB2107c, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYM8 (Residues: 1-145; Coverage: 100%)
Gene names: SAB2091c, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: AI, BI
Molecule details ›
Chains: AI, BI
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYK7 (Residues: 1-122; Coverage: 100%)
Gene names: SAB2112c, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
Length: 146 amino acids
Theoretical weight: 15.63 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL6 (Residues: 1-146; Coverage: 100%)
Gene names: SAB2103c, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: AK, BK
Molecule details ›
Chains: AK, BK
Length: 137 amino acids
Theoretical weight: 15.6 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYQ3 (Residues: 1-137; Coverage: 95%)
Gene names: SAB2115c, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: AL, BL
Molecule details ›
Chains: AL, BL
Length: 120 amino acids
Theoretical weight: 13.58 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYM3 (Residues: 3-122; Coverage: 98%)
Gene names: SAB2096c, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: AM, BM
Molecule details ›
Chains: AM, BM
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: W8TRE0 (Residues: 1-119; Coverage: 100%)
Gene names: A6760_13400, BN1321_380066, CV021_17995, E1948_03095, E1948_11800, EP54_02155, EQ90_01210, FAF17_03785, G6W63_05940, G6Y24_08820, GO793_01695, GO814_07330, GO941_09030, GO942_01070, GQX37_14855, GZ156_01250, GZ163_04620, H2639_07590, HMPREF3211_01559, M1K003_0777, NCTC13131_01577, NCTC5664_01678, NCTC6133_03024, NCTC7972_02476, QU38_04940, SAMEA1531744_00346, SAMEA2078260_00053, SAMEA2078588_00360, SAMEA2080344_00567, SAMEA2081063_01560, SAMEA4008575_01047, SAMEA70146418_00499, SAMEA70153168_01220, SAMEA70245418_00551, rplR, rplR_1
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: AN, BN
Molecule details ›
Chains: AN, BN
Length: 114 amino acids
Theoretical weight: 13.1 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YXM4 (Residues: 2-115; Coverage: 98%)
Gene names: SAB1105, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: AO, BO
Molecule details ›
Chains: AO, BO
Length: 116 amino acids
Theoretical weight: 13.46 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YTB1 (Residues: 2-117; Coverage: 98%)
Gene names: SAB1538c, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: AP, BP
Molecule details ›
Chains: AP, BP
Length: 102 amino acids
Theoretical weight: 11.35 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YT83 (Residues: 1-102; Coverage: 100%)
Gene names: SAB1516c, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: AQ, BQ
Molecule details ›
Chains: AQ, BQ
Length: 112 amino acids
Theoretical weight: 12.33 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYQ1 (Residues: 1-112; Coverage: 96%)
Gene names: SAB2117c, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: AR, BR
Molecule details ›
Chains: AR, BR
Length: 89 amino acids
Theoretical weight: 10.38 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYP8 (Residues: 2-90; Coverage: 98%)
Gene names: SAB2120c, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: AS, BS
Molecule details ›
Chains: AS, BS
Length: 103 amino acids
Theoretical weight: 11.32 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYK8 (Residues: 2-104; Coverage: 98%)
Gene names: SAB2111c, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: AT, BT
Molecule details ›
Chains: AT, BT
Length: 94 amino acids
Theoretical weight: 10.46 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A133Q8Z9 (Residues: 4-97; Coverage: 43%)
Gene names: HMPREF3211_00359, ctc, rplY
Sequence domains: Ribosomal L25p family
50S ribosomal protein L27 Chains: AU, BU
Molecule details ›
Chains: AU, BU
Length: 82 amino acids
Theoretical weight: 8.91 KDa
Source organism: Staphylococcus aureus
Large ribosomal subunit protein bL28 Chains: AV, BV
Molecule details ›
Chains: AV, BV
Length: 58 amino acids
Theoretical weight: 6.55 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YXJ2 (Residues: 3-60; Coverage: 94%)
Gene names: SAB1088c, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: AW, BW
Molecule details ›
Chains: AW, BW
Length: 67 amino acids
Theoretical weight: 7.85 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYN0 (Residues: 2-68; Coverage: 97%)
Gene names: SAB2114c, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: AX, BX
Molecule details ›
Chains: AX, BX
Length: 58 amino acids
Theoretical weight: 6.43 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YYL5 (Residues: 2-59; Coverage: 98%)
Gene names: SAB2104c, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31B Chains: AY, BY
Molecule details ›
Chains: AY, BY
Length: 59 amino acids
Theoretical weight: 6.91 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YUN3 (Residues: 1-59; Coverage: 70%)
Gene names: SAB2004c, rpmE2
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: AZ, BZ
Molecule details ›
Chains: AZ, BZ
Length: 48 amino acids
Theoretical weight: 5.57 KDa
Source organism: Staphylococcus aureus
Large ribosomal subunit protein bL33 Chains: A1, B1
Molecule details ›
Chains: A1, B1
Length: 47 amino acids
Theoretical weight: 5.68 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A077V2P0 (Residues: 2-48; Coverage: 96%)
Gene names: CD116_07290, ERS140147_01724, NCTC13712_01328, rpmG, rpmG2, rpmG2_1
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: A2, B2
Molecule details ›
Chains: A2, B2
Length: 43 amino acids
Theoretical weight: 5.25 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YZB6 (Residues: 2-44; Coverage: 96%)
Gene names: SAB2590c, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: A3, B3
Molecule details ›
Chains: A3, B3
Length: 64 amino acids
Theoretical weight: 7.46 KDa
Source organism: Staphylococcus aureus RF122
UniProt:
  • Canonical: Q2YTB0 (Residues: 2-65; Coverage: 97%)
Gene names: SAB1539c, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: A4, B4
Molecule details ›
Chains: A4, B4
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: A0A077UGV8 (Residues: 1-37; Coverage: 100%)
Gene names: CD116_01915, ERS140147_00615, NCTC13712_02175, rpmJ
Sequence domains: Ribosomal protein L36
16S ribosomal RNA Chains: Aa, Ba
Molecule details ›
Chains: Aa, Ba
Length: 1539 nucleotides
Theoretical weight: 498.06 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 2923 nucleotides
Theoretical weight: 946.7 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: AB, BB
Molecule details ›
Chains: AB, BB
Length: 115 nucleotides
Theoretical weight: 36.97 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.76Å
Relevant EMDB volumes: EMD-3637

Quick links

Citations

10 review citations

Ribosome Hibernation.
Prossliner et al. (2018)
9 more

6 mentions without citation

Translational regulation in mycobacteria and its implications for pathogenicity.
Sawyer et al. (2018)
5 more