› 8p2g

Electron Microscopy
2.02Å resolution

Staphylococcus aureus 70S ribosome with elongation factor G locked with fusidic acid cyclopentane with a tRNA in pe/E chimeric state

Released:
DOI: 10.2210/pdb8p2g/pdb
PDB entry 8p2g coloured by chain, front view.
PDB entry 8p2g coloured by chain, side view.
PDB entry 8p2g coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.
González-López A, Larsson DSD, Koripella RK, Cain BN, Chavez MG, Hergenrother PJ, Sanyal S, Selmer M
OpenAccess logo Sci Rep 14 14253 (2024)
PMID: 38902339
Related structures: EMD-17364

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-280386 (preferred)
Entry contents:
48 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (53 distinct):
Elongation factor G Chain: E
Molecule details ›
Chain: E
Length: 693 amino acids
Theoretical weight: 76.7 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2G0N1 (Residues: 1-693; Coverage: 100%)
Gene names: SAOUHSC_00529, fusA
Sequence domains:
Large ribosomal subunit protein uL2 Chain: G
Molecule details ›
Chain: G
Length: 277 amino acids
Theoretical weight: 30.22 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P60430 (Residues: 1-277; Coverage: 100%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 23.76 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW06 (Residues: 1-220; Coverage: 100%)
Gene names: SAOUHSC_02512, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: I
Molecule details ›
Chain: I
Length: 207 amino acids
Theoretical weight: 22.5 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW07 (Residues: 1-207; Coverage: 100%)
Gene names: SAOUHSC_02511, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: J
Molecule details ›
Chain: J
Length: 179 amino acids
Theoretical weight: 20.3 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW18 (Residues: 1-179; Coverage: 100%)
Gene names: SAOUHSC_02500, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: K
Molecule details ›
Chain: K
Length: 178 amino acids
Theoretical weight: 19.82 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW21 (Residues: 1-178; Coverage: 100%)
Gene names: SAOUHSC_02496, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: M
Molecule details ›
Chain: M
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW38 (Residues: 1-145; Coverage: 100%)
Gene names: SAOUHSC_02478, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: N
Molecule details ›
Chain: N
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW16 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02502, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: O
Molecule details ›
Chain: O
Length: 146 amino acids
Theoretical weight: 15.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0F8 (Residues: 1-146; Coverage: 100%)
Gene names: SAOUHSC_02492, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: P
Molecule details ›
Chain: P
Length: 144 amino acids
Theoretical weight: 16.27 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW13 (Residues: 1-144; Coverage: 100%)
Gene names: SAOUHSC_02505, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: Q
Molecule details ›
Chain: Q
Length: 122 amino acids
Theoretical weight: 13.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW33 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02484, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: R
Molecule details ›
Chain: R
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW22 (Residues: 1-119; Coverage: 100%)
Gene names: SAOUHSC_02495, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: S
Molecule details ›
Chain: S
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: T
Molecule details ›
Chain: T
Length: 118 amino acids
Theoretical weight: 13.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ1 (Residues: 1-118; Coverage: 100%)
Gene names: SAOUHSC_01784, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: U
Molecule details ›
Chain: U
Length: 102 amino acids
Theoretical weight: 11.35 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXS8 (Residues: 1-102; Coverage: 100%)
Gene names: SAOUHSC_01757, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: V
Molecule details ›
Chain: V
Length: 117 amino acids
Theoretical weight: 12.86 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW11 (Residues: 1-117; Coverage: 100%)
Gene names: SAOUHSC_02507, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: W
Molecule details ›
Chain: W
Length: 91 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW08 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_02510, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: X
Molecule details ›
Chain: X
Length: 105 amino acids
Theoretical weight: 11.56 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW17 (Residues: 1-105; Coverage: 100%)
Gene names: SAOUHSC_02501, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: Y
Molecule details ›
Chain: Y
Length: 217 amino acids
Theoretical weight: 23.81 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G0S0 (Residues: 1-217; Coverage: 100%)
Gene names: SAOUHSC_00474, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: Z
Molecule details ›
Chain: Z
Length: 94 amino acids
Theoretical weight: 10.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXT0 (Residues: 1-94; Coverage: 100%)
Gene names: SAOUHSC_01755, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: 1
Molecule details ›
Chain: 1
Length: 62 amino acids
Theoretical weight: 7 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ60 (Residues: 1-62; Coverage: 100%)
Gene names: SAOUHSC_01191, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 2
Molecule details ›
Chain: 2
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW14 (Residues: 1-69; Coverage: 100%)
Gene names: SAOUHSC_02504, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 3
Molecule details ›
Chain: 3
Length: 59 amino acids
Theoretical weight: 6.57 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0G2 (Residues: 1-59; Coverage: 100%)
Gene names: SAOUHSC_02493, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31B Chain: 4
Molecule details ›
Chain: 4
Length: 84 amino acids
Theoretical weight: 9.74 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FWD8 (Residues: 1-84; Coverage: 100%)
Gene names: SAOUHSC_02361, rpmE2
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 5
Molecule details ›
Chain: 5
Length: 57 amino acids
Theoretical weight: 6.5 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZF1 (Residues: 1-58; Coverage: 98%)
Gene names: SAOUHSC_01078, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33A Chain: 6
Molecule details ›
Chain: 6
Length: 49 amino acids
Theoretical weight: 5.94 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FYU6 (Residues: 1-49; Coverage: 100%)
Gene names: SAOUHSC_01328, rpmG1
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 7
Molecule details ›
Chain: 7
Length: 45 amino acids
Theoretical weight: 5.45 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FUQ0 (Residues: 1-45; Coverage: 100%)
Gene names: SAOUHSC_03055, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 8
Molecule details ›
Chain: 8
Length: 66 amino acids
Theoretical weight: 7.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ0 (Residues: 1-66; Coverage: 100%)
Gene names: SAOUHSC_01785, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 9
Molecule details ›
Chain: 9
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW29 (Residues: 1-37; Coverage: 100%)
Gene names: SAOUHSC_02488, rpmJ
Sequence domains: Ribosomal protein L36
Small ribosomal subunit protein uS2 Chain: c
Molecule details ›
Chain: c
Length: 255 amino acids
Theoretical weight: 29.14 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ25 (Residues: 1-255; Coverage: 100%)
Gene names: SAOUHSC_01232, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: d
Molecule details ›
Chain: d
Length: 217 amino acids
Theoretical weight: 24.14 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW12 (Residues: 1-217; Coverage: 100%)
Gene names: SAOUHSC_02506, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: e
Molecule details ›
Chain: e
Length: 200 amino acids
Theoretical weight: 23.05 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXK6 (Residues: 1-200; Coverage: 100%)
Gene names: SAOUHSC_01829, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: f
Molecule details ›
Chain: f
Length: 166 amino acids
Theoretical weight: 17.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW23 (Residues: 1-166; Coverage: 100%)
Gene names: SAOUHSC_02494, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: g
Molecule details ›
Chain: g
Length: 98 amino acids
Theoretical weight: 11.61 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G113 (Residues: 1-98; Coverage: 100%)
Gene names: SAOUHSC_00348, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: h
Molecule details ›
Chain: h
Length: 156 amino acids
Theoretical weight: 17.83 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P48940 (Residues: 1-156; Coverage: 100%)
Gene names: SAOUHSC_00528, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: i
Molecule details ›
Chain: i
Length: 132 amino acids
Theoretical weight: 14.85 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW20 (Residues: 1-132; Coverage: 100%)
Gene names: SAOUHSC_02498, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: j
Molecule details ›
Chain: j
Length: 132 amino acids
Theoretical weight: 14.86 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW39 (Residues: 1-132; Coverage: 100%)
Gene names: SAOUHSC_02477, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: k
Molecule details ›
Chain: k
Length: 102 amino acids
Theoretical weight: 11.6 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: A0A0D1JTN2 (Residues: 1-102; Coverage: 100%)
Gene names: ACR74_08305, AS572_10760, BN1321_380083, CNH36_12615, CV021_17910, E1948_03010, E1948_11885, EIH03_01515, EP54_02070, EQ90_01295, ERS1058648_01098, ERS329596_01247, G0Z31_10700, G6Y24_08905, GO793_01610, GO814_07415, GO941_08945, GO942_01155, GQX37_14770, GQX52_07235, GZ164_08470, HH313_002321, LB359_11515, M1K003_0794, NCTC10702_03549, NCTC13131_01594, NCTC6133_03041, NCTC7878_01007, NCTC7972_02459, QU38_05025, SAMEA1029528_02007, SAMEA1029536_00941, SAMEA1466929_00953, SAMEA1531725_01449, SAMEA2078260_00070, SAMEA2078588_00377, SAMEA2080344_00550, SAMEA2081063_01543, SAMEA4008575_01030, SAMEA4552975_02175, SAMEA70153168_01237, SAMEA70245418_00534, rpsJ, rpsJ_1
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: l
Molecule details ›
Chain: l
Length: 129 amino acids
Theoretical weight: 13.91 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW31 (Residues: 1-129; Coverage: 100%)
Gene names: SAOUHSC_02486, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: m
Molecule details ›
Chain: m
Length: 137 amino acids
Theoretical weight: 15.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0H0 (Residues: 1-137; Coverage: 100%)
Gene names: SAOUHSC_00527, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: n
Molecule details ›
Chain: n
Length: 121 amino acids
Theoretical weight: 13.75 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW30 (Residues: 1-121; Coverage: 100%)
Gene names: SAOUHSC_02487, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14B Chain: o
Molecule details ›
Chain: o
Length: 61 amino acids
Theoretical weight: 7.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW19 (Residues: 1-61; Coverage: 100%)
Gene names: SAOUHSC_02499, rpsN1, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: p
Molecule details ›
Chain: p
Length: 89 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G2Q1 (Residues: 1-89; Coverage: 100%)
Gene names: SAOUHSC_01250, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: q
Molecule details ›
Chain: q
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ45 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_01208, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: r
Molecule details ›
Chain: r
Length: 87 amino acids
Theoretical weight: 10.2 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW15 (Residues: 1-87; Coverage: 100%)
Gene names: SAOUHSC_02503, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: s
Molecule details ›
Chain: s
Length: 80 amino acids
Theoretical weight: 9.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G111 (Residues: 1-80; Coverage: 100%)
Gene names: SAOUHSC_00350, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: t
Molecule details ›
Chain: t
Length: 92 amino acids
Theoretical weight: 10.64 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW10 (Residues: 1-92; Coverage: 100%)
Gene names: SAOUHSC_02508, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: u
Molecule details ›
Chain: u
Length: 83 amino acids
Theoretical weight: 9.04 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXY6 (Residues: 1-83; Coverage: 100%)
Gene names: SAOUHSC_01689, rpsT
Sequence domains: Ribosomal protein S20
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2923 nucleotides
Theoretical weight: 946.78 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 115 nucleotides
Theoretical weight: 36.97 KDa
Sequence domains: 5S ribosomal RNA
tRNA Chain: D
Molecule details ›
Chain: D
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1555 nucleotides
Theoretical weight: 503.12 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: b
Molecule details ›
Chain: b
Length: 24 nucleotides
Theoretical weight: 7.89 KDa

Ligands and Environments

6 bound ligands:
Ligand MG 169 x MG
Ligand SPD 3 x SPD
Ligand PUT 1 x PUT
Ligand GDP 1 x GDP
Ligand WUX 1 x WUX
Ligand ZN 3 x ZN
11 modified residues:
Ligand 5MU 2 x 5MU
Ligand 3TD 1 x 3TD
Ligand OMG 1 x OMG
Ligand 2MG 2 x 2MG
Ligand H2U 1 x H2U
Ligand 2MA 1 x 2MA
Ligand G7M 1 x G7M
Ligand 5MC 1 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.02Å
Relevant EMDB volumes: EMD-17364
Expression system: Escherichia coli BL21(DE3)

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