› 7pib

Electron Microscopy
4.7Å resolution

70S ribosome with EF-G, A/P- and P/E-site tRNAs in spectinomycin-treated Mycoplasma pneumoniae cells

Released:
DOI: 10.2210/pdb7pib/pdb
PDB entry 7pib coloured by chain, front view.
PDB entry 7pib coloured by chain, side view.
PDB entry 7pib coloured by chain, top view.
Source organism: Mycoplasmoides pneumoniae M129
Primary publication:
Visualizing translation dynamics at atomic detail inside a bacterial cell.
Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J
OpenAccess logo Nature (2022)
PMID: 36171285
Related structures: EMD-13435

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
PDBe Complex ID:
PDB-CPX-154305 (preferred)
Entry contents:
51 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (55 distinct):
Large ribosomal subunit protein bL34 Chain: 0
Molecule details ›
Chain: 0
Length: 48 amino acids
Theoretical weight: 5.62 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P78006 (Residues: 1-48; Coverage: 100%)
Gene names: MP160, MPN_682, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 1
Molecule details ›
Chain: 1
Length: 59 amino acids
Theoretical weight: 6.79 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75447 (Residues: 1-59; Coverage: 100%)
Gene names: MP038, MPN_116, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 2
Molecule details ›
Chain: 2
Length: 37 amino acids
Theoretical weight: 4.4 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P52864 (Residues: 1-37; Coverage: 100%)
Gene names: MP643, MPN_188, rpmJ
Sequence domains: Ribosomal protein L36
Elongation factor G Chain: 9
Molecule details ›
Chain: 9
Length: 688 amino acids
Theoretical weight: 76.6 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75544 (Residues: 1-688; Coverage: 100%)
Gene names: MP604, MPN_227, fus, fusA
Sequence domains:
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 294 amino acids
Theoretical weight: 33.47 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75560 (Residues: 1-294; Coverage: 100%)
Gene names: MP623, MPN_208, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: B
Molecule details ›
Chain: B
Length: 273 amino acids
Theoretical weight: 30.66 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P41205 (Residues: 1-273; Coverage: 100%)
Gene names: MP660, MPN_171, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 23.82 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P46775 (Residues: 1-205; Coverage: 100%)
Gene names: MP395, MPN_446, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: D
Molecule details ›
Chain: D
Length: 219 amino acids
Theoretical weight: 24.14 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50301 (Residues: 1-219; Coverage: 100%)
Gene names: MP649, MPN_182, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.43 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75543 (Residues: 1-215; Coverage: 100%)
Gene names: MP603, MPN_228, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.9 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75545 (Residues: 1-155; Coverage: 100%)
Gene names: MP605, MPN_226, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: G
Molecule details ›
Chain: G
Length: 142 amino acids
Theoretical weight: 15.9 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50304 (Residues: 1-142; Coverage: 100%)
Gene names: MP652, MPN_179, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: H
Molecule details ›
Chain: H
Length: 132 amino acids
Theoretical weight: 15.15 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75179 (Residues: 1-132; Coverage: 100%)
Gene names: MP226, MPN_616, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: I
Molecule details ›
Chain: I
Length: 108 amino acids
Theoretical weight: 12.23 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75581 (Residues: 1-108; Coverage: 100%)
Gene names: MP667, MPN_164, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: J
Molecule details ›
Chain: J
Length: 121 amino acids
Theoretical weight: 12.71 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50296 (Residues: 1-121; Coverage: 100%)
Gene names: MP641, MPN_190, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: K
Molecule details ›
Chain: K
Length: 139 amino acids
Theoretical weight: 15.67 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75546 (Residues: 1-139; Coverage: 100%)
Gene names: MP606, MPN_225, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: L
Molecule details ›
Chain: L
Length: 124 amino acids
Theoretical weight: 14.21 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50297 (Residues: 1-124; Coverage: 100%)
Gene names: MP642, MPN_189, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: M
Molecule details ›
Chain: M
Length: 61 amino acids
Theoretical weight: 6.9 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50305 (Residues: 1-61; Coverage: 100%)
Gene names: MP653, MPN_178, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: N
Molecule details ›
Chain: N
Length: 86 amino acids
Theoretical weight: 9.92 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75173 (Residues: 1-86; Coverage: 100%)
Gene names: MP220, MPN_622, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: O
Molecule details ›
Chain: O
Length: 94 amino acids
Theoretical weight: 10.81 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75131 (Residues: 1-88; Coverage: 100%)
Gene names: MP182, MPN_660, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: P
Molecule details ›
Chain: P
Length: 85 amino acids
Theoretical weight: 9.86 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50309 (Residues: 1-85; Coverage: 100%)
Gene names: MP657, MPN_174, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: Q
Molecule details ›
Chain: Q
Length: 104 amino acids
Theoretical weight: 12.41 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75541 (Residues: 1-104; Coverage: 100%)
Gene names: MP601, MPN_230, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: R
Molecule details ›
Chain: R
Length: 87 amino acids
Theoretical weight: 10.06 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75576 (Residues: 1-87; Coverage: 100%)
Gene names: MP662, MPN_169, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: S
Molecule details ›
Chain: S
Length: 87 amino acids
Theoretical weight: 9.99 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75237 (Residues: 1-87; Coverage: 100%)
Gene names: MP301, MPN_541, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: T
Molecule details ›
Chain: T
Length: 60 amino acids
Theoretical weight: 7.54 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P57079 (Residues: 1-60; Coverage: 100%)
Gene names: MP539.1, MPN_296, rpsU
Large ribosomal subunit protein bL12 Chain: W
Molecule details ›
Chain: W
Length: 122 amino acids
Theoretical weight: 13.12 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75239 (Residues: 1-122; Coverage: 100%)
Gene names: MP303, MPN_539, rplL
Sequence domains:
Large ribosomal subunit protein uL2 Chain: a
Molecule details ›
Chain: a
Length: 287 amino acids
Theoretical weight: 31.97 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75577 (Residues: 1-287; Coverage: 100%)
Gene names: MP663, MPN_168, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: b
Molecule details ›
Chain: b
Length: 287 amino acids
Theoretical weight: 31.3 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75580 (Residues: 1-287; Coverage: 100%)
Gene names: MP666, MPN_165, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: c
Molecule details ›
Chain: c
Length: 212 amino acids
Theoretical weight: 23.63 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75579 (Residues: 1-212; Coverage: 100%)
Gene names: MP665, MPN_166, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: d
Molecule details ›
Chain: d
Length: 180 amino acids
Theoretical weight: 20.27 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50306 (Residues: 1-180; Coverage: 100%)
Gene names: MP654, MPN_177, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: e
Molecule details ›
Chain: e
Length: 184 amino acids
Theoretical weight: 20.62 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50303 (Residues: 1-184; Coverage: 100%)
Gene names: MP651, MPN_180, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: f
Molecule details ›
Chain: f
Length: 149 amino acids
Theoretical weight: 17.19 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75540 (Residues: 1-149; Coverage: 100%)
Gene names: MP600, MPN_231, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chain: g
Molecule details ›
Chain: g
Length: 161 amino acids
Theoretical weight: 17.65 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75240 (Residues: 1-161; Coverage: 100%)
Gene names: MP304, MPN_538, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: h
Molecule details ›
Chain: h
Length: 137 amino acids
Theoretical weight: 14.8 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75550 (Residues: 1-137; Coverage: 100%)
Gene names: MP612, MPN_219, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: i
Molecule details ›
Chain: i
Length: 146 amino acids
Theoretical weight: 16.82 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75178 (Residues: 1-146; Coverage: 100%)
Gene names: MP225, MPN_617, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: j
Molecule details ›
Chain: j
Length: 122 amino acids
Theoretical weight: 13.48 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50308 (Residues: 1-122; Coverage: 100%)
Gene names: MP656, MPN_175, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: k
Molecule details ›
Chain: k
Length: 151 amino acids
Theoretical weight: 16.77 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50300 (Residues: 1-151; Coverage: 100%)
Gene names: MP648, MPN_183, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: l
Molecule details ›
Chain: l
Length: 139 amino acids
Theoretical weight: 15.65 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P41204 (Residues: 1-139; Coverage: 100%)
Gene names: MP659, MPN_172, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: m
Molecule details ›
Chain: m
Length: 124 amino acids
Theoretical weight: 14.27 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q59547 (Residues: 1-124; Coverage: 100%)
Gene names: MP639, MPN_192, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: n
Molecule details ›
Chain: n
Length: 116 amino acids
Theoretical weight: 13.07 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50302 (Residues: 1-116; Coverage: 100%)
Gene names: MP650, MPN_181, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: o
Molecule details ›
Chain: o
Length: 119 amino acids
Theoretical weight: 13.87 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75133 (Residues: 1-119; Coverage: 100%)
Gene names: MP184, MPN_658, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: p
Molecule details ›
Chain: p
Length: 127 amino acids
Theoretical weight: 14.74 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P78023 (Residues: 1-127; Coverage: 100%)
Gene names: MP037, MPN_117, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: q
Molecule details ›
Chain: q
Length: 100 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P78026 (Residues: 1-100; Coverage: 100%)
Gene names: MP511, MPN_325, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: r
Molecule details ›
Chain: r
Length: 159 amino acids
Theoretical weight: 17.36 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75575 (Residues: 1-159; Coverage: 100%)
Gene names: MP661, MPN_170, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: s
Molecule details ›
Chain: s
Length: 237 amino acids
Theoretical weight: 25.89 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75578 (Residues: 1-237; Coverage: 100%)
Gene names: MP664, MPN_167, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: t
Molecule details ›
Chain: t
Length: 111 amino acids
Theoretical weight: 12.46 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50307 (Residues: 1-111; Coverage: 100%)
Gene names: MP655, MPN_176, rplX
Sequence domains:
Large ribosomal subunit protein bL27 Chain: u
Molecule details ›
Chain: u
Length: 104 amino acids
Theoretical weight: 11.53 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75458 (Residues: 1-104; Coverage: 100%)
Gene names: MP509, MPN_327, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: v
Molecule details ›
Chain: v
Length: 65 amino acids
Theoretical weight: 7.55 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75171 (Residues: 1-65; Coverage: 100%)
Gene names: MP218, MPN_624, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: w
Molecule details ›
Chain: w
Length: 111 amino acids
Theoretical weight: 13 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: Q50310 (Residues: 1-111; Coverage: 100%)
Gene names: MP658, MPN_173, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein bL31 Chain: x
Molecule details ›
Chain: x
Length: 97 amino acids
Theoretical weight: 10.98 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P78020 (Residues: 1-97; Coverage: 100%)
Gene names: MP476, MPN_360, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: y
Molecule details ›
Chain: y
Length: 57 amino acids
Theoretical weight: 6.64 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P75238 (Residues: 1-57; Coverage: 100%)
Gene names: MP302, MPN_540, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33A Chain: z
Molecule details ›
Chain: z
Length: 53 amino acids
Theoretical weight: 6.3 KDa
Source organism: Mycoplasmoides pneumoniae M129
UniProt:
  • Canonical: P78015 (Residues: 1-53; Coverage: 100%)
Gene names: MP370, MPN_471, rpmG, rpmG1
Sequence domains: Ribosomal protein L33
23S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 2907 nucleotides
Theoretical weight: 940.91 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 4
Molecule details ›
Chain: 4
Length: 108 nucleotides
Theoretical weight: 34.8 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 1520 nucleotides
Theoretical weight: 491.24 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNA-Phe Chains: 7, 8
Molecule details ›
Chains: 7, 8
Length: 76 nucleotides
Theoretical weight: 24.47 KDa
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand SCM 1 x SCM
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.7Å
Relevant EMDB volumes: EMD-13435

Quick links

Citations

8 review citations

Z-RNA biology: a central role in the innate immune response?
Nichols et al. (2023)
7 more