› 7pkt

Electron Microscopy
3Å resolution

Large subunit of the Chlamydomonas reinhardtii mitoribosome

Released:
DOI: 10.2210/pdb7pkt/pdb
PDB entry 7pkt coloured by chain, front view.
PDB entry 7pkt coloured by chain, side view.
PDB entry 7pkt coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
How to build a ribosome from RNA fragments in Chlamydomonas mitochondria.
Waltz F, Salinas-Giegé T, Englmeier R, Meichel H, Soufari H, Kuhn L, Pfeffer S, Förster F, Engel BD, Giegé P, Drouard L, Hashem Y
Nat Commun 12 7176 (2021)
PMID: 34887394
Related structures: EMD-13480

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
PDBe Complex ID:
PDB-CPX-104290 (preferred)
Entry contents:
45 distinct polypeptide molecules
9 distinct RNA molecules
Macromolecules (54 distinct):
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: a
Molecule details ›
Chain: a
Length: 383 amino acids
Theoretical weight: 41.09 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DL58 (Residues: 1-383; Coverage: 100%)
Gene name: CHLRE_07g348850v5
Sequence domains:
Mitochondrial ribosomal protein L3 Chain: b
Molecule details ›
Chain: b
Length: 417 amino acids
Theoretical weight: 44.94 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3E681 (Residues: 1-417; Coverage: 100%)
Gene name: CHLRE_01g022250v5
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: c
Molecule details ›
Chain: c
Length: 427 amino acids
Theoretical weight: 45.91 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3D422 (Residues: 1-427; Coverage: 100%)
Gene name: CHLRE_12g520400v5
Sequence domains: Ribosomal protein L4/L1 family
uL5m Chain: d
Molecule details ›
Chain: d
Length: 216 amino acids
Theoretical weight: 23.05 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DYN2 (Residues: 1-216; Coverage: 100%)
Gene name: CHLRE_03g196150v5
Large ribosomal subunit protein bL9c Chain: f
Molecule details ›
Chain: f
Length: 304 amino acids
Theoretical weight: 30.62 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DRF9 (Residues: 1-304; Coverage: 100%)
Gene name: CHLRE_06g307950v5
Sequence domains: Ribosomal protein L9, N-terminal domain
Mitochondrial ribosomal protein L13 Chain: i
Molecule details ›
Chain: i
Length: 277 amino acids
Theoretical weight: 29.71 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J810 (Residues: 1-277; Coverage: 100%)
Gene name: CHLRE_09g405200v5
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: j
Molecule details ›
Chain: j
Length: 120 amino acids
Theoretical weight: 13.36 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IYH4 (Residues: 1-120; Coverage: 100%)
Gene name: CHLRE_12g550650v5
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: k
Molecule details ›
Chain: k
Length: 337 amino acids
Theoretical weight: 35.53 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3D8F3 (Residues: 1-337; Coverage: 100%)
Gene name: CHLRE_11g476800v5
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Ribosomal_L16 domain-containing protein Chain: l
Molecule details ›
Chain: l
Length: 270 amino acids
Theoretical weight: 27.92 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DP67 (Residues: 1-270; Coverage: 100%)
Gene name: CHLRE_06g278224v5
Sequence domains: Ribosomal protein L16p/L10e
Mitochondrial ribosomal protein L17 Chain: m
Molecule details ›
Chain: m
Length: 183 amino acids
Theoretical weight: 21.38 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DXS2 (Residues: 1-157; Coverage: 100%)
Gene name: CHLRE_03g181350v5
Sequence domains: Ribosomal protein L17
Mitochondrial ribosomal protein L19 Chain: n
Molecule details ›
Chain: n
Length: 312 amino acids
Theoretical weight: 33.41 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8I7A8 (Residues: 1-312; Coverage: 100%)
Gene name: CHLRE_07g322500v5
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chain: o
Molecule details ›
Chain: o
Length: 115 amino acids
Theoretical weight: 13.14 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8HNL1 (Residues: 1-115; Coverage: 100%)
Gene name: CHLRE_01g052350v5
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21m Chain: p
Molecule details ›
Chain: p
Length: 370 amino acids
Theoretical weight: 40.17 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DDN8 (Residues: 1-370; Coverage: 100%)
Gene name: CHLRE_09g388550v5
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22m Chain: q
Molecule details ›
Chain: q
Length: 377 amino acids
Theoretical weight: 39.18 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DSG6 (Residues: 1-377; Coverage: 100%)
Gene name: CHLRE_05g242950v5
Sequence domains: Ribosomal protein L22p/L17e
Mitochondrial ribosomal protein L23 Chain: r
Molecule details ›
Chain: r
Length: 226 amino acids
Theoretical weight: 25.59 KDa
Source organism: Chlamydomonas reinhardtii
KOW domain-containing protein Chain: s
Molecule details ›
Chain: s
Length: 309 amino acids
Theoretical weight: 31.16 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DJU3 (Residues: 1-180; Coverage: 58%)
Gene name: CHLRE_07g330450v5
Sequence domains:
Large ribosomal subunit protein bL25 beta domain-containing protein Chain: t
Molecule details ›
Chain: t
Length: 366 amino acids
Theoretical weight: 38.73 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3E0K7 (Residues: 1-366; Coverage: 100%)
Gene name: CHLRE_02g081450v5
Sequence domains: Ribosomal protein TL5, C-terminal domain
Ribosomal protein L27 Chain: u
Molecule details ›
Chain: u
Length: 173 amino acids
Theoretical weight: 18.01 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3E880 (Residues: 1-167; Coverage: 100%)
Gene name: CHLRE_01g053600v5
Sequence domains: Ribosomal L27 protein
Mitochondrial ribosomal protein L28 Chain: v
Molecule details ›
Chain: v
Length: 153 amino acids
Theoretical weight: 17 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3D077 (Residues: 1-153; Coverage: 100%)
Gene name: CHLRE_13g579150v5
uL29m Chain: w
Molecule details ›
Chain: w
Length: 127 amino acids
Theoretical weight: 14.8 KDa
Source organism: Chlamydomonas reinhardtii
Large ribosomal subunit protein uL30m Chain: x
Molecule details ›
Chain: x
Length: 214 amino acids
Theoretical weight: 24.37 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DSP9 (Residues: 1-214; Coverage: 100%)
Gene name: CHLRE_05g234659v5
Sequence domains: Ribosomal protein L30p/L7e
bL32m Chain: y
Molecule details ›
Chain: y
Length: 123 amino acids
Theoretical weight: 13.37 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8JGW4 (Residues: 1-123; Coverage: 100%)
Gene name: CHLRE_12g558750v5
Sequence domains: Ribosomal L32p protein family
Mitochondrial ribosomal protein L33 Chain: z
Molecule details ›
Chain: z
Length: 59 amino acids
Theoretical weight: 6.86 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J9C3 (Residues: 1-59; Coverage: 100%)
Gene name: CHLRE_16g653601v5
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34m Chain: A
Molecule details ›
Chain: A
Length: 280 amino acids
Theoretical weight: 29.65 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3CX36 (Residues: 1-280; Coverage: 100%)
Gene name: CHLRE_14g608970v5
Sequence domains: Ribosomal protein L34
bL35m Chain: B
Molecule details ›
Chain: B
Length: 151 amino acids
Theoretical weight: 17.49 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DKX8 (Residues: 1-151; Coverage: 100%)
Gene name: CHLRE_07g345850v5
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: e
Molecule details ›
Chain: e
Length: 207 amino acids
Theoretical weight: 22.28 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J503 (Residues: 1-207; Coverage: 100%)
Gene name: CHLRE_09g415950v5
Sequence domains: Ribosomal protein L6
mL40 Chain: D
Molecule details ›
Chain: D
Length: 172 amino acids
Theoretical weight: 17.75 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3D9N2 (Residues: 1-172; Coverage: 100%)
Gene name: CHLRE_10g428350v5
mL41 Chain: E
Molecule details ›
Chain: E
Length: 112 amino acids
Theoretical weight: 12.62 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J2J1 (Residues: 1-112; Coverage: 100%)
Gene name: CHLRE_06g291300v5
mL43 Chain: F
Molecule details ›
Chain: F
Length: 141 amino acids
Theoretical weight: 16.22 KDa
Source organism: Chlamydomonas reinhardtii
Mitochondrial ribosomal protein L17 Chain: G
Molecule details ›
Chain: G
Length: 259 amino acids
Theoretical weight: 27.32 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IWI1 (Residues: 1-259; Coverage: 100%)
Gene name: CHLRE_03g193550v5
mL63/57/60 Chain: I
Molecule details ›
Chain: I
Length: 132 amino acids
Theoretical weight: 14.65 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8IS96 (Residues: 1-132; Coverage: 100%)
Gene name: CHLRE_16g684950v5
mL59/64 Chain: J
Molecule details ›
Chain: J
Length: 134 amino acids
Theoretical weight: 14.37 KDa
Source organism: Chlamydomonas reinhardtii
mL80 Chain: K
Molecule details ›
Chain: K
Length: 249 amino acids
Theoretical weight: 27.18 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DBX4 (Residues: 1-249; Coverage: 100%)
Gene name: CHLRE_10g461650v5
mL87 Chain: L
Molecule details ›
Chain: L
Length: 206 amino acids
Theoretical weight: 23.54 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J535 (Residues: 1-206; Coverage: 100%)
Gene name: CHLRE_09g417100v5
bL36m Chain: C
Molecule details ›
Chain: C
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Chlamydomonas reinhardtii
mL113 Chain: M
Molecule details ›
Chain: M
Length: 876 amino acids
Theoretical weight: 84.44 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DVD3 (Residues: 1-523; Coverage: 60%)
Gene name: CHLRE_03g145867v5
mL114 Chain: N
Molecule details ›
Chain: N
Length: 455 amino acids
Theoretical weight: 48.76 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DR53 (Residues: 1-455; Coverage: 100%)
Gene name: CHLRE_06g303850v5
mL115 Chain: O
Molecule details ›
Chain: O
Length: 688 amino acids
Theoretical weight: 72.34 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A8J070 (Residues: 1-596; Coverage: 87%)
Gene name: CHLRE_09g392579v5
mL116 Chain: P
Molecule details ›
Chain: P
Length: 530 amino acids
Theoretical weight: 53.02 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DXQ3 (Residues: 1-530; Coverage: 100%)
Gene name: CHLRE_03g179901v5
mL117 Chain: Q
Molecule details ›
Chain: Q
Length: 820 amino acids
Theoretical weight: 75.8 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3CXJ4 (Residues: 1-693; Coverage: 85%)
Gene name: CHLRE_14g615450v5
mL118 Chain: R
Molecule details ›
Chain: R
Length: 653 amino acids
Theoretical weight: 64.12 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3DTE5 (Residues: 1-477; Coverage: 73%)
Gene name: CHLRE_04g217904v5
Flagellar associated protein Chain: S
Molecule details ›
Chain: S
Length: 334 amino acids
Theoretical weight: 36.81 KDa
Source organism: Chlamydomonas reinhardtii
UniProt:
  • Canonical: A0A2K3D424 (Residues: 1-334; Coverage: 100%)
Gene name: CHLRE_12g521050v5
Unk1 Chain: X
Molecule details ›
Chain: X
Length: 31 amino acids
Theoretical weight: 2.66 KDa
Source organism: Chlamydomonas reinhardtii
PPR* Chain: Y
Molecule details ›
Chain: Y
Length: 172 amino acids
Theoretical weight: 14.66 KDa
Source organism: Chlamydomonas reinhardtii
Unk2 Chain: Z
Molecule details ›
Chain: Z
Length: 49 amino acids
Theoretical weight: 4.19 KDa
Source organism: Chlamydomonas reinhardtii
L1 rRNA Chain: 1
Molecule details ›
Chain: 1
Length: 162 nucleotides
Theoretical weight: 51.98 KDa
L2a rRNA Chain: 2
Molecule details ›
Chain: 2
Length: 86 nucleotides
Theoretical weight: 27.51 KDa
L3a rRNA (5S) Chain: 0
Molecule details ›
Chain: 0
Length: 75 nucleotides
Theoretical weight: 24.03 KDa
L3b rRNA Chain: 3
Molecule details ›
Chain: 3
Length: 184 nucleotides
Theoretical weight: 59.4 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
L4 rRNA Chain: 4
Molecule details ›
Chain: 4
Length: 118 nucleotides
Theoretical weight: 38.25 KDa
L5 rRNA Chain: 5
Molecule details ›
Chain: 5
Length: 149 nucleotides
Theoretical weight: 47.72 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
L6 rRNA Chain: 6
Molecule details ›
Chain: 6
Length: 136 nucleotides
Theoretical weight: 43.92 KDa
L7 rRNA Chain: 7
Molecule details ›
Chain: 7
Length: 578 nucleotides
Theoretical weight: 186.48 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
L8 rRNA Chain: 8
Molecule details ›
Chain: 8
Length: 413 nucleotides
Theoretical weight: 132.91 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 69 x MG
Ligand FES 1 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-13480

Quick links

Citations

6 review citations

The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain.
Maclean et al. (2022)
5 more