› 3j6b

Electron Microscopy
3.2Å resolution

Structure of the yeast mitochondrial large ribosomal subunit

Released:
DOI: 10.2210/pdb3j6b/pdb
PDB entry 3j6b coloured by chain, front view.
PDB entry 3j6b coloured by chain, side view.
PDB entry 3j6b coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of the yeast mitochondrial large ribosomal subunit.
Amunts A, Brown A, Bai XC, Llácer JL, Hussain T, Emsley P, Long F, Murshudov G, Scheres SHW, Ramakrishnan V
Science 343 1485-1489 (2014)
PMID: 24675956
Related structures: EMD-2566

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 41-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126975 (preferred)
Entry contents:
39 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (41 distinct):
Large ribosomal subunit protein uL2m Chain: B
Molecule details ›
Chain: B
Length: 393 amino acids
Theoretical weight: 43.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32611 (Residues: 1-393; Coverage: 100%)
Gene names: RML2, SYGP-ORF37, YEL050C
Sequence domains:
Large ribosomal subunit protein uL3m Chain: C
Molecule details ›
Chain: C
Length: 269 amino acids
Theoretical weight: 29.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P31334 (Residues: 1-269; Coverage: 100%)
Gene names: G8520, MRPL9, YGR220C
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: D
Molecule details ›
Chain: D
Length: 286 amino acids
Theoretical weight: 32.01 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P51998 (Residues: 1-286; Coverage: 100%)
Gene names: YML025C, YML6
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5m Chain: E
Molecule details ›
Chain: E
Length: 292 amino acids
Theoretical weight: 33.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36519 (Residues: 1-292; Coverage: 100%)
Gene names: MRPL7, YD8419.04, YDR237W
Sequence domains:
Large ribosomal subunit protein uL6m Chain: F
Molecule details ›
Chain: F
Length: 214 amino acids
Theoretical weight: 23.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32904 (Residues: 1-214; Coverage: 100%)
Gene names: MRPL6, YHR147C
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9m Chain: G
Molecule details ›
Chain: G
Length: 139 amino acids
Theoretical weight: 16.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53724 (Residues: 1-139; Coverage: 100%)
Gene names: MRPL50, N3220, YNR022C
Large ribosomal subunit protein uL13m Chain: H
Molecule details ›
Chain: H
Length: 163 amino acids
Theoretical weight: 18.5 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12487 (Residues: 1-163; Coverage: 100%)
Gene names: MRPL23, O3530, YOR150W
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14m Chain: I
Molecule details ›
Chain: I
Length: 138 amino acids
Theoretical weight: 14.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35996 (Residues: 1-138; Coverage: 100%)
Gene names: MRPL34, MRPL38, YKL170W, YKL634
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15m Chain: J
Molecule details ›
Chain: J
Length: 322 amino acids
Theoretical weight: 36.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36520 (Residues: 1-322; Coverage: 100%)
Gene names: MRPL10, MRPL18, N0580, YNL284C
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16m Chain: K
Molecule details ›
Chain: K
Length: 232 amino acids
Theoretical weight: 26.57 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38064 (Residues: 1-232; Coverage: 100%)
Gene names: MRPL16, RML16, YBL038W, YBL0411
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: L
Molecule details ›
Chain: L
Length: 238 amino acids
Theoretical weight: 26.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22353 (Residues: 1-238; Coverage: 100%)
Gene names: HRD238, J1125, MRPL8, YJL063C
Sequence domains:
Large ribosomal subunit protein bL19m Chain: M
Molecule details ›
Chain: M
Length: 169 amino acids
Theoretical weight: 19.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25626 (Residues: 1-169; Coverage: 100%)
Gene names: IMG1, PETCR46, YCR046C, YCR46C
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL21m Chain: N
Molecule details ›
Chain: N
Length: 161 amino acids
Theoretical weight: 18.42 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40858 (Residues: 1-161; Coverage: 100%)
Gene names: J0904, MRPL49, YJL096W
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22m Chain: O
Molecule details ›
Chain: O
Length: 309 amino acids
Theoretical weight: 34.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53881 (Residues: 1-309; Coverage: 100%)
Gene names: MRPL22, N1657, YNL177C
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23m Chain: P
Molecule details ›
Chain: P
Length: 263 amino acids
Theoretical weight: 30.62 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32387 (Residues: 1-263; Coverage: 100%)
Gene names: D9509.23, MRP20, MRPL41, YDR405W
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24m Chain: Q
Molecule details ›
Chain: Q
Length: 297 amino acids
Theoretical weight: 33.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36534 (Residues: 1-297; Coverage: 100%)
Gene names: MRPL40, YPL173W
Large ribosomal subunit protein bL27m Chain: R
Molecule details ›
Chain: R
Length: 371 amino acids
Theoretical weight: 43.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P12687 (Residues: 1-371; Coverage: 100%)
Gene names: MRP7, MRPL2, N2007, YNL005C
Sequence domains:
Large ribosomal subunit protein bL28m Chain: S
Molecule details ›
Chain: S
Length: 258 amino acids
Theoretical weight: 30.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36525 (Residues: 1-258; Coverage: 100%)
Gene names: MRPL14, MRPL24, YM9646.05, YMR193W
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m Chain: T
Molecule details ›
Chain: T
Length: 319 amino acids
Theoretical weight: 37.02 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36517 (Residues: 1-319; Coverage: 100%)
Gene names: L9753.1, MRPL4, YLR439W
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: U
Molecule details ›
Chain: U
Length: 86 amino acids
Theoretical weight: 9.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20084 (Residues: 1-86; Coverage: 100%)
Gene names: MRPL33, YM8021.12, YMR286W
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31m Chain: V
Molecule details ›
Chain: V
Length: 177 amino acids
Theoretical weight: 20.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36531 (Residues: 1-177; Coverage: 100%)
Gene names: MRPL36, YBR0918, YBR122C
Sequence domains: Ribosomal protein L31p, N-terminal
Large ribosomal subunit protein bL32m Chain: W
Molecule details ›
Chain: W
Length: 183 amino acids
Theoretical weight: 21.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25348 (Residues: 1-183; Coverage: 100%)
Gene names: MRPL32, YCR003W, YCR041, YCR3W
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33m Chain: X
Molecule details ›
Chain: X
Length: 70 amino acids
Theoretical weight: 7.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36533 (Residues: 1-70; Coverage: 100%)
Gene names: MRPL39, YM9571.09C, YML009C
Large ribosomal subunit protein bL34m Chain: Y
Molecule details ›
Chain: Y
Length: 105 amino acids
Theoretical weight: 12.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04598 (Residues: 1-105; Coverage: 100%)
Gene names: YD9727.10, YDR115W
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35m Chain: Z
Molecule details ›
Chain: Z
Length: 115 amino acids
Theoretical weight: 13.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53921 (Residues: 1-115; Coverage: 100%)
Gene names: MRP35, N1901, YNL122C
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36m Chain: 0
Molecule details ›
Chain: 0
Length: 93 amino acids
Theoretical weight: 10.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O14464 (Residues: 1-93; Coverage: 100%)
Gene names: RTC6, TAE4, YPL183BW, YPL183W-A
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein mL38 Chain: 1
Molecule details ›
Chain: 1
Length: 367 amino acids
Theoretical weight: 42.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06678 (Residues: 1-367; Coverage: 100%)
Gene names: D9798.5, MRPL35, YDR322W
Sequence domains: Phosphatidylethanolamine-binding protein
Large ribosomal subunit protein mL40 Chain: 2
Molecule details ›
Chain: 2
Length: 147 amino acids
Theoretical weight: 17.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36527 (Residues: 1-147; Coverage: 100%)
Gene names: D8035.6, MRPL28, YDR462W
Sequence domains: Mitochondrial ribosomal protein L28
Large ribosomal subunit protein mL41 Chain: 3
Molecule details ›
Chain: 3
Length: 146 amino acids
Theoretical weight: 16.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36526 (Residues: 1-146; Coverage: 100%)
Gene names: MRPL27, YBR2019, YBR282W
Sequence domains: Mitochondrial ribosomal protein L27
Large ribosomal subunit protein mL43 Chain: 4
Molecule details ›
Chain: 4
Length: 140 amino acids
Theoretical weight: 16.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06090 (Residues: 1-140; Coverage: 100%)
Gene names: MRPL51, P8283.12, YPR100W
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: 5
Molecule details ›
Chain: 5
Length: 390 amino acids
Theoretical weight: 44.06 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36516 (Residues: 1-390; Coverage: 100%)
Gene names: MRPL3, YM9711.14, YMR024W
Sequence domains:
Large ribosomal subunit protein mL46 Chain: 6
Molecule details ›
Chain: 6
Length: 281 amino acids
Theoretical weight: 32.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36528 (Residues: 1-281; Coverage: 100%)
Gene names: MRPL17, MRPL30, N0864, YNL252C
Sequence domains: 39S mitochondrial ribosomal protein L46
Large ribosomal subunit protein mL49 Chain: 7
Molecule details ›
Chain: 7
Length: 146 amino acids
Theoretical weight: 16.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25642 (Residues: 1-146; Coverage: 100%)
Gene names: IMG2, YCR071C, YCR71C
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
Large ribosomal subunit protein mL50 Chain: 8
Molecule details ›
Chain: 8
Length: 264 amino acids
Theoretical weight: 30.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02204 (Residues: 1-264; Coverage: 100%)
Gene names: MRPL13, YK105, YKR006C
Sequence domains: Ribosomal subunit 39S
Large ribosomal subunit protein mL57 Chain: 9
Molecule details ›
Chain: 9
Length: 253 amino acids
Theoretical weight: 28.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36523 (Residues: 1-253; Coverage: 100%)
Gene names: MRPL15, YLR312BW, YLR312W-A
Sequence domains: Ribonuclease III domain
Large ribosomal subunit protein mL58 Chain: a
Molecule details ›
Chain: a
Length: 195 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22354 (Residues: 1-195; Coverage: 100%)
Gene names: MRPL20, YKR085C, YKR405
Sequence domains: Mitochondrial ribosomal protein subunit L20
Large ribosomal subunit protein mL59 Chain: b
Molecule details ›
Chain: b
Length: 157 amino acids
Theoretical weight: 18.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23369 (Residues: 1-157; Coverage: 100%)
Gene names: MRPL25, YGR076C, YMR26
Sequence domains: Mitochondrial ribosomal protein mL59
Large ribosomal subunit protein mL60 Chain: c
Molecule details ›
Chain: c
Length: 131 amino acids
Theoretical weight: 15.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14063 (Residues: 1-131; Coverage: 100%)
Gene names: MRPL31, YKL138C
Sequence domains: Mitochondrial ribosomal protein L31
Large ribosomal subunit protein mL67 Chain: d
Molecule details ›
Chain: d
Length: 226 amino acids
Theoretical weight: 26.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06630 (Residues: 1-226; Coverage: 100%)
Gene names: MHR1, XTC1, YDR296W
Sequence domains: Transcriptional regulation of mitochondrial recombination
21S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3296 nucleotides
Theoretical weight: 1057.81 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
E-site tRNA Chain: e
Molecule details ›
Chain: e
Length: 20 nucleotides
Theoretical weight: 6.45 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 110 x MG
Ligand NA 1 x NA
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-2566

Quick links

Citations

70 review citations

Cancer metabolism: a therapeutic perspective.
Martinez-Outschoorn et al. (2017)
69 more

12 mentions without citation

Structure of the yeast mitochondrial large ribosomal subunit.
Amunts et al. (2014)
11 more