› 3iy9

Electron Microscopy
14.1Å resolution

Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model

Released:
DOI: 10.2210/pdb3iy9/pdb
PDB 3iy9 coloured by chain and viewed from the front.
PDB 3iy9 coloured by chain and viewed from the side.
PDB 3iy9 coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Structure of a mitochondrial ribosome with minimal RNA.
Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK
Proc. Natl. Acad. Sci. U.S.A. 106 9637-42 (2009)
PMID: 19497863
Related structures: EMD-5113

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
Entry contents:
19 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (20 distinct):
39S ribosomal protein L2, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 136 amino acids
Theoretical weight: 14.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2TA12 (Residues: 127-262; Coverage: 44%)
Gene name: MRPL2
Sequence domains:
50S ribosomal protein L3 Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
39S ribosomal protein L4, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 175 amino acids
Theoretical weight: 19.71 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYD3 (Residues: 97-271; Coverage: 56%)
Gene names: CDABP0091, CGI-28, MRPL4
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L9 Chain: H
Molecule details ›
Chain: H
Length: 60 amino acids
Theoretical weight: 6.58 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R1 (Residues: 1-60; Coverage: 40%)
Gene names: JW4161, b4203, rplI
Sequence domains: Ribosomal protein L9, N-terminal domain
39S ribosomal protein L11, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 145 amino acids
Theoretical weight: 15.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q2YDI0 (Residues: 13-157; Coverage: 76%)
Gene name: MRPL11
Sequence domains:
50S ribosomal protein L13 Chain: J
Molecule details ›
Chain: J
Length: 140 amino acids
Theoretical weight: 15.82 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AA10 (Residues: 1-140; Coverage: 99%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: K
Molecule details ›
Chain: K
Length: 121 amino acids
Theoretical weight: 13.32 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY3 (Residues: 2-122; Coverage: 98%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
39S ribosomal protein L16, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 118 amino acids
Theoretical weight: 13.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NX20 (Residues: 71-188; Coverage: 47%)
Gene names: MRPL16, PNAS-111
Sequence domains: Ribosomal protein L16p/L10e
39S ribosomal protein L17, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 116 amino acids
Theoretical weight: 13.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q3T0L3 (Residues: 11-127; Coverage: 67%)
Gene name: MRPL17
Sequence domains: Ribosomal protein L17
50S ribosomal protein L20 Chain: Q
Molecule details ›
Chain: Q
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: 99%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chain: R
Molecule details ›
Chain: R
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
39S ribosomal protein L22, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 110 amino acids
Theoretical weight: 12.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q3SZX5 (Residues: 67-176; Coverage: 54%)
Gene name: MRPL22
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chain: T
Molecule details ›
Chain: T
Length: 99 amino acids
Theoretical weight: 11.09 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-99; Coverage: 99%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
39S ribosomal protein L24, mitochondrial Chain: N
Molecule details ›
Chain: N
Length: 96 amino acids
Theoretical weight: 11.01 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q3SYS0 (Residues: 59-154; Coverage: 44%)
Gene name: MRPL24
Sequence domains:
39S ribosomal protein L27, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 69 amino acids
Theoretical weight: 7.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9P0M9 (Residues: 31-99; Coverage: 47%)
Gene names: HSPC250, MRPL27
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L29 Chain: X
Molecule details ›
Chain: X
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: Y
Molecule details ›
Chain: Y
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG51 (Residues: 2-59; Coverage: 98%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
39S ribosomal protein L33, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 52 amino acids
Theoretical weight: 6.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75394 (Residues: 9-60; Coverage: 80%)
Gene names: C2orf1, MRPL33
Sequence domains: Ribosomal protein L33
Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Chain: A
Molecule details ›
Chain: A
Length: 1027 nucleotides
Theoretical weight: 327.98 KDa
Sequence domains: Trypanosomatid mitochondrial large subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 14.1Å
Relevant EMDB volumes: EMD-5113

Quick links

Citations

22 review citations

Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes.
Scaltsoyiannes et al. (2022)
21 more

2 mentions without citation

Structure of a mitochondrial ribosome with minimal RNA.
Sharma et al. (2009)
1 more