› 3iy9

Electron Microscopy
14.1Å resolution

Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model

Released:
DOI: 10.2210/pdb3iy9/pdb
PDB entry 3iy9 coloured by chain, front view.
PDB entry 3iy9 coloured by chain, side view.
PDB entry 3iy9 coloured by chain, top view.
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)
Assembly name:
PDBe Complex ID:
PDB-CPX-130942 (preferred)
Entry contents:
19 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (20 distinct):
Large ribosomal subunit protein uL2m 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:
Large ribosomal subunit protein uL3 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
Large ribosomal subunit protein uL4m 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
Large ribosomal subunit protein bL9 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
Large ribosomal subunit protein uL11m 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:
Large ribosomal subunit protein uL13 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
Large ribosomal subunit protein uL14 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
Large ribosomal subunit protein uL15 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
Large ribosomal subunit protein uL16m 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
Large ribosomal subunit protein bL17m 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
Large ribosomal subunit protein bL20 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
Large ribosomal subunit protein bL21 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
Large ribosomal subunit protein uL22m 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
Large ribosomal subunit protein uL23 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
Large ribosomal subunit protein uL24m 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:
Large ribosomal subunit protein bL27m 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
Large ribosomal subunit protein uL29 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
Large ribosomal subunit protein uL30 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
Large ribosomal subunit protein bL33m 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

23 review citations

Mitochondrial evolution.
Gray MW. (2012)
22 more

2 mentions without citation

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