› 6yws

Electron Microscopy
2.74Å resolution

The structure of the large subunit of the mitoribosome from Neurospora crassa

Released:
DOI: 10.2210/pdb6yws/pdb
PDB entry 6yws coloured by chain, front view.
PDB entry 6yws coloured by chain, side view.
PDB entry 6yws coloured by chain, top view.
Source organism: Neurospora crassa OR74A
Primary publication:
Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
OpenAccess logo Nat Commun 11 5187 (2020)
PMID: 33056988
Related structures: EMD-10973

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-245032 (preferred)
Entry contents:
44 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (45 distinct):
Large ribosomal subunit protein uL2m Chain: B
Molecule details ›
Chain: B
Length: 383 amino acids
Theoretical weight: 42.26 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SCX7 (Residues: 1-383; Coverage: 100%)
Gene names: NCU02757, rml2
Sequence domains:
Large ribosomal subunit protein uL3m Chain: C
Molecule details ›
Chain: C
Length: 384 amino acids
Theoretical weight: 41.26 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K8T6 (Residues: 1-384; Coverage: 100%)
Gene names: NCU06749, mrpl9
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: D
Molecule details ›
Chain: D
Length: 325 amino acids
Theoretical weight: 36.4 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: V5IMN1 (Residues: 1-325; Coverage: 100%)
Gene names: NCU01474, yml6
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5m Chain: E
Molecule details ›
Chain: E
Length: 352 amino acids
Theoretical weight: 39.17 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K6P0 (Residues: 1-352; Coverage: 100%)
Gene names: NCU04171, mrpl7
Sequence domains: ribosomal L5P family C-terminus
Large ribosomal subunit protein uL6m Chain: F
Molecule details ›
Chain: F
Length: 255 amino acids
Theoretical weight: 28.63 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RZF0 (Residues: 1-255; Coverage: 100%)
Gene names: NCU04068, mrpl6
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9m Chain: G
Molecule details ›
Chain: G
Length: 300 amino acids
Theoretical weight: 33.17 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S054 (Residues: 1-300; Coverage: 100%)
Gene names: NCU09999, mrpl50
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL10m Chain: f
Molecule details ›
Chain: f
Length: 347 amino acids
Theoretical weight: 37.36 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RZ62 (Residues: 1-347; Coverage: 100%)
Gene names: NCU04412, mrpl11
Large ribosomal subunit protein uL11m Chain: g
Molecule details ›
Chain: g
Length: 158 amino acids
Theoretical weight: 16.63 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RX40 (Residues: 1-158; Coverage: 100%)
Gene names: NCU04336, mrpl19
Sequence domains:
Large ribosomal subunit protein uL13m Chain: H
Molecule details ›
Chain: H
Length: 183 amino acids
Theoretical weight: 20.33 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SBV6 (Residues: 1-183; Coverage: 100%)
Gene names: NCU07852, mrpl23
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14m Chain: I
Molecule details ›
Chain: I
Length: 131 amino acids
Theoretical weight: 14.14 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SBJ8 (Residues: 1-131; Coverage: 100%)
Gene names: NCU08552, mrpl38
Sequence domains: Ribosomal protein L14p/L23e
Ribosomal protein L15 Chain: J
Molecule details ›
Chain: J
Length: 312 amino acids
Theoretical weight: 33.95 KDa
Source organism: Neurospora crassa OR74A
Large ribosomal subunit protein uL16m Chain: K
Molecule details ›
Chain: K
Length: 249 amino acids
Theoretical weight: 27.44 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: F5HIJ5 (Residues: 1-249; Coverage: 100%)
Gene names: NCU06768, mrpl16
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17m Chain: L
Molecule details ›
Chain: L
Length: 193 amino acids
Theoretical weight: 22.18 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K8C8 (Residues: 1-193; Coverage: 100%)
Gene names: NCU01023, mrpl8
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein bL19m Chain: M
Molecule details ›
Chain: M
Length: 258 amino acids
Theoretical weight: 28.24 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RYW8 (Residues: 1-258; Coverage: 100%)
Gene names: NCU06450, img1
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL21m Chain: N
Molecule details ›
Chain: N
Length: 217 amino acids
Theoretical weight: 23.95 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SGE5 (Residues: 1-217; Coverage: 100%)
Gene names: NCU00977, mrpl49
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22m Chain: O
Molecule details ›
Chain: O
Length: 364 amino acids
Theoretical weight: 41.57 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S5N0 (Residues: 1-364; Coverage: 100%)
Gene names: NCU05813, mrpl22
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23m Chain: P
Molecule details ›
Chain: P
Length: 228 amino acids
Theoretical weight: 26.01 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SA60 (Residues: 1-228; Coverage: 100%)
Gene names: NCU08329, mrp20
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24m Chain: Q
Molecule details ›
Chain: Q
Length: 396 amino acids
Theoretical weight: 45.46 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RXU7 (Residues: 1-396; Coverage: 100%)
Gene names: NCU01485, mrpl40
Sequence domains:
Large ribosomal subunit protein bL27m Chain: R
Molecule details ›
Chain: R
Length: 447 amino acids
Theoretical weight: 49.55 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K730 (Residues: 1-447; Coverage: 100%)
Gene names: NCU08861, mrp7
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28m Chain: S
Molecule details ›
Chain: S
Length: 274 amino acids
Theoretical weight: 31.5 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SC44 (Residues: 1-274; Coverage: 100%)
Gene names: NCU08410, mrpl24
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29m Chain: T
Molecule details ›
Chain: T
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S910 (Residues: 1-263; Coverage: 100%)
Gene names: NCU05287, mrpl4
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Large ribosomal subunit protein uL30m Chain: U
Molecule details ›
Chain: U
Length: 161 amino acids
Theoretical weight: 18.2 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K8Y7 (Residues: 1-161; Coverage: 100%)
Gene names: NCU06786, mrpl33
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31m Chain: V
Molecule details ›
Chain: V
Length: 219 amino acids
Theoretical weight: 23.77 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K7L7 (Residues: 1-219; Coverage: 100%)
Gene names: NCU04138, mrpl36
Sequence domains: Ribosomal protein L31p, N-terminal
Large ribosomal subunit protein bL32m Chain: W
Molecule details ›
Chain: W
Length: 129 amino acids
Theoretical weight: 14.11 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K4P1 (Residues: 1-129; Coverage: 100%)
Gene names: NCU03516, mrpl32
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33m Chain: X
Molecule details ›
Chain: X
Length: 59 amino acids
Theoretical weight: 7.03 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: V5IM60 (Residues: 1-59; Coverage: 100%)
Gene names: NCU17114, mrpl39
Sequence domains: Ribosomal protein L33
Related to ribosomal protein L34, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 140 amino acids
Theoretical weight: 14.85 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q96U95 (Residues: 1-140; Coverage: 100%)
Gene name: B11N2.075
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL36m Chain: 0
Molecule details ›
Chain: 0
Length: 124 amino acids
Theoretical weight: 13.96 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S4E7 (Residues: 1-124; Coverage: 100%)
Gene names: NCU06038, rtc6
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein mL38 Chain: 1
Molecule details ›
Chain: 1
Length: 449 amino acids
Theoretical weight: 50.75 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RXV8 (Residues: 1-449; Coverage: 100%)
Gene names: NCU01473, mrpl35
Sequence domains: Phosphatidylethanolamine-binding protein
Uncharacterized protein Chain: 2
Molecule details ›
Chain: 2
Length: 370 amino acids
Theoretical weight: 41.5 KDa
Source organism: Neurospora crassa OR74A
Large ribosomal subunit protein mL41 Chain: 3
Molecule details ›
Chain: 3
Length: 103 amino acids
Theoretical weight: 11.8 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S5W0 (Residues: 1-103; Coverage: 100%)
Gene names: NCU07057, mrpl27
Sequence domains: Mitochondrial ribosomal protein L27
Large ribosomal subunit protein mL43 Chain: 4
Molecule details ›
Chain: 4
Length: 138 amino acids
Theoretical weight: 15.13 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S300 (Residues: 1-138; Coverage: 100%)
Gene names: NCU07549, mrpl51
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Large ribosomal subunit protein mL44 Chain: 5
Molecule details ›
Chain: 5
Length: 439 amino acids
Theoretical weight: 48.11 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SA88 (Residues: 1-439; Coverage: 100%)
Gene names: NCU08299, mrpl3
Sequence domains: Double-stranded RNA binding motif
Large ribosomal subunit protein mL46 Chain: 6
Molecule details ›
Chain: 6
Length: 368 amino acids
Theoretical weight: 41.32 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S1Z3 (Residues: 1-368; Coverage: 100%)
Gene names: NCU07560, mrpl17
Sequence domains:
Large ribosomal subunit protein mL49 Chain: 7
Molecule details ›
Chain: 7
Length: 165 amino acids
Theoretical weight: 18.18 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S518 (Residues: 1-165; Coverage: 100%)
Gene names: NCU05890, img2
Sequence domains: Mitochondrial large subunit ribosomal protein (Img2)
Large ribosomal subunit protein mL50 Chain: 8
Molecule details ›
Chain: 8
Length: 443 amino acids
Theoretical weight: 49.75 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S711 (Residues: 1-443; Coverage: 100%)
Gene names: NCU05552, mrpl13
Sequence domains: Ribosomal subunit 39S
Large ribosomal subunit protein mL53 Chain: h
Molecule details ›
Chain: h
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SGH0 (Residues: 1-98; Coverage: 100%)
Gene names: NCU00952, mrpl44
Sequence domains: 39S ribosomal protein L53/MRP-L53
Large ribosomal subunit protein mL54 Chain: i
Molecule details ›
Chain: i
Length: 218 amino acids
Theoretical weight: 23.18 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7SCZ3 (Residues: 1-218; Coverage: 100%)
Gene names: NCU03094, mrpl37
Sequence domains: Mitochondrial ribosomal protein L37
Large ribosomal subunit protein mL57 Chain: 9
Molecule details ›
Chain: 9
Length: 267 amino acids
Theoretical weight: 29.63 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7S1R6 (Residues: 1-267; Coverage: 100%)
Gene names: NCU09826, mrpl15
Sequence domains: Ribonuclease-III-like
Large ribosomal subunit protein mL58 Chain: a
Molecule details ›
Chain: a
Length: 225 amino acids
Theoretical weight: 25.44 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K6U7 (Residues: 1-225; Coverage: 100%)
Gene names: NCU04225, mrpl20
Sequence domains: Mitochondrial ribosomal protein subunit L20
Mitoc_mL59 domain-containing protein Chain: b
Molecule details ›
Chain: b
Length: 162 amino acids
Theoretical weight: 18.75 KDa
Source organism: Neurospora crassa OR74A
Large ribosomal subunit protein mL60 Chain: c
Molecule details ›
Chain: c
Length: 110 amino acids
Theoretical weight: 13.13 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: U9W8F2 (Residues: 1-110; Coverage: 100%)
Gene names: NCU00211, mrpl31
Sequence domains: Mitochondrial ribosomal protein L31
Large ribosomal subunit protein mL67 Chain: d
Molecule details ›
Chain: d
Length: 292 amino acids
Theoretical weight: 32.52 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RYM5 (Residues: 1-292; Coverage: 100%)
Gene names: NCU00103, mhr1
Sequence domains: Transcriptional regulation of mitochondrial recombination
Large ribosomal subunit protein uL1m Chain: e
Molecule details ›
Chain: e
Length: 303 amino acids
Theoretical weight: 33.33 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q1K699 (Residues: 1-303; Coverage: 100%)
Gene names: NCU08893, mrpl1
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein mL61 Chain: j
Molecule details ›
Chain: j
Length: 201 amino acids
Theoretical weight: 22.73 KDa
Source organism: Neurospora crassa OR74A
UniProt:
  • Canonical: Q7RWZ7 (Residues: 1-201; Coverage: 100%)
Gene names: NCU01650, mrp49
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
RNA (2820-MER) Chain: A
Molecule details ›
Chain: A
Length: 3464 nucleotides
Theoretical weight: 1114.86 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

5 bound ligands:
Ligand MG 163 x MG
Ligand SPM 1 x SPM
Ligand K 12 x K
Ligand ZN 2 x ZN
Ligand NAD 1 x NAD
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.74Å
Relevant EMDB volumes: EMD-10973

Quick links

Citations

3 review citations

The Diseased Mitoribosome.
Ferrari et al. (2021)
2 more

2 mentions without citation

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins.
Bykov et al. (2022)
1 more