› 6ywe

Electron Microscopy
2.99Å resolution

The structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state

Released:
DOI: 10.2210/pdb6ywe/pdb
PDB entry 6ywe coloured by chain, front view.
PDB entry 6ywe coloured by chain, side view.
PDB entry 6ywe coloured by chain, top view.
Source organism: Neurospora crassa
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-10965

Function and Biology Details

Reaction catalysed: 
3-hydroxy-2-methylpropanoyl-CoA + H(2)O = CoA + 3-hydroxy-2-methylpropanoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 84-mer (preferred)
PDBe Complex ID:
PDB-CPX-245944 (preferred)
Entry contents:
78 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (82 distinct):
Related to ribosomal protein L1 Chain: e
Molecule details ›
Chain: e
Length: 303 amino acids
Theoretical weight: 33.33 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q870V5 (Residues: 1-303; Coverage: 100%)
Gene name: B14A21.170
Sequence domains: Ribosomal protein L1p/L10e family
60S ribosomal protein L2, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 383 amino acids
Theoretical weight: 42.26 KDa
Source organism: Neurospora crassa
Related to ribosomal protein L3, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 384 amino acids
Theoretical weight: 41.26 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q873B3 (Residues: 1-384; Coverage: 100%)
Gene name: B24N11.110
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
UniProt:
  • Canonical: V5IMN1 (Residues: 1-325; Coverage: 100%)
Gene names: NCU01474, yml6
Sequence domains: Ribosomal protein L4/L1 family
Related to ribosomal protein L5, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 352 amino acids
Theoretical weight: 39.17 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q96U12 (Residues: 1-352; Coverage: 100%)
Gene name: B7A16.090
Sequence domains: ribosomal L5P family C-terminus
uL6m Chain: F
Molecule details ›
Chain: F
Length: 255 amino acids
Theoretical weight: 28.63 KDa
Source organism: Neurospora crassa
RIBOSOMAL_L9 domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 300 amino acids
Theoretical weight: 33.17 KDa
Source organism: Neurospora crassa
Related to ribosomal protein YmL11, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 347 amino acids
Theoretical weight: 37.36 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q6M9C4 (Residues: 1-347; Coverage: 100%)
Gene name: 29E8.010
uL11m Chain: g
Molecule details ›
Chain: g
Length: 158 amino acids
Theoretical weight: 16.63 KDa
Source organism: Neurospora crassa
uL13m Chain: H
Molecule details ›
Chain: H
Length: 183 amino acids
Theoretical weight: 20.33 KDa
Source organism: Neurospora crassa
Ribosomal protein L14 Chain: I
Molecule details ›
Chain: I
Length: 131 amino acids
Theoretical weight: 14.14 KDa
Source organism: Neurospora crassa
Ribosomal protein L15 Chain: J
Molecule details ›
Chain: J
Length: 312 amino acids
Theoretical weight: 33.95 KDa
Source organism: Neurospora crassa
Related to ribosomal protein L16, mitochondrial Chain: K
Molecule details ›
Chain: K
Length: 249 amino acids
Theoretical weight: 27.44 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8X081 (Residues: 1-249; Coverage: 100%)
Gene name: B14D6.470
Sequence domains: Ribosomal protein L16p/L10e
uL17m Chain: L
Molecule details ›
Chain: L
Length: 193 amino acids
Theoretical weight: 22.18 KDa
Source organism: Neurospora crassa
bL19m Chain: M
Molecule details ›
Chain: M
Length: 258 amino acids
Theoretical weight: 28.24 KDa
Source organism: Neurospora crassa
Large ribosomal subunit protein bL21m Chain: N
Molecule details ›
Chain: N
Length: 217 amino acids
Theoretical weight: 23.95 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q6MVF2 (Residues: 1-217; Coverage: 100%)
Gene name: B20J13.280
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
UniProt:
  • Canonical: Q7S5N0 (Residues: 1-364; Coverage: 100%)
Gene names: NCU05813, mrpl22
Sequence domains: Ribosomal protein L22p/L17e
uL23m Chain: P
Molecule details ›
Chain: P
Length: 228 amino acids
Theoretical weight: 26.01 KDa
Source organism: Neurospora crassa
KOW domain-containing protein Chain: Q
Molecule details ›
Chain: Q
Length: 396 amino acids
Theoretical weight: 45.46 KDa
Source organism: Neurospora crassa
Large ribosomal subunit protein bL27m Chain: R
Molecule details ›
Chain: R
Length: 447 amino acids
Theoretical weight: 49.55 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8X0Q2 (Residues: 1-447; Coverage: 100%)
Gene name: 5E6.150
Sequence domains: Ribosomal L27 protein
bL28m Chain: S
Molecule details ›
Chain: S
Length: 274 amino acids
Theoretical weight: 31.5 KDa
Source organism: Neurospora crassa
54S ribosomal protein L4, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 263 amino acids
Theoretical weight: 29.65 KDa
Source organism: Neurospora crassa
Large ribosomal subunit protein uL30m Chain: U
Molecule details ›
Chain: U
Length: 161 amino acids
Theoretical weight: 18.2 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8X098 (Residues: 1-161; Coverage: 100%)
Gene name: B14D6.300
Sequence domains: Ribosomal protein L30p/L7e
Related to ribosomal protein YmL36, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 219 amino acids
Theoretical weight: 23.77 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q9C2E5 (Residues: 1-219; Coverage: 100%)
Gene name: 9G6.200
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
UniProt:
  • Canonical: Q9HFL0 (Residues: 1-129; Coverage: null%)
Gene name: B11E6.060
Sequence domains: Ribosomal L32p protein family
bL33m Chain: X
Molecule details ›
Chain: X
Length: 59 amino acids
Theoretical weight: 7.03 KDa
Source organism: Neurospora crassa
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
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
UniProt:
  • Canonical: Q7S4E7 (Residues: 1-124; Coverage: 100%)
Gene names: NCU06038, rtc6
Sequence domains: Ribosomal protein L36
PEBP-like protein Chain: 1
Molecule details ›
Chain: 1
Length: 449 amino acids
Theoretical weight: 50.75 KDa
Source organism: Neurospora crassa
mL40 Chain: 2
Molecule details ›
Chain: 2
Length: 370 amino acids
Theoretical weight: 41.5 KDa
Source organism: Neurospora crassa
mL41 Chain: 3
Molecule details ›
Chain: 3
Length: 103 amino acids
Theoretical weight: 11.8 KDa
Source organism: Neurospora crassa
L51_S25_CI-B8 domain-containing protein Chain: 4
Molecule details ›
Chain: 4
Length: 138 amino acids
Theoretical weight: 15.13 KDa
Source organism: Neurospora crassa
Ribonuclease III Chain: 5
Molecule details ›
Chain: 5
Length: 439 amino acids
Theoretical weight: 48.11 KDa
Source organism: Neurospora crassa
MRP-L46 domain-containing protein Chain: 6
Molecule details ›
Chain: 6
Length: 368 amino acids
Theoretical weight: 41.32 KDa
Source organism: Neurospora crassa
Large ribosomal subunit protein mL49 Chain: 7
Molecule details ›
Chain: 7
Length: 165 amino acids
Theoretical weight: 18.18 KDa
Source organism: Neurospora crassa
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
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
UniProt:
  • Canonical: Q6MVH6 (Residues: 1-98; Coverage: 100%)
Gene name: B20J13.030
Sequence domains: 39S ribosomal protein L53/MRP-L53
mL54 Chain: i
Molecule details ›
Chain: i
Length: 218 amino acids
Theoretical weight: 23.18 KDa
Source organism: Neurospora crassa
RNase III domain-containing protein Chain: 9
Molecule details ›
Chain: 9
Length: 267 amino acids
Theoretical weight: 29.63 KDa
Source organism: Neurospora crassa
Related to ribosomal protein YmL20, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 225 amino acids
Theoretical weight: 25.44 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8NIR6 (Residues: 1-225; Coverage: 100%)
Gene name: G15D1.090
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
54S ribosomal protein L31, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 110 amino acids
Theoretical weight: 13.13 KDa
Source organism: Neurospora crassa
mL67 Chain: d
Molecule details ›
Chain: d
Length: 292 amino acids
Theoretical weight: 32.52 KDa
Source organism: Neurospora crassa
Large ribosomal subunit protein mL61 Chain: j
Molecule details ›
Chain: j
Length: 201 amino acids
Theoretical weight: 22.73 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7RWZ7 (Residues: 1-201; Coverage: 100%)
Gene names: NCU01650, mrp49
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
bS1m Chain: AA
Molecule details ›
Chain: AA
Length: 470 amino acids
Theoretical weight: 51.6 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein uS2m Chain: BB
Molecule details ›
Chain: BB
Length: 428 amino acids
Theoretical weight: 47.2 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: V5ILE0 (Residues: 1-428; Coverage: 100%)
Gene names: NCU12023, mrp4
Sequence domains: Ribosomal protein S2
Ribosomal protein S5 Chain: CC
Molecule details ›
Chain: CC
Length: 508 amino acids
Theoretical weight: 58.91 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: A0A1W5YJW8 (Residues: 1-508; Coverage: 100%)
Gene name: rps3
S4 RNA-binding domain-containing protein Chain: DD
Molecule details ›
Chain: DD
Length: 453 amino acids
Theoretical weight: 51.61 KDa
Source organism: Neurospora crassa
Related to ribosomal protein S5 (Mitochondrial) Chain: EE
Molecule details ›
Chain: EE
Length: 477 amino acids
Theoretical weight: 53.3 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8X048 (Residues: 1-477; Coverage: 100%)
Gene name: B1K11.100
Sequence domains:
Ribosomal protein S6 Chain: FF
Molecule details ›
Chain: FF
Length: 117 amino acids
Theoretical weight: 13.3 KDa
Source organism: Neurospora crassa
Ribosomal_S7 domain-containing protein Chain: GG
Molecule details ›
Chain: GG
Length: 309 amino acids
Theoretical weight: 33.82 KDa
Source organism: Neurospora crassa
uS8m Chain: HH
Molecule details ›
Chain: HH
Length: 161 amino acids
Theoretical weight: 17.74 KDa
Source organism: Neurospora crassa
uS9m Chain: II
Molecule details ›
Chain: II
Length: 315 amino acids
Theoretical weight: 35.32 KDa
Source organism: Neurospora crassa
30S ribosomal protein S10, mitochondrial Chain: JJ
Molecule details ›
Chain: JJ
Length: 268 amino acids
Theoretical weight: 30.38 KDa
Source organism: Neurospora crassa
Translational machinery component Chain: KK
Molecule details ›
Chain: KK
Length: 376 amino acids
Theoretical weight: 42.16 KDa
Source organism: Neurospora crassa
Ribosomal protein S12 Chain: LL
Molecule details ›
Chain: LL
Length: 174 amino acids
Theoretical weight: 18.66 KDa
Source organism: Neurospora crassa
Probable ribosomal protein S13 Chain: MM
Molecule details ›
Chain: MM
Length: 119 amino acids
Theoretical weight: 13.5 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q6MVY0 (Residues: 1-119; Coverage: 100%)
Gene name: B11E5.360
Sequence domains: Ribosomal protein S13/S18
Mitochondrial 37S ribosomal protein MRP2 Chain: NN
Molecule details ›
Chain: NN
Length: 113 amino acids
Theoretical weight: 13.21 KDa
Source organism: Neurospora crassa
Related to ribosomal protein S15 (Mitochondrial) Chain: OO
Molecule details ›
Chain: OO
Length: 320 amino acids
Theoretical weight: 35.8 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q8X067 (Residues: 1-320; Coverage: 100%)
Gene name: B19C19.050
Sequence domains: Ribosomal protein S15
bS16m Chain: PP
Molecule details ›
Chain: PP
Length: 107 amino acids
Theoretical weight: 12.14 KDa
Source organism: Neurospora crassa
uS17m Chain: QQ
Molecule details ›
Chain: QQ
Length: 165 amino acids
Theoretical weight: 18.51 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein bS18m Chain: RR
Molecule details ›
Chain: RR
Length: 256 amino acids
Theoretical weight: 28.47 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q872A7 (Residues: 1-256; Coverage: 100%)
Gene name: B11O8.090
Sequence domains: Ribosomal protein S18
Ribosomal protein S19/S15 Chain: SS
Molecule details ›
Chain: SS
Length: 91 amino acids
Theoretical weight: 10.41 KDa
Source organism: Neurospora crassa
bS21m Chain: TT
Molecule details ›
Chain: TT
Length: 236 amino acids
Theoretical weight: 25.68 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein mS23 Chain: UU
Molecule details ›
Chain: UU
Length: 253 amino acids
Theoretical weight: 29.55 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q873E4 (Residues: 1-128, 129-240; Coverage: 100%)
Gene names: NCU03343, rsm25
Sequence domains: Mitochondrial ribosomal protein S25
Small ribosomal subunit protein mS26 Chain: VV
Molecule details ›
Chain: VV
Length: 316 amino acids
Theoretical weight: 35.31 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7SHR9 (Residues: 1-316; Coverage: 100%)
Gene names: NCU02545, pet123
Small ribosomal subunit protein mS27 Chain: WW
Molecule details ›
Chain: WW
Length: 396 amino acids
Theoretical weight: 44.92 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7RYW7 (Residues: 1-396; Coverage: 100%)
Gene names: NCU06451, mrp13
Small ribosomal subunit protein mS29 Chain: XX
Molecule details ›
Chain: XX
Length: 469 amino acids
Theoretical weight: 51.45 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7SD06 (Residues: 1-469; Coverage: 100%)
Gene names: NCU08120, rsm23
Sequence domains: Mitochondrial ribosomal death-associated protein 3
mS33 Chain: YY
Molecule details ›
Chain: YY
Length: 108 amino acids
Theoretical weight: 12.17 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein mS35 Chain: ZZ
Molecule details ›
Chain: ZZ
Length: 382 amino acids
Theoretical weight: 44.06 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q9P5J2 (Residues: 1-382; Coverage: 100%)
Gene name: B23L21.370
Sequence domains: Mitochondrial ribosomal subunit protein
37S ribosomal protein mrp10, mitochondrial Chain: 11
Molecule details ›
Chain: 11
Length: 90 amino acids
Theoretical weight: 9.91 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein mS38 Chain: 22
Molecule details ›
Chain: 22
Length: 344 amino acids
Theoretical weight: 38.13 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7SHR6 (Residues: 1-344; Coverage: 100%)
Gene names: NCU02548, cox24
Sequence domains: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS41 Chain: 33
Molecule details ›
Chain: 33
Length: 236 amino acids
Theoretical weight: 26.61 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q9HE52 (Residues: 77-312; Coverage: 76%)
Gene name: B2F7.100
Sequence domains: IGR protein motif
Manganese and iron superoxide dismutase Chains: 44, 55
Molecule details ›
Chains: 44, 55
Length: 310 amino acids
Theoretical weight: 34.27 KDa
Source organism: Neurospora crassa
Small ribosomal subunit protein mS45 Chain: 66
Molecule details ›
Chain: 66
Length: 348 amino acids
Theoretical weight: 39.27 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q7SHB2 (Residues: 1-348; Coverage: 100%)
Gene names: NCU01894, mrps35
Sequence domains: Eukaryotic mitochondrial regulator protein
mS46 Chain: 77
Molecule details ›
Chain: 77
Length: 414 amino acids
Theoretical weight: 43.11 KDa
Source organism: Neurospora crassa
3-hydroxyisobutyryl-CoA hydrolase Chain: 88
Molecule details ›
Chain: 88
Length: 508 amino acids
Theoretical weight: 56.4 KDa
Source organism: Neurospora crassa
UniProt:
  • Canonical: Q9C251 (Residues: 1-508; Coverage: 100%)
Gene name: B18D24.230
Sequence domains: Enoyl-CoA hydratase/isomerase
IF1 Chains: 00, 99
Molecule details ›
Chains: 00, 99
Length: 95 amino acids
Theoretical weight: 10.66 KDa
Source organism: Neurospora crassa
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 3464 nucleotides
Theoretical weight: 1114.86 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
tRNA P/E state Chain: bb
Molecule details ›
Chain: bb
Length: 74 nucleotides
Theoretical weight: 23.71 KDa
Sequence domains: tRNA
16S ribosomal RNA Chain: aa
Molecule details ›
Chain: aa
Length: 1864 nucleotides
Theoretical weight: 600.34 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: ee
Molecule details ›
Chain: ee
Length: 11 nucleotides
Theoretical weight: 3.45 KDa

Ligands and Environments

6 bound ligands:
Ligand MG 242 x MG
Ligand SPM 1 x SPM
Ligand K 55 x K
Ligand ZN 2 x ZN
Ligand NAD 1 x NAD
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.99Å
Relevant EMDB volumes: EMD-10965

Quick links

Citations

3 review citations

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