[English] 日本語
Yorodumi
- EMDB-16547: Structure of human mitochondrial MRPP1-MRPP2 in complex with mito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16547
TitleStructure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile
Map data
Sample
  • Complex: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle
    • Complex: Human mitochondrial MRPP1-MRPP2
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: tRNA methyltransferase 10 homolog C
    • Complex: Mitochondrial pre-tRNAIle
      • RNA: Mitochondrial Precursor tRNA-Ile(5,4)
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsRNA maturation / RNA modification / mitochondrial tRNA / RNA methyltransferase / MRPP1 / MRPP2 / MRPP3 / RNA binding protein / m6A / RNA binding / RNA recognition
Function / homology
Function and homology information


brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / mitochondrial tRNA methylation / tRNA (adenine9-N1)-methyltransferase / mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / tRNA (adenine(9)-N1)-methyltransferase activity ...brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / mitochondrial tRNA methylation / tRNA (adenine9-N1)-methyltransferase / mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA (guanine9-N1)-methyltransferase / mitochondrial ribonuclease P complex / tRNA (guanosine(9)-N1)-methyltransferase activity / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / tRNA modification in the mitochondrion / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial tRNA 3'-end processing / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase (NAD+) activity / C21-steroid hormone metabolic process / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / L-isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / bile acid biosynthetic process / testosterone dehydrogenase (NAD+) activity / positive regulation of mitochondrial translation / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Branched-chain amino acid catabolism / estrogen metabolic process / fatty acid beta-oxidation / androgen metabolic process / mitochondrial nucleoid / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / mRNA processing / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. ...tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
tRNA methyltransferase 10 homolog C / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMEYNIER V / HARDWICK S / CATALA M / ROSKE J / OERUM S / CHIRGADZE D / BARRAUD P / LUISI B / TISNE C
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE07-0028 France
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for human mitochondrial tRNA maturation.
Authors: Vincent Meynier / Steven W Hardwick / Marjorie Catala / Johann J Roske / Stephanie Oerum / Dimitri Y Chirgadze / Pierre Barraud / Wyatt W Yue / Ben F Luisi / Carine Tisné /
Abstract: The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by ...The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by the mitochondrial endoribonucleases (mt-RNase), P and Z, releases all RNA species from the two RNA transcripts. The tRNAs then undergo 3'-CCA addition. In metazoan mitochondria, RNase P is a multi-enzyme assembly that comprises the endoribonuclease PRORP and a tRNA methyltransferase subcomplex. The requirement for this tRNA methyltransferase subcomplex for mt-RNase P cleavage activity, as well as the mechanisms of pre-tRNA 3'-cleavage and 3'-CCA addition, are still poorly understood. Here, we report cryo-EM structures that visualise four steps of mitochondrial tRNA maturation: 5' and 3' tRNA-end processing, methylation and 3'-CCA addition, and explain the defined sequential order of the tRNA processing steps. The methyltransferase subcomplex recognises the pre-tRNA in a distinct mode that can support tRNA-end processing and 3'-CCA addition, likely resulting from an evolutionary adaptation of mitochondrial tRNA maturation complexes to the structurally-fragile mitochondrial tRNAs. This subcomplex can also ensure a tRNA-folding quality-control checkpoint before the sequential docking of the maturation enzymes. Altogether, our study provides detailed molecular insight into RNA-transcript processing and tRNA maturation in human mitochondria.
History
DepositionJan 25, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16547.png

Downloads & links

-
Map

FileDownload / File: emd_16547.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 320 pix.
= 231.36 Å		0.72 Å/pix.
x 320 pix.
= 231.36 Å		0.72 Å/pix.
x 320 pix.
= 231.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.022064975 - 0.054834947
Average (Standard dev.)-0.000007821941 (±0.0018989918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 231.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_16547_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16547_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre...

EntireName: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle
Components
  • Complex: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle
    • Complex: Human mitochondrial MRPP1-MRPP2
      • Protein or peptide: 3-hydroxyacyl-CoA dehydrogenase type-2
      • Protein or peptide: tRNA methyltransferase 10 homolog C
    • Complex: Mitochondrial pre-tRNAIle
      • RNA: Mitochondrial Precursor tRNA-Ile(5,4)
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

-
Supramolecule #1: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre...

SupramoleculeName: Human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNAIle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 170 KDa

-
Supramolecule #2: Human mitochondrial MRPP1-MRPP2

SupramoleculeName: Human mitochondrial MRPP1-MRPP2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Mitochondrial pre-tRNAIle

SupramoleculeName: Mitochondrial pre-tRNAIle / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: 3-hydroxyacyl-CoA dehydrogenase type-2

MacromoleculeName: 3-hydroxyacyl-CoA dehydrogenase type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: 3-hydroxyacyl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.342254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SVKGLVAVIT GGASGLGLAT AERLVGQGAS AVLLDLPNSG GEAQAKKLGN NCVFAPADVT SEKDVQTALA LAKGKFGRVD VAVNCAGIA VASKTYNLKK GQTHTLEDFQ RVLDVNLMGT FNVIRLVAGE MGQNEPDQGG QRGVIINTAS VAAFEGQVGQ A AYSASKGG ...String:
SVKGLVAVIT GGASGLGLAT AERLVGQGAS AVLLDLPNSG GEAQAKKLGN NCVFAPADVT SEKDVQTALA LAKGKFGRVD VAVNCAGIA VASKTYNLKK GQTHTLEDFQ RVLDVNLMGT FNVIRLVAGE MGQNEPDQGG QRGVIINTAS VAAFEGQVGQ A AYSASKGG IVGMTLPIAR DLAPIGIRVM TIAPGLFGTP LLTSLPEKVC NFLASQVPFP SRLGDPAEYA HLVQAIIENP FL NGEVIRL DGAIRMQP

UniProtKB: 3-hydroxyacyl-CoA dehydrogenase type-2

-
Macromolecule #2: tRNA methyltransferase 10 homolog C

MacromoleculeName: tRNA methyltransferase 10 homolog C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.857826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KNFLFLRLWD RNMDIAMGWK GAQAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQ EKWDKLLLTS TEKSHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT E CLPLDKYL ...String:
KNFLFLRLWD RNMDIAMGWK GAQAMQFGQP LVFDMAYENY MKRKELQNTV SQLLESEGWN RRNVDPFHIY FCNLKIDGAL HRELVKRYQ EKWDKLLLTS TEKSHVDLFP KDSIIYLTAD SPNVMTTFRH DKVYVIGSFV DKSMQPGTSL AKAKRLNLAT E CLPLDKYL QWEIGNKNLT LDQMIRILLC LKNNGNWQEA LQFVPKRKHT GFL

UniProtKB: tRNA methyltransferase 10 homolog C

-
Macromolecule #3: Mitochondrial Precursor tRNA-Ile(5,4)

MacromoleculeName: Mitochondrial Precursor tRNA-Ile(5,4) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.118934 KDa
SequenceString:
GGGUAAGAAA UAUGUCUGAU AAAAGAGUUA CUUUGAUAGA GUAAAUAAUA GGAGCUUAAA CCCCCUUAUU UCUAGGAC

-
Macromolecule #4: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

-
Macromolecule #5: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO32-Amino-2-hydroxymethyl-propane-1,3-diol
100.0 mMNaClSodium chloride
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 3 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7onu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 141653
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 133.7 / Target criteria: Cross-correlation coefficient
Output model

PDB-8cbo:
Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more