Uniprot accession / id : O08756  OR   Uniprot accession / id : Q99714
 
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Entry Information
Entry status  (1)
REL
(15)
 
Experimental methods  (2)
Electron Microscopy
(12)
X-ray diffraction
(3)
 
Authors  (91)
BARRAUD P
(4)
Barraud P
(4)
Bhatta A
(4)
CATALA M
(4)
CHIRGADZE D
(4)
Catala M
(4)
Chirgadze DY
(4)
HARDWICK S
(4)
Hallberg BM
(4)
Hardwick SW
(4)
Hillen HS
(4)
Hällberg BM
(4)
LUISI B
(4)
Luisi BF
(4)
MEYNIER V
(4)
Meynier V
(4)
OERUM S
(4)
Oerum S
(4)
ROSKE J
(4)
Roske JJ
(4)
TISNE C
(4)
Tisne C
(4)
Tisné C
(4)
Valentin Gese G
(4)
Valentín Gesé G
(4)
Yue WW
(4)
Bohnsack KE
(3)
Ditter K
(3)
Kuhle B
(3)
Spanaus L
(3)
Yu RD
(3)
ARROWSMITH C
(1)
Abreo MA
(1)
Agree CS
(1)
Arancio O
(1)
Arrowsmith C
(1)
Aust RM
(1)
Caspersen C
(1)
Chaney M
(1)
Chen X
(1)
Cirilli M
(1)
Cramer P
(1)
DEBRECZENI J
(1)
Debreczeni J
(1)
Dienemann C
(1)
EDWARDS A
(1)
Edwards A
(1)
Gunn-Moore F
(1)
KAVANAGH KL
(1)
Kavanagh KL
(1)
Kissinger CR
(1)
Kuppusamy P
(1)
Li B
(1)
Lin C
(1)
Liu S
(1)
Lue LF
(1)
Lustbader JW
(1)
Margosiak S
(1)
Meng JJ
(1)
OPPERMANN U
(1)
Oppermann U
(1)
Pelletier LA
(1)
Pollak S
(1)
Rejto PA
(1)
SCHOLER K
(1)
SHAFQAT N
(1)
SUNDSTROM M
(1)
Scholer K
(1)
Shafqat N
(1)
Showalter RE
(1)
Stern D
(1)
Structural Genomics Consortium (SGC)
(1)
Sundstrom M
(1)
Takuma K
(1)
Tempczyk-Russell A
(1)
Thomson JA
(1)
Trinchese F
(1)
Vanderpool D
(1)
Villafranca JE
(1)
WEIGELT J
(1)
Walker DG
(1)
Wang N
(1)
Weigelt J
(1)
Wu H
(1)
Xu HW
(1)
YU W
(1)
Yan SS
(1)
ZSCHOCKE J
(1)
Zewier ZL
(1)
Zschocke J
(1)
von Delft F
(1)
 
Homo / hetero assembly  (2)
hetero
(12)
homo
(3)
 
Assembly composition  (2)
RNA/protein complex
(12)
protein structure
(3)
 
Assembly polymer count  (3)
heptamer
(10)
tetramer
(3)
hexamer
(2)
 
Resolution distribution
1.0 - 1.5
(1)
1.5 - 2
(2)
2.0 - 2.5
(1)
2.5 - 3
(7)
3.0 - 3.5
(4)
 
Release year distribution
2000 - 2005
(2)
2005 - 2010
(1)
2020 - 2025
(12)
2025 - 2030
(3)
 
Journal  (6)
EMBO J
(4)
Nat Commun
(4)
Nat Struct Mol Biol
(4)
J Mol Biol
(1)
Science
(1)
To be published
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(15)
 
Organism name  (1)
Homo sapiens
(15)
 
Molecule name  (15)
17-beta-estradiol 17-dehydrogenase
(15)
2-methyl-3-hydroxybutyryl-CoA dehydrogenase
(15)
3-alpha-(17-beta)-hydroxysteroid dehydrogenase (NAD(+))
(15)
3-hydroxy-2-methylbutyryl-CoA dehydrogenase
(15)
3-hydroxyacyl-CoA dehydrogenase type II
(15)
3-hydroxyacyl-CoA dehydrogenase type-2
(15)
3alpha(or 20beta)-hydroxysteroid dehydrogenase
(15)
7-alpha-hydroxysteroid dehydrogenase
(15)
Endoplasmic reticulum-associated amyloid beta-peptide-binding protein
(15)
MHBD
(15)
Mitochondrial RNase P protein 2
(15)
Mitochondrial ribonuclease P protein 2
(15)
Short chain dehydrogenase/reductase family 5C member 1
(15)
Short-chain type dehydrogenase/reductase XH98G2
(15)
Type II HADH
(15)
 
Molecule type  (1)
Protein
(15)
 
Gene names  (7)
ERAB
(15)
HADH2
(15)
HSD17B10
(15)
MRPP2
(15)
SCHAD
(15)
SDR5C1
(15)
XH98G2
(15)
 
Interacting Molecules  (15)
tRNA methyltransferase 10 homolog C
(12)
Zinc phosphodiesterase ELAC protein 2
(7)
Mitochondrial ribonuclease P catalytic subunit
(2)
mt-tRNA-His-CCA
(2)
CCA tRNA nucleotidyltransferase 1, mitochondrial
(1)
Human mitochondria tRNA-Tyr precursor with 3' trailer
(1)
Human mitochondrial tRNA-Gln precursor with 3' trailer RNA
(1)
Human mitochondrial tRNA-Tyr precursor with 3' trailer
(1)
Mitochondrial Precursor tRNA-His(0,Ser)
(1)
Mitochondrial Precursor tRNA-His(5,Ser)
(1)
Mitochondrial Precursor tRNA-Ile(0,0)
(1)
Mitochondrial Precursor tRNA-Ile(5,4)
(1)
Mitochondrial Precursor tRNA-Tyr
(1)
mt-tRNA-His
(1)
tRNA-His-tRNA-Ser
(1)
 
Interacting ligands  (5)
NAD : NICOTINAMIDE-ADENINE-DINUCLEOTIDE
(7)
CL : CHLORIDE ION
(1)
GOL : GLYCEROL
(1)
NA : SODIUM ION
(1)
TDT : 1-AZEPAN-1-YL-2-PHENYL-2-(4-THIOXO-1,4-DIHYDRO-PYRAZOLO[3,4-D]PYRIMIDIN-5-YL)ETHANONE ADDUCT
(1)
 
Function and Biology
EC number / name  (6)
1.1.1.159 : 7-alpha-hydroxysteroid dehydrogenase
(15)
1.1.1.178 : 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
(15)
1.1.1.239 : 3-alpha-(17-beta)-hydroxysteroid dehydrogenase (NAD(+))
(15)
1.1.1.35 : 3-hydroxyacyl-CoA dehydrogenase
(15)
1.1.1.53 : 3-alpha(or 20-beta)-hydroxysteroid dehydrogenase
(15)
1.1.1.62 : 17-beta-estradiol 17-dehydrogenase
(15)
 
Biological function  (15)
17-beta-hydroxysteroid dehydrogenase (NAD+) activity
(15)
3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity
(15)
3-hydroxyacyl-CoA dehydrogenase activity
(15)
RNA binding
(15)
androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity
(15)
chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity
(15)
cholate 7-alpha-dehydrogenase (NAD+) activity
(15)
estradiol 17-beta-dehydrogenase [NAD(P)+] activity
(15)
isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
(15)
oxidoreductase activity
(15)
protein binding
(15)
tRNA binding
(15)
testosterone dehydrogenase (NAD+) activity
(15)
testosterone dehydrogenase [NAD(P)+] activity
(15)
ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
(15)
 
Biological process  (16)
C21-steroid hormone metabolic process
(15)
androgen metabolic process
(15)
bile acid biosynthetic process
(15)
brexanolone metabolic process
(15)
estrogen metabolic process
(15)
fatty acid beta-oxidation
(15)
fatty acid metabolic process
(15)
isoleucine catabolic process
(15)
lipid metabolic process
(15)
mitochondrial tRNA 3'-end processing
(15)
mitochondrial tRNA 5'-end processing
(15)
mitochondrial tRNA methylation
(15)
mitochondrion organization
(15)
protein homotetramerization
(15)
steroid metabolic process
(15)
tRNA processing
(15)
 
Biological cell component  (7)
cytoplasm
(15)
mitochondrial matrix
(15)
mitochondrial nucleoid
(15)
mitochondrial ribonuclease P complex
(15)
mitochondrion
(15)
plasma membrane
(15)
tRNA methyltransferase complex
(15)
 
Compound cofactor class  (1)
Nicotinamide-adenine dinucleotide
(7)
 
Sequence and Structure classification
SCOP fold  (1)
NAD(P)-binding Rossmann-fold domains
(3)
 
SCOP family  (1)
Tyrosine-dependent oxidoreductases
(3)
 
CATH class  (1)
Alpha Beta
(3)
 
CATH topology  (1)
Rossmann fold
(3)
 
Pfam accession / name  (1)
PF00106 : adh_short
(15)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(3)
 
Diffraction radiation source type  (2)
Synchrotron
(2)
Rotating anode
(1)
 
Diffraction source  (3)
APS BEAMLINE 32-ID
(1)
RIGAKU RU200
(1)
SLS BEAMLINE X10SA
(1)
 
Synchrotron site  (2)
APS
(1)
SLS
(1)
 
Diffraction detector type  (2)
CCD
(1)
Image plate
(1)
 
Refinement software  (4)
CNS
(1)
PHENIX
(1)
REFMAC
(1)
SHELXL-97
(1)
 
EM microscope model  (2)
TFS KRIOS
(8)
FEI TITAN KRIOS
(4)
 
EM detector name  (2)
GATAN K3 (6k x 4k)
(8)
GATAN K3 BIOQUANTUM (6k x 4k)
(4)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 15
Entries 1 to 10 of 15
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Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant with ordered flexible arm and tRNA-Tyr precursor - (Composite model)
Bhatta A, Yu RD, Kuhle B, Hillen HS
Nat Struct Mol Biol (2025) [PMID: 39747487  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: ZN    SAH    ZN    SAH   
PDBe complex ID: PDB-CPX-284681 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
3.2Å resolution
Released: 8 Jan 2025
Model geometry
Fit model/data
Data not analysed
8rr4
8rr4
8rr4
Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant and tRNA-Gln precursor (Composite model)
Bhatta A, Yu RD, Kuhle B, Hillen HS
Nat Struct Mol Biol (2025) [PMID: 39747487  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: ZN    SAH    ZN    SAH   
PDBe complex ID: PDB-CPX-284680 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
3.4Å resolution
Released: 8 Jan 2025
Model geometry
Fit model/data
Data not analysed
8rr3
8rr3
8rr3
Human mitochondrial RNase Z complex with ELAC2-D550N catalytic mutant and tRNA-Tyr precursor (Composite model)
Bhatta A, Yu RD, Kuhle B, Hillen HS
Nat Struct Mol Biol (2025) [PMID: 39747487  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: ZN    SAH    ZN    SAH   
PDBe complex ID: PDB-CPX-286269 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
2.93Å resolution
Released: 8 Jan 2025
Model geometry
Fit model/data
Data not analysed
8rr1
8rr1
8rr1
Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-Tyr
Bhatta A, Dienemann C, Cramer P, Hillen HS
Nat Struct Mol Biol (2021) [PMID: 34489609  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    ZN    NAD    ZN    MG   
PDBe complex ID: PDB-CPX-127288 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    O15091   
Electron Microscopy
3Å resolution
Released: 11 Aug 2021
Model geometry
Fit model/data
Data not analysed
7onu
7onu
7onu
Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile
MEYNIER V, HARDWICK S, CATALA M, ROSKE J, OERUM S, CHIRGADZE D, BARRAUD P, LUISI B, TISNE C
Nat Commun (2024) [PMID: 38824131  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: SAH    NAD    SAH   
Assembly name: tRNA methyltransferase 10 homolog C and 3-hydroxyacyl-CoA dehydrogenase type-2 and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-274996 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3   
Electron Microscopy
3.2Å resolution
Released: 12 Jun 2024
Model geometry
Fit model/data
Data not analysed
8cbo
8cbo
8cbo
Human mitochondrial RNase Z with tRNA-His-CCA, SDR5C1/TRMT10C focus
Valentin Gese G, Hallberg BM
EMBO J (2024) [PMID: 39516281  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: MG    SAM    SAM    GTP    GTP    MG   
Assembly name: tRNA methyltransferase 10 homolog C and 3-hydroxyacyl-CoA dehydrogenase type-2 and RNA (Preferred)   search this complex
PDBe complex ID: PDB-CPX-281893 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3   
Electron Microscopy
1.9Å resolution
Released: 20 Nov 2024
Model geometry
Fit model/data
Data not analysed
9gch
9gch
9gch
Structure of human mitochondrial CCA-adding enzyme in complex with mitochondrial pre-tRNA-Ile
MEYNIER V, HARDWICK S, CATALA M, ROSKE J, OERUM S, CHIRGADZE D, BARRAUD P, LUISI B, TISNE C
Nat Commun (2024) [PMID: 38824131  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: CDP    SAH    NAD    SAH    CDP   
PDBe complex ID: PDB-CPX-274994 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q96Q11   
Electron Microscopy
3.14Å resolution
Released: 12 Jun 2024
Model geometry
Fit model/data
Data not analysed
8cbm
8cbm
8cbm
Human mitochondrial RNase Z with tRNA-His-CCA
Valentin Gese G, Hallberg BM
EMBO J (2024) [PMID: 39516281  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: SAM    SAM    ZN    GTP    ZN    GTP   
PDBe complex ID: PDB-CPX-281892 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
2.96Å resolution
Released: 27 Nov 2024
Model geometry
Fit model/data
Data not analysed
9ey2
9ey2
9ey2
Human mitochondrial RNase Z with tRNA-His precursor
Valentin Gese G, Hallberg BM
EMBO J (2024) [PMID: 39516281  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: ZN    GTP    SAH    ZN    GTP    SAH   
Modified residues: 1MA    1MA   
PDBe complex ID: PDB-CPX-281891 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
2.9Å resolution
Released: 13 Nov 2024
Model geometry
Fit model/data
Data not analysed
9ey1
9ey1
9ey1
Human mitochondrial RNase Z with tRNA-His
Valentin Gese G, Hallberg BM
EMBO J (2024) [PMID: 39516281  ]
Source organism: Homo sapiens  
Assembly composition: RNA/protein complex
Bound ligands: SAM    SAM    ZN    GTP    ZN    GTP   
PDBe complex ID: PDB-CPX-281890 (Preferred)   search this ID
PDBe-KB: Q99714    Q7L0Y3    Q9BQ52   
Electron Microscopy
2.78Å resolution
Released: 13 Nov 2024
Model geometry
Fit model/data
Data not analysed
9ey0
9ey0
9ey0
Entries 1 to 10 of 15
Entries 1 to 10 of 15