[English] 日本語
Yorodumi
- PDB-7qh7: Cryo-EM structure of the human mtLSU assembly intermediate upon M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qh7
TitleCryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4
Components
  • (39S ribosomal protein ...) x 41
  • 16S ribosomal RNA
  • Acyl carrier protein, mitochondrial
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • MIEF1 upstream open reading frame protein
  • Mitochondrial assembly of ribosomal large subunit protein 1
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrialRibosome
  • mitochondrial tRNAVal
KeywordsRIBOSOME / Mitochondria / Assembly / Methyltransferase / MRM2 / RNA modification
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational elongation / iron-sulfur cluster assembly complex ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational elongation / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / [2Fe-2S] cluster assembly / Glyoxylate metabolism and glycine degradation / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial small ribosomal subunit / acyl binding / mitochondrial ribosome / iron-sulfur cluster assembly / acyl carrier activity / mitochondrial translation / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / ribosomal large subunit binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / RNA processing / aerobic respiration / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / small ribosomal subunit rRNA binding / fatty acid biosynthetic process / double-stranded RNA binding / 5S rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / calcium ion binding / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 ...MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Double-stranded RNA-binding domain / : / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / Beta-grasp domain superfamily / NTF2-like domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Nucleotidyltransferase superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL24m / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsRebelo-Guiomar, P. / Pellegrino, S. / Dent, K.C. / Warren, A.J. / Minczuk, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/4 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.
Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron ...Authors: Pedro Rebelo-Guiomar / Simone Pellegrino / Kyle C Dent / Aldema Sas-Chen / Leonor Miller-Fleming / Caterina Garone / Lindsey Van Haute / Jack F Rogan / Adam Dinan / Andrew E Firth / Byron Andrews / Alexander J Whitworth / Schraga Schwartz / Alan J Warren / Michal Minczuk /
Abstract: Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that ...Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by cryo-EM at the resolution of 2.6 Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module, allowing five mtLSU biogenesis intermediates with different intersubunit interface configurations to be placed along the assembly pathway. However, mitoribosome biogenesis does not depend on the methyltransferase activity of MRM2. Disruption of the MRM2 Drosophila melanogaster orthologue leads to mitochondria-related developmental arrest. This work identifies a key checkpoint during mtLSU assembly, essential to maintain mitochondrial homeostasis.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: 39S ribosomal protein L2, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
P: 39S ribosomal protein L18, mitochondrial
Q: 39S ribosomal protein L19, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
0: 39S ribosomal protein L32, mitochondrial
1: 39S ribosomal protein L33, mitochondrial
2: 39S ribosomal protein L34, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
7: 39S ribosomal protein L39, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
b: 39S ribosomal protein L43, mitochondrial
c: 39S ribosomal protein L44, mitochondrial
d: 39S ribosomal protein L45, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
j: 39S ribosomal protein L52, mitochondrial
o: Ribosomal protein 63, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
r: 39S ribosomal protein S18a, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
u: Mitochondrial assembly of ribosomal large subunit protein 1
v: MIEF1 upstream open reading frame protein
w: Acyl carrier protein, mitochondrial
A: 16S ribosomal RNA
B: mitochondrial tRNAVal
4: 39S ribosomal protein L36, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,248,836102
Polymers1,247,42449
Non-polymers1,41153
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
39S ribosomal protein ... , 41 types, 41 molecules DEFHIKLMNOPQRSTUVWXYZ01235679a...

#1: Protein 39S ribosomal protein L2, mitochondrial / Ribosome / L2mt / MRP-L2 / Mitochondrial large ribosomal subunit protein uL2m


Mass: 23834.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#2: Protein 39S ribosomal protein L3, mitochondrial / Ribosome / L3mt / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 34023.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#3: Protein 39S ribosomal protein L4, mitochondrial / Ribosome / L4mt / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 28528.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#4: Protein 39S ribosomal protein L9, mitochondrial / Ribosome / L9mt / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 11127.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#5: Protein/peptide 39S ribosomal protein L10, mitochondrial / Ribosome / L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / MRP-L8 / Mitochondrial large ...L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 3552.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#6: Protein 39S ribosomal protein L13, mitochondrial / Ribosome / L13mt / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20591.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#7: Protein 39S ribosomal protein L14, mitochondrial / Ribosome / L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Mitochondrial large ...L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 12710.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#8: Protein 39S ribosomal protein L15, mitochondrial / Ribosome / L15mt / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 32704.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#9: Protein 39S ribosomal protein L16, mitochondrial / Ribosome / L16mt / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 23069.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#10: Protein 39S ribosomal protein L17, mitochondrial / Ribosome / L17mt / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 17761.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#11: Protein 39S ribosomal protein L18, mitochondrial / Ribosome / L18mt / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 16335.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#12: Protein 39S ribosomal protein L19, mitochondrial / Ribosome / L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / Mitochondrial large ...L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 25674.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#13: Protein 39S ribosomal protein L20, mitochondrial / Ribosome / L20mt / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 16251.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#14: Protein 39S ribosomal protein L21, mitochondrial / Ribosome / L21mt / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 17794.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#15: Protein 39S ribosomal protein L22, mitochondrial / Ribosome / L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ...L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 19466.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#16: Protein 39S ribosomal protein L23, mitochondrial / Ribosome


Mass: 14562.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#17: Protein/peptide 39S ribosomal protein L24, mitochondrial / Ribosome / L24mt / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 5751.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#18: Protein 39S ribosomal protein L27, mitochondrial / Ribosome / L27mt / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 11364.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#19: Protein 39S ribosomal protein L28, mitochondrial / Ribosome / L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 28818.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#20: Protein 39S ribosomal protein L47, mitochondrial / Ribosome / L47mt / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma ...L47mt / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 21360.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#21: Protein 39S ribosomal protein L30, mitochondrial / Ribosome / L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Mitochondrial large ...L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 13332.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#22: Protein 39S ribosomal protein L32, mitochondrial / Ribosome / L32mt / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 12606.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#23: Protein/peptide 39S ribosomal protein L33, mitochondrial / Ribosome / L33mt / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 5831.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#24: Protein/peptide 39S ribosomal protein L34, mitochondrial / Ribosome / L34mt / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 5239.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#25: Protein 39S ribosomal protein L35, mitochondrial / Ribosome / L35mt / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 11788.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#26: Protein 39S ribosomal protein L37, mitochondrial / Ribosome / L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / Mitochondrial large ...L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 45302.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#27: Protein 39S ribosomal protein L38, mitochondrial / Ribosome


Mass: 34730.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#28: Protein 39S ribosomal protein L39, mitochondrial / Ribosome / L39mt / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / L5mt / MRP-L5 / Mitochondrial large ...L39mt / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / L5mt / MRP-L5 / Mitochondrial large ribosomal subunit protein mL39


Mass: 33289.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#29: Protein 39S ribosomal protein L41, mitochondrial / Ribosome / L41mt / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal ...L41mt / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 / Cell proliferation-inducing gene 3 protein / MRP-L27 homolog / Mitochondrial large ribosomal subunit protein mL41


Mass: 14032.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#30: Protein 39S ribosomal protein L42, mitochondrial / Ribosome


Mass: 9578.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#31: Protein 39S ribosomal protein L43, mitochondrial / Ribosome / L43mt / MRP-L43 / Mitochondrial large ribosomal subunit protein mL43 / Mitochondrial ribosomal protein bMRP36a


Mass: 16741.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#32: Protein 39S ribosomal protein L44, mitochondrial / Ribosome / L44mt / MRP-L44 / Mitochondrial large ribosomal subunit protein mL44


Mass: 32773.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9H9J2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#33: Protein 39S ribosomal protein L45, mitochondrial / Ribosome / L45mt / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 19852.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRJ2
#34: Protein/peptide 39S ribosomal protein L48, mitochondrial / Ribosome


Mass: 2019.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#35: Protein 39S ribosomal protein L49, mitochondrial / Ribosome / L49mt / MRP-L49 / Mitochondrial large ribosomal subunit protein mL49 / Neighbor of FAU / NOF / Protein NOF1


Mass: 15087.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13405
#36: Protein 39S ribosomal protein L50, mitochondrial / Ribosome / L50mt / MRP-L50 / Mitochondrial large ribosomal subunit protein mL50


Mass: 12107.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5N7
#37: Protein 39S ribosomal protein L51, mitochondrial / Ribosome / L51mt / MRP-L51 / Mitochondrial large ribosomal subunit protein mL51 / bMRP-64 / bMRP64


Mass: 11739.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q4U2R6
#38: Protein 39S ribosomal protein L52, mitochondrial / Ribosome / L52mt / MRP-L52 / Mitochondrial large ribosomal subunit protein mL52


Mass: 9801.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86TS9
#42: Protein 39S ribosomal protein S18a, mitochondrial / Ribosome / MRP-S18-a / Mrps18a / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / ...MRP-S18-a / Mrps18a / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal subunit protein bS18a / Mitochondrial large ribosomal subunit protein mL66


Mass: 16351.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVS2
#43: Protein 39S ribosomal protein S30, mitochondrial / Ribosome / MRP-S30 / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ...MRP-S30 / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit protein mS30 / Programmed cell death protein 9


Mass: 45204.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NP92
#49: Protein/peptide 39S ribosomal protein L36, mitochondrial / Ribosome / L36mt / MRP-L36 / BRCA1-interacting protein 1 / Mitochondrial large ribosomal subunit protein bL36m


Mass: 4768.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J6

-
Protein , 6 types, 6 molecules opquvw

#39: Protein Ribosomal protein 63, mitochondrial / Ribosome / hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / ...hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57


Mass: 9768.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6
#40: Protein Peptidyl-tRNA hydrolase ICT1, mitochondrial


Mass: 14901.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#41: Protein Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6- ...39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6-interacting factor 1 / CRIF1 / Mitochondrial large ribosomal subunit protein mL64 / Papillomavirus L2-interacting nuclear protein 1 / PLINP / PLINP-1 / p53-responsive gene 6 protein


Mass: 11942.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#44: Protein Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 13280.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3
#45: Protein MIEF1 upstream open reading frame protein / Alternative MIEF1 protein / AltMIEF1 / MIEF1 microprotein / MIEF1-MP


Mass: 8329.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8
#46: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 9144.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561

-
RNA chain , 2 types, 2 molecules AB

#47: RNA chain 16S ribosomal RNA /


Mass: 403061.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#48: RNA chain mitochondrial tRNAVal


Mass: 19530.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Non-polymers , 3 types, 67 molecules

#50: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: Mg
#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#52: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human mitochondrial ribosome large subunit / Type: RIBOSOME / Entity ID: #1-#49 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2709521
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224933 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5OOL

5ool

+
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