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- PDB-7po4: Assembly intermediate of human mitochondrial ribosome large subun... -

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Basic information

Entry
Database: PDB / ID: 7po4
TitleAssembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP)
Components
  • (39S ribosomal protein ...) x 47
  • 16SrRNA
  • 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, mitochondrial
  • tRNAVal
KeywordsRIBOSOME / Small subunit / mitochondrion / biogenesis / maturation
Function / homology
Function and homology information


negative regulation of mitochondrial translation / iron-sulfur cluster assembly complex / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex I biogenesis / positive regulation of mitochondrial translation / Respiratory electron transport / mitochondrial transcription / rRNA import into mitochondrion ...negative regulation of mitochondrial translation / iron-sulfur cluster assembly complex / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex I biogenesis / positive regulation of mitochondrial translation / Respiratory electron transport / mitochondrial transcription / rRNA import into mitochondrion / rescue of stalled mitochondrial ribosome / mitochondrial translational termination / mitochondrial translational elongation / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit assembly / protein lipoylation / mitochondrial fission / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / mitochondrial ribosome / mitochondrial small ribosomal subunit / peptidyl-tRNA hydrolase activity / [2Fe-2S] cluster assembly / mitochondrial translation / iron-sulfur cluster assembly / ribosomal large subunit binding / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / acyl binding / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / anatomical structure morphogenesis / acyl carrier activity / RNA processing / Mitochondrial protein degradation / fatty acid binding / aerobic respiration / ribosomal large subunit biogenesis / mitochondrial membrane / fatty acid biosynthetic process / regulation of translation / double-stranded RNA binding / 5S rRNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / negative regulation of translation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / calcium ion binding / apoptotic process / positive regulation of DNA-templated transcription / structural molecule activity / mitochondrion / : / RNA binding / nucleoplasm / nucleus
Similarity search - Function
MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial ...MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L37 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / : / Large ribosomal subunit protein mL44, endonuclease domain / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / : / : / Large ribosomal subunit protein bL9m C-terminal domain / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L50, mitochondria / MRPL44, double-stranded RNA binding domain / Ribosomal subunit 39S / MRPL44 dsRNA-binding domain / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / : / Beta-grasp domain superfamily / NTF2-like domain superfamily / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Phosphopantetheine attachment site / Ribosomal protein L11, N-terminal
Similarity search - Domain/homology
Chem-8Q1 / FE2/S2 (INORGANIC) CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m ...Chem-8Q1 / FE2/S2 (INORGANIC) CLUSTER / : / 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 bL12m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL55 / 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 / Large ribosomal subunit protein mL38 / Mitochondrial assembly of ribosomal large subunit protein 1 / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL48 / 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 mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / 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 bL27m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsItoh, Y. / Khawaja, A. / Rorbach, J. / Amunts, A.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
The Swedish Foundation for Strategic ResearchFFL15:0325European Union
European Commission799399-ItohriboEuropean Union
CitationJournal: Nature / Year: 2022
Title: Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Authors: Yuzuru Itoh / Anas Khawaja / Ivan Laptev / Miriam Cipullo / Ilian Atanassov / Petr Sergiev / Joanna Rorbach / Alexey Amunts /
Abstract: Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) ...Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 2.0Jun 22, 2022Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.1Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16SrRNA
B: tRNAVal
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
J: 39S ribosomal protein L11, 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
8: 39S ribosomal protein L40, 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
e: 39S ribosomal protein L46, 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
k: 39S ribosomal protein L53, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
m: 39S ribosomal protein L55, 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
t: 39S ribosomal protein L12, mitochondrial
u: 39S ribosomal protein L12, mitochondrial
v: 39S ribosomal protein L12, mitochondrial
w: 39S ribosomal protein L12, mitochondrial
x: 39S ribosomal protein L12, mitochondrial
y: 39S ribosomal protein L12, mitochondrial
za: Mitochondrial assembly of ribosomal large subunit protein 1
zb: MIEF1 upstream open reading frame protein
zc: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,911,857106
Polymers1,909,91160
Non-polymers1,94546
Water45,8122543
1


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

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 16SrRNA


Mass: 500671.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human)
#2: RNA chain tRNAVal


Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human)

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39S ribosomal protein ... , 47 types, 52 molecules DEFHIJKLMNOPQRSTUVWXYZ01235678...

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


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#4: Protein 39S ribosomal protein L3, mitochondrial / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#5: Protein 39S ribosomal protein L4, mitochondrial / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein 39S ribosomal protein L9, mitochondrial / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#7: Protein 39S ribosomal protein L10, mitochondrial / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit ...MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#8: Protein 39S ribosomal protein L11, mitochondrial / MRP-L11 / Mitochondrial large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#9: Protein 39S ribosomal protein L13, mitochondrial / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20633.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#10: Protein 39S ribosomal protein L14, mitochondrial / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal ...MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#11: Protein 39S ribosomal protein L15, mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#12: Protein 39S ribosomal protein L16, mitochondrial / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#13: Protein 39S ribosomal protein L17, mitochondrial / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#14: Protein 39S ribosomal protein L18, mitochondrial / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#15: Protein 39S ribosomal protein L19, mitochondrial / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal ...MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#16: Protein 39S ribosomal protein L20, mitochondrial / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#17: Protein 39S ribosomal protein L21, mitochondrial / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#18: Protein 39S ribosomal protein L22, mitochondrial / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / MRP-L25 / Mitochondrial large ribosomal ...MRP-L22 / 39S ribosomal protein L25 / mitochondrial / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#19: Protein 39S ribosomal protein L23, mitochondrial / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / ...MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17718.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#20: Protein 39S ribosomal protein L24, mitochondrial / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#21: Protein 39S ribosomal protein L27, mitochondrial / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#22: Protein 39S ribosomal protein L28, mitochondrial / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#23: Protein 39S ribosomal protein L47, mitochondrial / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis- ...MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 29508.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#24: Protein 39S ribosomal protein L30, mitochondrial / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal ...MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#25: Protein 39S ribosomal protein L32, mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#26: Protein 39S ribosomal protein L33, mitochondrial / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#27: Protein 39S ribosomal protein L34, mitochondrial / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#28: Protein 39S ribosomal protein L35, mitochondrial / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#29: Protein 39S ribosomal protein L37, mitochondrial / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit ...MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#30: Protein 39S ribosomal protein L38, mitochondrial / MRP-L38 / Mitochondrial large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4
#31: Protein 39S ribosomal protein L39, mitochondrial / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit ...MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit protein mL39


Mass: 38764.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#32: Protein 39S ribosomal protein L40, mitochondrial / MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal- ...MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal-containing protein deleted in velocardiofacial syndrome / Up-regulated in metastasis


Mass: 24534.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NQ50
#33: Protein 39S ribosomal protein L41, mitochondrial / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 ...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: 15404.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#34: Protein 39S ribosomal protein L42, mitochondrial / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal ...MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal subunit protein mL42


Mass: 16691.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6G3
#35: Protein 39S ribosomal protein L43, mitochondrial / MRP-L43 / Mitochondrial large ribosomal subunit protein mL43 / Mitochondrial ribosomal protein bMRP36a


Mass: 23368.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#36: Protein 39S ribosomal protein L44, mitochondrial / MRP-L44 / Mitochondrial large ribosomal subunit protein mL44


Mass: 37583.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human)
References: UniProt: Q9H9J2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#37: Protein 39S ribosomal protein L45, mitochondrial / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 35402.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRJ2
#38: Protein 39S ribosomal protein L46, mitochondrial / MRP-L46 / Mitochondrial large ribosomal subunit protein mL46 / P2ECSL


Mass: 31748.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2W6
#39: Protein 39S ribosomal protein L48, mitochondrial / MRP-L48 / Mitochondrial large ribosomal subunit protein mL48


Mass: 23970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#40: Protein 39S ribosomal protein L49, mitochondrial / MRP-L49 / Mitochondrial large ribosomal subunit protein mL49 / Neighbor of FAU / NOF / Protein NOF1


Mass: 19225.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q13405
#41: Protein 39S ribosomal protein L50, mitochondrial / MRP-L50 / Mitochondrial large ribosomal subunit protein mL50


Mass: 18349.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5N7
#42: Protein 39S ribosomal protein L51, mitochondrial / MRP-L51 / Mitochondrial large ribosomal subunit protein mL51 / bMRP-64 / bMRP64


Mass: 15125.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q4U2R6
#43: Protein 39S ribosomal protein L52, mitochondrial / L52mt / MRP-L52 / Mitochondrial large ribosomal subunit protein mL52


Mass: 13682.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q86TS9
#44: Protein 39S ribosomal protein L53, mitochondrial / MRP-L53 / Mitochondrial large ribosomal subunit protein mL53


Mass: 12036.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL3
#45: Protein 39S ribosomal protein L54, mitochondrial / MRP-L54 / Mitochondrial large ribosomal subunit protein mL54


Mass: 15844.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P161
#46: Protein 39S ribosomal protein L55, mitochondrial / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal ...MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7F7
#50: Protein 39S ribosomal protein S18a, mitochondrial / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal ...S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal subunit protein bS18a / Mitochondrial large ribosomal subunit protein mL66


Mass: 22224.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVS2
#51: Protein 39S ribosomal protein S30, mitochondrial / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit ...S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit protein mS30 / Programmed cell death protein 9


Mass: 50429.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NP92
#52: Protein
39S ribosomal protein L12, mitochondrial / MRP-L12 / 5c5-2 / Mitochondrial large ribosomal subunit protein bL12m


Mass: 21378.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P52815

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Protein , 6 types, 6 molecules opqzazbzc

#47: Protein Ribosomal protein 63, mitochondrial / 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: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6
#48: Protein Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature ...39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature colon carcinoma transcript 1 protein / Mitochondrial large ribosomal subunit protein mL62


Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase
#49: 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-1 / p53-responsive gene 6 protein


Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#53: Protein Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3
#54: Protein MIEF1 upstream open reading frame protein


Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8
#55: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O14561

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Non-polymers , 6 types, 2589 molecules

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


Mass: 24.305 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#60: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2543 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Assembly intermediate of the large subunit of human mitochondrial ribosome
Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.20 Mpotassium chlorideKCl1
25.0 mMmagnesium acetateMg(CH3COO)21
325 mMHEPES-KOH buffer pH 7.51
40.05 % (w/v)n-dodecyl-beta-D-maltopyranosideC24H46O111
50.25 mM5'-guanylyl imidodiphosphateC10H17N6O13P31
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: 297 K

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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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 31 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 20583
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.9model fitting
9RELION3initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1073141
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180400 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6ZM6

6zm6


Accession code: 6ZM6 / Source name: PDB / Type: experimental model

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