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Basic information

Entry
Database: PDB / ID: 9rov
TitleAssembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA (Inward conformation) (State M2)
Components
  • (28S ribosomal protein ...) x 26
  • 12S mitochondrial rRNA
  • 12S rRNA N4-methylcytidine (m4C) methyltransferase
  • Aurora kinase A-interacting protein
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Putative ribosome-binding factor A, mitochondrial
  • Small ribosomal subunit protein bS21m
KeywordsRIBOSOME / mitochondrial gene expression / mitoribosome / mitoribosome assembly factors / cryoEM
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial small ribosomal subunit assembly / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / rRNA base methylation / mitochondrial ribosome / mitochondrial small ribosomal subunit ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial small ribosomal subunit assembly / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / rRNA base methylation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / sperm head-tail coupling apparatus / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / apoptotic signaling pathway / rRNA processing / cell junction / regulation of translation / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell population proliferation / mitochondrial inner membrane / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / protein domain specific binding / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / 28S ribosomal protein S26 ...Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Putative ribosome-binding factor A, mitochondrial / Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S22, mitochondrial / 28S ribosomal protein S10, mitochondrial / : / Mitochondrial 28S ribosomal protein S22 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S18b, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 28S ribosomal protein S24, mitochondrial / Mitochondrial 28S ribosomal protein S34 / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / : / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / 12S rRNA N(4)-cytidine methyltransferase METTL15 / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein uS10m / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS11m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein bS21m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Putative ribosome-binding factor A, mitochondrial / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein bS22, mitochondrial / Small ribosomal subunit protein mS33 / Small ribosomal subunit protein bS1m / Small ribosomal subunit protein uS17m / Small ribosomal subunit protein uS7m / Small ribosomal subunit protein uS2m / Small ribosomal subunit protein bS16m / Small ribosomal subunit protein bS18m / Small ribosomal subunit protein mS23 / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKhawaja, A. / Singh, V. / Shiriaev, D.I. / Rorbach, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation023405053 Sweden
CitationJournal: Nat Commun / Year: 2026
Title: Pseudouridine synthase PUS1 and initiation factor mtIF2 are human mitoribosomal small subunit assembly factors.
Authors: Vivek Singh / Dmitrii Shiriaev / Lorina Bilalli / Anas Khawaja / Joanna Rorbach /
Abstract: Assembly of the mitochondrial ribosome (mitoribosome) is a crucial step in mitochondrial gene expression. This process facilitates mitochondrial translation, which produces essential subunits of the ...Assembly of the mitochondrial ribosome (mitoribosome) is a crucial step in mitochondrial gene expression. This process facilitates mitochondrial translation, which produces essential subunits of the oxidative phosphorylation machinery-the cell's primary energy-producing machinery. Disruptions in mitoribosome assembly can lead to severe human diseases. Given its fundamental importance, detailed structural analysis of mitoribosome assembly pathways is essential for advancing our understanding of mitochondrial function in both health and disease. In this study, we characterize twelve distinct assembly states of the mitoribosomal small subunit (mtSSU) isolated from human cells. Our findings reveal the intricate details of the final maturation stages of the mtSSU platform, decoding center, and the 3'-end of 12S rRNA. This process is governed by coordinated actions of assembly factors that ensure precise, stepwise rRNA folding and the integration of mitoribosomal proteins into the developing subunit. Our approach identifies pseudouridine synthase PUS1 and initiation factor mtIF2 as assembly factors, expanding their known roles beyond mt-tRNA maturation and translation, respectively. In addition, the identified assembly intermediates provide insight into the modular nature of mtSSU biogenesis in mitochondria and further link late-stage assembly to the acquisition of translational competence.
History
DepositionJun 23, 2025Deposition site: PDBE / Processing site: PDBE
SupersessionJul 1, 2026ID: 9IGU
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 28S ribosomal protein S34, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
3: Aurora kinase A-interacting protein
B: 28S ribosomal protein S2, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
H: 28S ribosomal protein S10, mitochondrial
I: 28S ribosomal protein S11, mitochondrial
J: 28S ribosomal protein S12, mitochondrial
K: 28S ribosomal protein S14, mitochondrial
L: 28S ribosomal protein S15, mitochondrial
M: 28S ribosomal protein S16, mitochondrial
N: 28S ribosomal protein S17, mitochondrial
O: 28S ribosomal protein S18b, mitochondrial
P: 28S ribosomal protein S18c, mitochondrial
Q: Small ribosomal subunit protein bS21m
R: 28S ribosomal protein S22, mitochondrial
S: 28S ribosomal protein S23, mitochondrial
T: 28S ribosomal protein S25, mitochondrial
U: 28S ribosomal protein S26, mitochondrial
W: 28S ribosomal protein S28, mitochondrial
X: 28S ribosomal protein S29, mitochondrial
Y: 28S ribosomal protein S31, mitochondrial
Z: 28S ribosomal protein S33, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
G: 28S ribosomal protein S9, mitochondrial
V: 28S ribosomal protein S27, mitochondrial
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
b: 12S rRNA N4-methylcytidine (m4C) methyltransferase
A: 12S mitochondrial rRNA
a: Putative ribosome-binding factor A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,216,12677
Polymers1,212,86532
Non-polymers3,26045
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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28S ribosomal protein ... , 26 types, 26 molecules 01BCEFHIJKLMNOPRSTUWXYZDGV

#1: Protein 28S ribosomal protein S34, mitochondrial / S34mt / Mitochondrial small ribosomal subunit protein mS34


Mass: 25695.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82930
#2: Protein 28S ribosomal protein S35, mitochondrial / MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ...MRP-S35 / S35mt / 28S ribosomal protein S28 / mitochondrial / MRP-S28 / S28mt / Mitochondrial small ribosomal subunit protein mS35


Mass: 36898.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82673
#4: Protein 28S ribosomal protein S2, mitochondrial / MRP-S2 / S2mt / Mitochondrial small ribosomal subunit protein uS2m


Mass: 33298.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y399
#5: Protein 28S ribosomal protein S24, mitochondrial / MRP-S24 / S24mt / Mitochondrial small ribosomal subunit protein uS3m / bMRP-47 / bMRP47


Mass: 19046.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL2
#6: Protein 28S ribosomal protein S6, mitochondrial / MRP-S6 / S6mt / Mitochondrial small ribosomal subunit protein bS6m


Mass: 14250.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82932
#7: Protein 28S ribosomal protein S7, mitochondrial / MRP-S7 / S7mt / Mitochondrial small ribosomal subunit protein uS7m / bMRP-27a / bMRP27a


Mass: 28186.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R9
#8: Protein 28S ribosomal protein S10, mitochondrial / MRP-S10 / S10mt / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23033.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82664
#9: Protein 28S ribosomal protein S11, mitochondrial / MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal ...MRP-S11 / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal subunit protein uS11m


Mass: 20663.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82912
#10: Protein 28S ribosomal protein S12, mitochondrial / MRP-S12 / S12mt / MT-RPS12 / Mitochondrial small ribosomal subunit protein uS12m


Mass: 15200.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15235
#11: Protein 28S ribosomal protein S14, mitochondrial / MRP-S14 / S14mt / Mitochondrial small ribosomal subunit protein uS14m


Mass: 15168.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60783
#12: Protein 28S ribosomal protein S15, mitochondrial / MRP-S15 / S15mt / Mitochondrial small ribosomal subunit protein uS15m


Mass: 29903.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82914
#13: Protein 28S ribosomal protein S16, mitochondrial / MRP-S16 / S16mt / Mitochondrial small ribosomal subunit protein bS16m


Mass: 15371.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D3
#14: Protein 28S ribosomal protein S17, mitochondrial / MRP-S17 / S17mt / Mitochondrial small ribosomal subunit protein uS17m


Mass: 14526.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R5
#15: Protein 28S ribosomal protein S18b, mitochondrial / MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / ...MRP-S18-b / Mrps18-b / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / Mitochondrial small ribosomal subunit protein bS18b / Mitochondrial small ribosomal subunit protein mS40


Mass: 29440.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y676
#16: Protein 28S ribosomal protein S18c, mitochondrial / MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / ...MRP-S18-c / Mrps18-c / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / Mitochondrial small ribosomal subunit protein bS18c / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15876.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D5
#18: Protein 28S ribosomal protein S22, mitochondrial / MRP-S22 / S22mt / Mitochondrial small ribosomal subunit protein mS22


Mass: 41337.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82650
#19: Protein 28S ribosomal protein S23, mitochondrial / MRP-S23 / S23mt / Mitochondrial small ribosomal subunit protein mS23


Mass: 21805.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D9
#20: Protein 28S ribosomal protein S25, mitochondrial / MRP-S25 / S25mt / Mitochondrial small ribosomal subunit protein mS25


Mass: 20146.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82663
#21: Protein 28S ribosomal protein S26, mitochondrial / MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ...MRP-S26 / S26mt / 28S ribosomal protein S13 / mitochondrial / MRP-S13 / S13mt / Mitochondrial small ribosomal subunit protein mS26


Mass: 24259.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYN8
#22: Protein 28S ribosomal protein S28, mitochondrial / MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ...MRP-S28 / S28mt / 28S ribosomal protein S35 / mitochondrial / MRP-S35 / S35mt / Mitochondrial small ribosomal subunit protein bS1m


Mass: 20878.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2Q9
#23: Protein 28S ribosomal protein S29, mitochondrial / MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring ...MRP-S29 / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein / Mitochondrial small ribosomal subunit protein mS29


Mass: 45634.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51398
#24: Protein 28S ribosomal protein S31, mitochondrial / MRP-S31 / S31mt / Imogen 38 / Mitochondrial small ribosomal subunit protein mS31


Mass: 45391.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92665
#25: Protein 28S ribosomal protein S33, mitochondrial / MRP-S33 / S33mt / Mitochondrial small ribosomal subunit protein mS33


Mass: 12657.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y291
#26: Protein 28S ribosomal protein S5, mitochondrial / MRP-S5 / S5mt / Mitochondrial small ribosomal subunit protein uS5m


Mass: 48094.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82675
#27: Protein 28S ribosomal protein S9, mitochondrial / MRP-S9 / S9mt / Mitochondrial small ribosomal subunit protein uS9m


Mass: 45909.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82933
#28: Protein 28S ribosomal protein S27, mitochondrial / MRP-S27 / S27mt / Mitochondrial ribosomal protein S27 / Mitochondrial small ribosomal subunit protein mS27


Mass: 47669.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92552

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Protein , 5 types, 5 molecules 3Q4ba

#3: Protein Aurora kinase A-interacting protein / AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial ...AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial small ribosomal subunit protein mS38


Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8
#17: Protein Small ribosomal subunit protein bS21m / 28S ribosomal protein S21 / mitochondrial / MRP-S21 / S21mt


Mass: 10659.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P82921
#29: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein mS39 / Transformation-related gene 15 protein / TRG-15


Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7
#30: Protein 12S rRNA N4-methylcytidine (m4C) methyltransferase / 12S rRNA m4C methyltransferase / Methyltransferase 5 domain-containing protein 1 / ...12S rRNA m4C methyltransferase / Methyltransferase 5 domain-containing protein 1 / Methyltransferase-like protein 15


Mass: 46184.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases
#32: Protein Putative ribosome-binding factor A, mitochondrial


Mass: 38417.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N0V3

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RNA chain , 1 types, 1 molecules A

#31: RNA chain 12S mitochondrial rRNA


Mass: 306214.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1858621102

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Non-polymers , 9 types, 48 molecules

#33: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#34: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#36: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#37: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#40: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Maturation state of mitochondria ribosomal 28S subunit.
Type: CELL / Entity ID: #1-#32 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.1_5286:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9007 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00271988
ELECTRON MICROSCOPYf_angle_d0.386101765
ELECTRON MICROSCOPYf_dihedral_angle_d19.00420223
ELECTRON MICROSCOPYf_chiral_restr0.03211950
ELECTRON MICROSCOPYf_plane_restr0.0049511

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