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- PDB-9h52: Assembly intermediate of human mitochondrial ribosome small subun... -

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Basic information

Entry
Database: PDB / ID: 9h52
TitleAssembly intermediate of human mitochondrial ribosome small subunit in complex with NOA1, ERAL1, METTL17, MCAT and TFB1M (state N1)
Components
  • (28S ribosomal protein ...) x 21
  • 12S mitochondrial rRNA
  • Dimethyladenosine transferase 1, mitochondrial
  • GTPase Era, mitochondrial
  • Isoform 2 of Ribosome assembly protein METTL17, mitochondrial
  • MRPS21 isoform 1
  • Malonyl-CoA-acyl carrier protein transacylase, mitochondrial
  • Nitric oxide-associated protein 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Small ribosomal subunit protein mS34
KeywordsRIBOSOME / mitochondria / small subunit / assembly / NOA1
Function / homology
Function and homology information


mitochondrial ribosome binding / rRNA modification in the mitochondrion / mitochondrial small ribosomal subunit assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / Mitochondrial Fatty Acid Beta-Oxidation / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity ...mitochondrial ribosome binding / rRNA modification in the mitochondrion / mitochondrial small ribosomal subunit assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / Mitochondrial Fatty Acid Beta-Oxidation / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / RNA folding chaperone / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation / Mitochondrial ribosome-associated quality control / S-adenosyl-L-methionine binding / Mitochondrial translation termination / rRNA methylation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / fatty acid beta-oxidation / apoptotic mitochondrial changes / mitochondrial nucleoid / ribosomal small subunit binding / sperm head-tail coupling apparatus / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrion organization / apoptotic signaling pathway / Transcriptional activation of mitochondrial biogenesis / fatty acid biosynthetic process / cell junction / regulation of translation / ribosomal small subunit assembly / 4 iron, 4 sulfur cluster binding / ribosomal small subunit biogenesis / 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 / apoptotic process / GTP binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / YqeH-like, C-terminal / GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 ...: / : / : / YqeH-like, C-terminal / GTP-binding protein Era / Era-type guanine nucleotide-binding (G) domain / Era-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / 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 / : / 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 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 / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Malonyl-CoA ACP transacylase, ACP-binding / 50S ribosome-binding GTPase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / GTP binding domain / Acyl transferase/acyl hydrolase/lysophospholipase / 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. / Small GTP-binding protein domain / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / K homology domain superfamily, prokaryotic type / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / MRPS21 isoform 1 / Small ribosomal subunit protein uS12m ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / MRPS21 isoform 1 / Small ribosomal subunit protein uS12m / GTPase Era, mitochondrial / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS22 / Small ribosomal subunit protein mS25 / Small ribosomal subunit protein mS35 / Small ribosomal subunit protein uS5m / Small ribosomal subunit protein uS15m / Small ribosomal subunit protein mS34 / Small ribosomal subunit protein bS6m / Small ribosomal subunit protein uS9m / Malonyl-CoA-acyl carrier protein transacylase, mitochondrial / Nitric oxide-associated protein 1 / Dimethyladenosine transferase 1, 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 / Ribosome assembly protein METTL17, mitochondrial / 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: 3.9 Å
AuthorsSingh, V. / Shiriaev, D. / Khawaja, A. / Rorbach, J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW2019.0109 Sweden
Swedish Research CouncilVR2016-02179 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
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: GTPase Era, mitochondrial
0: Small ribosomal subunit protein mS34
9: Nitric oxide-associated protein 1
D: 28S ribosomal protein S5, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
J: 28S ribosomal protein S12, 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: MRPS21 isoform 1
R: 28S ribosomal protein S22, mitochondrial
S: 28S ribosomal protein S23, mitochondrial
T: 28S ribosomal protein S25, mitochondrial
U: 28S ribosomal protein S26, mitochondrial
A: 12S mitochondrial rRNA
B: 28S ribosomal protein S2, mitochondrial
W: 28S ribosomal protein S28, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
G: 28S ribosomal protein S9, mitochondrial
X: 28S ribosomal protein S29, mitochondrial
Y: 28S ribosomal protein S31, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
8: Malonyl-CoA-acyl carrier protein transacylase, mitochondrial
7: Isoform 2 of Ribosome assembly protein METTL17, mitochondrial
5: Dimethyladenosine transferase 1, mitochondrial
V: 28S ribosomal protein S27, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,296,83939
Polymers1,294,62830
Non-polymers2,2119
Water00
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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Protein , 8 types, 8 molecules a09Q4875

#1: Protein GTPase Era, mitochondrial / H-ERA / hERA / Conserved ERA-like GTPase / CEGA / ERA-W / ERA-like protein 1


Mass: 48413.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAL1, HERA / Production host: Homo sapiens (human) / References: UniProt: O75616
#2: Protein Small ribosomal subunit protein mS34 / 28S ribosomal protein S34 / mitochondrial / MRP-S34 / S34mt


Mass: 25336.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS34 / Production host: Homo sapiens (human) / References: UniProt: P82930
#3: Protein Nitric oxide-associated protein 1


Mass: 78565.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOA1, C4orf14 / Production host: Homo sapiens (human) / References: UniProt: Q8NC60
#12: Protein MRPS21 isoform 1 / MRPS21 isoform 2 / Mitochondrial ribosomal protein S21


Mass: 10659.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS21, CR201_G0018851 / Production host: Homo sapiens (human) / References: UniProt: A0A2J8VEN6
#26: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTCD3, MRPS39, TRG15 / Production host: Homo sapiens (human) / References: UniProt: Q96EY7
#27: Protein Malonyl-CoA-acyl carrier protein transacylase, mitochondrial / MCT / Mitochondrial malonyl CoA:ACP acyltransferase / Mitochondrial malonyltransferase / [Acyl- ...MCT / Mitochondrial malonyl CoA:ACP acyltransferase / Mitochondrial malonyltransferase / [Acyl-carrier-protein] malonyltransferase


Mass: 43019.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCAT, MT / Production host: Homo sapiens (human)
References: UniProt: Q8IVS2, [acyl-carrier-protein] S-malonyltransferase
#28: Protein Isoform 2 of Ribosome assembly protein METTL17, mitochondrial / False p73 target gene protein / Methyltransferase 11 domain-containing protein 1 / ...False p73 target gene protein / Methyltransferase 11 domain-containing protein 1 / Methyltransferase-like protein 17 / Protein RSM22 homolog / mitochondrial


Mass: 50807.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL17, METT11D1 / Production host: Homo sapiens (human) / References: UniProt: Q9H7H0
#29: Protein Dimethyladenosine transferase 1, mitochondrial / Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / h-mtTFB / h-mtTFB1 / ...Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / h-mtTFB / h-mtTFB1 / hTFB1M / mtTFB1 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 1


Mass: 39600.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFB1M, CGI-75 / Production host: Homo sapiens (human)
References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases

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28S ribosomal protein ... , 21 types, 21 molecules DEJLMNOPRSTUBWCFGXY1V

#4: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS5 / Production host: Homo sapiens (human) / References: UniProt: P82675
#5: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS6, C21orf101, RPMS6 / Production host: Homo sapiens (human) / References: UniProt: P82932
#6: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS12, RPMS12, RPSM12 / Production host: Homo sapiens (human) / References: UniProt: O15235
#7: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS15, RPMS15, DC37 / Production host: Homo sapiens (human) / References: UniProt: P82914
#8: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS16, RPMS16, CGI-132 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3D3
#9: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS17, RPMS17, HSPC011 / Production host: Homo sapiens (human) / References: UniProt: Q9Y2R5
#10: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS18B, C6orf14, HSPC183, PTD017 / Production host: Homo sapiens (human) / References: UniProt: Q9Y676
#11: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS18C, CGI-134 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3D5
#13: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS22, C3orf5, RPMS22, GK002 / Production host: Homo sapiens (human) / References: UniProt: P82650
#14: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS23, CGI-138, HSPC329 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3D9
#15: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS25, RPMS25 / Production host: Homo sapiens (human) / References: UniProt: P82663
#16: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS26, C20orf193, RPMS13 / Production host: Homo sapiens (human) / References: UniProt: Q9BYN8
#18: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS2, CGI-91 / Production host: Homo sapiens (human) / References: UniProt: Q9Y399
#19: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS28, MRPS35, HSPC007 / Production host: Homo sapiens (human) / References: UniProt: Q9Y2Q9
#20: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS24, HSPC335 / Production host: Homo sapiens (human) / References: UniProt: Q96EL2
#21: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS7 / Production host: Homo sapiens (human) / References: UniProt: Q9Y2R9
#22: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS9, RPMS9 / Production host: Homo sapiens (human) / References: UniProt: P82933
#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAP3, MRPS29 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS31, IMOGN38 / Production host: Homo sapiens (human) / References: UniProt: Q92665
#25: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS35, MRPS28, HDCMD11P, MDS023, PSEC0213 / Production host: Homo sapiens (human) / References: UniProt: P82673
#30: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS27, KIAA0264 / Production host: Homo sapiens (human) / References: UniProt: Q92552

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RNA chain , 1 types, 1 molecules A

#17: RNA chain 12S mitochondrial rRNA


Mass: 306449.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 1858621102

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Non-polymers , 6 types, 9 molecules

#31: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#32: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#35: 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
#36: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN
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: mitoribosomal small subunit assembly intermediate / Type: RIBOSOME / Entity ID: #2-#16, #1, #17-#30 / 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: 1800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warp4particle selection
2PHENIX1.20.1_4487model refinement
12RELION3.1classification
13cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11115 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00370792
ELECTRON MICROSCOPYf_angle_d0.48599286
ELECTRON MICROSCOPYf_dihedral_angle_d13.14916027
ELECTRON MICROSCOPYf_chiral_restr0.03411553
ELECTRON MICROSCOPYf_plane_restr0.00810005

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