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- PDB-9h51: Assembly intermediate of human mitochondrial ribosome small subun... -

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Basic information

Entry
Database: PDB / ID: 9h51
TitleAssembly intermediate of human mitochondrial ribosome small subunit in complex with PUS1, METTL15 and RBFA(IN conformation) (state M1)
Components
  • (28S ribosomal protein ...) x 25
  • (Small ribosomal subunit protein ...) x 2
  • 12S rRNA N4-methylcytidine (m4C) methyltransferase
  • Aurora kinase A-interacting protein
  • Nitric oxide-associated protein 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Pseudouridylate synthase 1 homolog
  • Putative ribosome-binding factor A, mitochondrial
  • RNA (969-MER)
KeywordsRIBOSOME / mitochondria / small subunit / assembly / NOA1
Function / homology
Function and homology information


mitochondrial tRNA pseudouridine(27/28) synthase activity / mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA pseudouridine(38-40) synthase activity / rRNA (cytosine-N4-)-methyltransferase activity / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthesis / mitochondrial small ribosomal subunit assembly ...mitochondrial tRNA pseudouridine(27/28) synthase activity / mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA pseudouridine(38-40) synthase activity / rRNA (cytosine-N4-)-methyltransferase activity / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthesis / mitochondrial small ribosomal subunit assembly / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / RNA folding chaperone / 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 / RNA splicing / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrion organization / apoptotic signaling pathway / mRNA processing / rRNA processing / cell junction / regulation of translation / small ribosomal subunit / small ribosomal subunit rRNA binding / transcription regulator complex / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / transcription coactivator activity / 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 / chromatin binding / GTP binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pseudouridine synthase PUS1/ PUS2-like / : / : / YqeH-like, C-terminal / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Ribosomal RNA small subunit methyltransferase H ...Pseudouridine synthase PUS1/ PUS2-like / : / : / YqeH-like, C-terminal / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / 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 / Pseudouridine synthase, catalytic domain superfamily / 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 / 28S ribosomal protein S10, 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 / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / 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. / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / 50S ribosome-binding GTPase / GTP binding domain / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-ADENOSYL-L-HOMOCYSTEINE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-ADENOSYL-L-HOMOCYSTEINE / 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 / Nitric oxide-associated protein 1 / 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 / Pseudouridylate synthase 1 homolog / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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: To Be Published
Title: Structural analysis reveals alternative pathways for assembly of the human mitoribosome small subunit
Authors: Singh, V. / Shiriaev, D. / Bilalli, L. / Khawaja, A. / Rorbach, J.
History
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0May 27, 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
c: Pseudouridylate synthase 1 homolog
A: RNA (969-MER)
B: 28S ribosomal protein S2, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
I: 28S ribosomal protein S11, 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: 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
V: 28S ribosomal protein S27, mitochondrial
W: 28S ribosomal protein S28, mitochondrial
0: Small ribosomal subunit protein mS34
3: Aurora kinase A-interacting protein
b: 12S rRNA N4-methylcytidine (m4C) methyltransferase
a: Putative ribosome-binding factor A, mitochondrial
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
H: 28S ribosomal protein S10, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
Z: 28S ribosomal protein S33, mitochondrial
X: 28S ribosomal protein S29, mitochondrial
K: 28S ribosomal protein S14, mitochondrial
Y: 28S ribosomal protein S31, mitochondrial
G: 28S ribosomal protein S9, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
9: Nitric oxide-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,339,45988
Polymers1,335,63434
Non-polymers3,82454
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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Protein , 6 types, 6 molecules c3ba49

#1: Protein Pseudouridylate synthase 1 homolog / tRNA pseudouridine synthase 1 / tRNA pseudouridine(38-40) synthase / tRNA pseudouridylate synthase ...tRNA pseudouridine synthase 1 / tRNA pseudouridine(38-40) synthase / tRNA pseudouridylate synthase I / tRNA-uridine isomerase I


Mass: 42987.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUS1, PP8985 / Production host: Homo sapiens (human)
References: UniProt: Q9Y606, Isomerases; Intramolecular transferases; Transferring other groups, tRNA pseudouridine38-40 synthase
#21: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKAIP1, AIP, AKIP, MRPS38 / Production host: Homo sapiens (human) / References: UniProt: Q9NWT8
#22: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL15, METT5D1 / Production host: Homo sapiens (human)
References: UniProt: A6NJ78, Transferases; Transferring one-carbon groups; Methyltransferases
#23: Protein Putative ribosome-binding factor A, mitochondrial


Mass: 38417.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBFA, C18orf22 / Production host: Homo sapiens (human) / References: UniProt: Q8N0V3
#24: 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
#34: 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

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RNA chain , 1 types, 1 molecules A

#2: RNA chain RNA (969-MER)


Mass: 307789.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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28S ribosomal protein ... , 25 types, 25 molecules BDEIJLMNOPRSTUVWH1ZXKYGFC

#3: 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
#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 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS11, RPMS11, HCC2 / Production host: Homo sapiens (human) / References: UniProt: P82912
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#14: 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
#15: 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
#16: 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
#17: 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 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
#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
#25: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS10, MSTP040 / Production host: Homo sapiens (human) / References: UniProt: P82664
#26: 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
#27: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS33, CGI-139, PTD003 / Production host: Homo sapiens (human) / References: UniProt: Q9Y291
#28: 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
#29: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS14 / Production host: Homo sapiens (human) / References: UniProt: O60783
#30: 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
#31: 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
#32: 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
#33: 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

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Small ribosomal subunit protein ... , 2 types, 2 molecules Q0

#13: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS21, RPMS21, MDS016 / Production host: Homo sapiens (human) / References: UniProt: P82921
#20: 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

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Non-polymers , 10 types, 57 molecules

#35: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Mg
#38: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#39: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#41: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#42: 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
#43: 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
#44: 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 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: #1-#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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16442 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00374953
ELECTRON MICROSCOPYf_angle_d0.456105629
ELECTRON MICROSCOPYf_dihedral_angle_d12.43818237
ELECTRON MICROSCOPYf_chiral_restr0.03412337
ELECTRON MICROSCOPYf_plane_restr0.00410160

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