[English] 日本語
Yorodumi
- PDB-9h55: Assembly intermediate of human mitochondrial ribosome small subun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h55
TitleAssembly intermediate of human mitochondrial ribosome small subunit in complex with NOA1 and TFB1M (state N3)
Components
  • (28S ribosomal protein ...) x 25
  • (Small ribosomal subunit protein ...) x 2
  • 12S mitochondrial rRNA
  • Dimethyladenosine transferase 1, mitochondrial
  • Nitric oxide-associated protein 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Putative ribosome-binding factor A, mitochondrial
KeywordsRIBOSOME / mitochondria / small subunit / assembly / NOA1
Function / homology
Function and homology information


rRNA modification in the mitochondrion / mitochondrial small ribosomal subunit assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / RNA folding chaperone / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation initiation ...rRNA modification in the mitochondrion / mitochondrial small ribosomal subunit assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase 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 / 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 / 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 / apoptotic process / GTP binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / YqeH-like, C-terminal / 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 / rRNA adenine dimethylase-like, C-terminal ...: / : / YqeH-like, C-terminal / 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 / 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 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / 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. / 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 / Ribosomal protein S5, C-terminal domain / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / Small ribosomal subunit protein uS14m ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / 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 / 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 / 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: 3.4 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 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 12S mitochondrial rRNA
B: 28S ribosomal protein S2, mitochondrial
C: 28S ribosomal protein S24, mitochondrial
D: 28S ribosomal protein S5, mitochondrial
E: 28S ribosomal protein S6, mitochondrial
F: 28S ribosomal protein S7, mitochondrial
G: 28S ribosomal protein S9, 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
V: 28S ribosomal protein S27, 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
0: Small ribosomal subunit protein mS34
1: 28S ribosomal protein S35, mitochondrial
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
9: Nitric oxide-associated protein 1
5: Dimethyladenosine transferase 1, mitochondrial
a: Putative ribosome-binding factor A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,265,52689
Polymers1,262,32832
Non-polymers3,19857
Water00
1


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

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: 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

+
28S ribosomal protein ... , 25 types, 25 molecules BCDEFGHIJKLMNOPRSTUVWXYZ1

#2: 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
#3: 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
#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 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
#7: 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
#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS10, MSTP040 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS11, RPMS11, HCC2 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS12, RPMS12, RPSM12 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS14 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS15, RPMS15, DC37 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS16, RPMS16, CGI-132 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS17, RPMS17, HSPC011 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS18B, C6orf14, HSPC183, PTD017 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS18C, CGI-134 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS22, C3orf5, RPMS22, GK002 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS23, CGI-138, HSPC329 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS25, RPMS25 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS26, C20orf193, RPMS13 / Production host: Homo sapiens (human) / References: UniProt: Q9BYN8
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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 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

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

#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRPS21, RPMS21, MDS016 / Production host: Homo sapiens (human) / References: UniProt: P82921
#27: 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

-
Protein , 4 types, 4 molecules 495a

#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTCD3, MRPS39, TRG15 / Production host: Homo sapiens (human) / References: UniProt: Q96EY7
#30: 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
#31: 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
#32: 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

-
Non-polymers , 6 types, 57 molecules

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


Mass: 24.305 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Mg
#34: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#35: Chemical ChemComp-ZN / ZINC ION


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#37: 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
#38: 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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mitoribosomal small subunit assembly intermediate / Type: RIBOSOME / Entity ID: #1-#18, #21-#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

-
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 defocus max: 1800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 16018 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00372048
ELECTRON MICROSCOPYf_angle_d0.435101416
ELECTRON MICROSCOPYf_dihedral_angle_d11.6417152
ELECTRON MICROSCOPYf_chiral_restr0.03311847
ELECTRON MICROSCOPYf_plane_restr0.0059882

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more