[English] 日本語
Yorodumi
- PDB-6rw4: Structure of human mitochondrial 28S ribosome in complex with mit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rw4
TitleStructure of human mitochondrial 28S ribosome in complex with mitochondrial IF3
Components
  • (28S ribosomal protein ...) x 27
  • 12S mitochondrial rRNA
  • Aurora kinase A-interacting protein
  • Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Translation initiation factor IF-3, mitochondrial
KeywordsRIBOSOME / ribosomal small subunit / initiation complex / initiation factor 3 / mitochondria
Function / homology
Function and homology information


mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / ribosome disassembly / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division ...mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / ribosome disassembly / mitochondrial ribosome assembly / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / translation initiation factor activity / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / ribosome binding / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / mRNA binding / intracellular membrane-bounded organelle / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / PPR repeat family / Cysteine alpha-hairpin motif superfamily ...Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / PPR repeat family / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S27, mitochondrial / MRPS27/PTCD2 / Mitochondrial 28S ribosomal protein S27 / Ribosomal protein S22, mitochondrial / Ribosomal protein S23, mitochondrial / Ribosomal protein S23/S25, mitochondrial / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal protein S23 / Mitochondrial 28S ribosomal protein S31 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, 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 / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / 40S ribosomal protein rpS2 (S5p), N-terminal / 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. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 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 S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein S10p/S20e / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S5, C-terminal domain / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S11 / Ribosomal protein S17/S11 / Ribosomal_S15
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / STREPTOMYCIN / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / STREPTOMYCIN / 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 / Small ribosomal subunit protein mS27 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein mS37 / Small ribosomal subunit protein uS3m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS26 / Translation initiation factor IF-3, mitochondrial / Small ribosomal subunit protein mS38 / 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: 2.97 Å
Model detailsRibosome small subunit with initiation factors
AuthorsItoh, Y. / Khawaja, A. / Rorbach, J. / Amunts, A.
CitationJournal: Nat Commun / Year: 2020
Title: Distinct pre-initiation steps in human mitochondrial translation.
Authors: Anas Khawaja / Yuzuru Itoh / Cristina Remes / Henrik Spåhr / Olessya Yukhnovets / Henning Höfig / Alexey Amunts / Joanna Rorbach /
Abstract: Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two ...Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.
History
DepositionJun 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10021
  • Imaged by UCSF Chimera
  • Download
Movie viewer
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: 28S ribosomal protein S21, mitochondrial
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: 28S ribosomal protein S34, mitochondrial
1: 28S ribosomal protein S35, mitochondrial
2: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
3: Aurora kinase A-interacting protein
4: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
8: Translation initiation factor IF-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,179,570117
Polymers1,174,55332
Non-polymers5,01785
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area215150 Å2
ΔGint-1932 kcal/mol
Surface area380130 Å2
MethodPISA

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain 12S mitochondrial rRNA


Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T

+
28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01

#2: Protein 28S ribosomal protein S2, mitochondrial / Ribosome / S2mt / Mitochondrial small ribosomal subunit protein uS2m


Mass: 33298.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y399
#3: Protein 28S ribosomal protein S24, mitochondrial / Ribosome / S24mt / Mitochondrial small ribosomal subunit protein uS3m / bMRP-47 / bMRP47


Mass: 19046.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96EL2
#4: Protein 28S ribosomal protein S5, mitochondrial / Ribosome / S5mt / Mitochondrial small ribosomal subunit protein uS5m


Mass: 48094.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82675
#5: Protein 28S ribosomal protein S6, mitochondrial / Ribosome / S6mt / Mitochondrial small ribosomal subunit protein bS6m


Mass: 14250.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82932
#6: Protein 28S ribosomal protein S7, mitochondrial / Ribosome / S7mt / Mitochondrial small ribosomal subunit protein uS7m / bMRP-27a / bMRP27a


Mass: 28186.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y2R9
#7: Protein 28S ribosomal protein S9, mitochondrial / Ribosome / S9mt / Mitochondrial small ribosomal subunit protein uS9m


Mass: 45909.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82933
#8: Protein 28S ribosomal protein S10, mitochondrial / Ribosome / S10mt / Mitochondrial small ribosomal subunit protein uS10m


Mass: 23033.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82664
#9: Protein 28S ribosomal protein S11, mitochondrial / Ribosome / S11mt / Cervical cancer proto-oncogene 2 protein / HCC-2 / Mitochondrial small ribosomal subunit protein uS11m


Mass: 20648.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82912
#10: Protein 28S ribosomal protein S12, mitochondrial / Ribosome / S12mt / MT-RPS12 / Mitochondrial small ribosomal subunit protein uS12m


Mass: 15200.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: O15235
#11: Protein 28S ribosomal protein S14, mitochondrial / Ribosome / S14mt / Mitochondrial small ribosomal subunit protein uS14m


Mass: 15168.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: O60783
#12: Protein 28S ribosomal protein S15, mitochondrial / Ribosome / S15mt / Mitochondrial small ribosomal subunit protein uS15m


Mass: 29903.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82914
#13: Protein 28S ribosomal protein S16, mitochondrial / Ribosome / S16mt / Mitochondrial small ribosomal subunit protein bS16m


Mass: 15371.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y3D3
#14: Protein 28S ribosomal protein S17, mitochondrial / Ribosome / S17mt / Mitochondrial small ribosomal subunit protein uS17m


Mass: 14526.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y2R5
#15: Protein 28S ribosomal protein S18b, mitochondrial / Ribosome / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / Mitochondrial small ribosomal ...S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2 / Mitochondrial small ribosomal subunit protein bS18b / Mitochondrial small ribosomal subunit protein mS40


Mass: 29440.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y676
#16: Protein 28S ribosomal protein S18c, mitochondrial / Ribosome / S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / Mitochondrial small ribosomal ...S18mt-c / 28S ribosomal protein S18-1 / mitochondrial / MRP-S18-1 / Mitochondrial small ribosomal subunit protein bS18c / Mitochondrial small ribosomal subunit protein bS18m


Mass: 15876.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y3D5
#17: Protein 28S ribosomal protein S21, mitochondrial / Ribosome / S21mt / Mitochondrial small ribosomal subunit protein bS21m


Mass: 10675.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82921
#18: Protein 28S ribosomal protein S22, mitochondrial / Ribosome / S22mt / Mitochondrial small ribosomal subunit protein mS22


Mass: 41337.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82650
#19: Protein 28S ribosomal protein S23, mitochondrial / Ribosome / S23mt / Mitochondrial small ribosomal subunit protein mS23


Mass: 21805.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y3D9
#20: Protein 28S ribosomal protein S25, mitochondrial / Ribosome / S25mt / Mitochondrial small ribosomal subunit protein mS25


Mass: 20146.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82663
#21: Protein 28S ribosomal protein S26, mitochondrial / Ribosome / S26mt / 28S ribosomal protein S13 / mitochondrial / S13mt / Mitochondrial small ribosomal subunit protein mS26


Mass: 24259.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9BYN8
#22: Protein 28S ribosomal protein S27, mitochondrial / Ribosome / S27mt / Mitochondrial ribosomal protein S27 / Mitochondrial small ribosomal subunit protein mS27


Mass: 47669.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q92552
#23: Protein 28S ribosomal protein S28, mitochondrial / Ribosome / S28mt / 28S ribosomal protein S35 / mitochondrial / S35mt / Mitochondrial small ribosomal subunit protein bS1m


Mass: 20878.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y2Q9
#24: Protein 28S ribosomal protein S29, mitochondrial / Ribosome / S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein / ...S29mt / Death-associated protein 3 / DAP-3 / Ionizing radiation resistance conferring protein / Mitochondrial small ribosomal subunit protein mS29


Mass: 45634.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P51398
#25: Protein 28S ribosomal protein S31, mitochondrial / Ribosome / S31mt / Imogen 38 / Mitochondrial small ribosomal subunit protein mS31


Mass: 45391.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q92665
#26: Protein 28S ribosomal protein S33, mitochondrial / Ribosome / S33mt / Mitochondrial small ribosomal subunit protein mS33


Mass: 12657.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9Y291
#27: Protein 28S ribosomal protein S34, mitochondrial / Ribosome / S34mt / Mitochondrial small ribosomal subunit protein mS34


Mass: 25695.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82930
#28: Protein 28S ribosomal protein S35, mitochondrial / Ribosome / S35mt / 28S ribosomal protein S28 / mitochondrial / S28mt / Mitochondrial small ribosomal subunit protein mS35


Mass: 36898.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: P82673

-
Protein , 4 types, 4 molecules 2348

#29: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S37 / mitochondrial / MRP-S37 / Mitochondrial small ribosomal subunit protein mS37 / Nuclear protein C2360


Mass: 13409.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96BP2
#30: Protein Aurora kinase A-interacting protein / AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial ...AURKA-interacting protein / 28S ribosomal protein S38 / mitochondrial / MRP-S38 / Mitochondrial small ribosomal subunit protein mS38


Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q9NWT8
#31: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial / 28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein ...28S ribosomal protein S39 / mitochondrial / MRP-S39 / Mitochondrial small ribosomal subunit protein mS39 / Transformation-related gene 15 protein / TRG-15


Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / References: UniProt: Q96EY7
#32: Protein Translation initiation factor IF-3, mitochondrial / IF3mt


Mass: 32545.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTIF3, DC38 / Plasmid: pCDNA5/FRT/TO / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9H2K0

-
Non-polymers , 10 types, 144 molecules

#33: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#35: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / Streptomycin


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Mg
#37: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#38: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#41: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#42: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1IF3 bound mitochondrial translation pre-initiation complexRIBOSOMESmall subunit of mitochondrial ribosome in complex with mitochondrial IF3#1-#320MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#311NATURAL
3IF3COMPLEX#321RECOMBINANT
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.10 MPotassium chlorideKCl1
225 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-potassium hydroxide bufferHEPES-KOH1
35.0 mMMagnesium acetateMg(CH3COO)21
40.25 mM5'-Guanylyl imidodiphosphateC10H17N6O13P31
50.05 %n-Dodecyl-beta-D-maltopyranosideC24H46O111
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was coated with 3 nm carbon film prior to use
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Calibrated magnification: 165000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 250 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13831
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 2-20

-
Processing

EM software
IDNameVersionCategory
1Gautomatch0.55particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.88 ELmodel fitting
9RELION2.1.0initial Euler assignment
10RELION2.1.0final Euler assignment
11RELION3.0.2classification
12RELION3.0.23D reconstruction
13PHENIX1.15rc2-3428model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1103314
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 379761 / Symmetry type: POINT
Atomic model buildingB value: 36 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 3J9M

3j9m


Accession code: 3J9M / Source name: PDB / Type: experimental model

+
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