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- PDB-7p2e: Human mitochondrial ribosome small subunit in complex with IF3, G... -

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Basic information

Entry
Database: PDB / ID: 7p2e
TitleHuman mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
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 / Initiation factor 3 / translation / antibiotic / streptomycin
Function / homology
Function and homology information


mitochondrial translational initiation / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial ribosome / mitochondrial small ribosomal subunit / ribosome disassembly ...mitochondrial translational initiation / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial ribosome / mitochondrial small ribosomal subunit / ribosome disassembly / mitochondrial translation / apoptotic mitochondrial changes / positive regulation of proteolysis / ribosomal small subunit binding / translation initiation factor activity / Mitochondrial protein degradation / apoptotic signaling pathway / fibrillar center / cell junction / regulation of translation / ribosome binding / ribosomal small subunit assembly / 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 / intracellular membrane-bounded organelle / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 28S ribosomal protein S27, mitochondrial ...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 / Cysteine alpha-hairpin motif superfamily / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / 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 / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S34 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / : / Mitochondrial ribosome subunit S24 / 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. / 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. / 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 S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / 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 / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Tetratricopeptide-like helical domain superfamily / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S12 signature.
Similarity search - Domain/homology
Chem-5I0 / ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / RNA / RNA (> 10) / RNA (> 100) ...Chem-5I0 / ADENOSINE-5'-TRIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMINE / 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: 2.4 Å
AuthorsItoh, Y. / Khawaja, A. / Singh, V. / Rorbach, J. / Amunts, A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230 Sweden
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
CitationJournal: Elife / Year: 2022
Title: Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Authors: Yuzuru Itoh / Vivek Singh / Anas Khawaja / Andreas Naschberger / Minh Duc Nguyen / Joanna Rorbach / Alexey Amunts /
Abstract: The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was ...The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.
History
DepositionJul 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 30, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / citation_author / em_software / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _chem_comp.pdbx_synonyms / _em_software.category / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_close_contact.label_alt_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Provider: author / Type: Coordinate replacement
Revision 2.1Feb 8, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 3.1Jan 17, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 3.2Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)1,179,811123
Polymers1,174,56832
Non-polymers5,24391
Water55,5763085
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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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 / Details: cell / Source: (natural) Homo sapiens (human)

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

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


Mass: 33298.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y399
#3: Protein 28S ribosomal protein S24, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL2
#4: Protein 28S ribosomal protein S5, mitochondrial / S5mt / Mitochondrial small ribosomal subunit protein uS5m


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


Mass: 14250.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P82932
#6: Protein 28S ribosomal protein S7, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R9
#7: Protein 28S ribosomal protein S9, mitochondrial / S9mt / Mitochondrial small ribosomal subunit protein uS9m


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


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


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


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


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


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


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


Mass: 14526.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2R5
#15: Protein 28S ribosomal protein S18b, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y676
#16: Protein 28S ribosomal protein S18c, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3D5
#17: Protein 28S ribosomal protein S21, mitochondrial / S21mt / Mitochondrial small ribosomal subunit protein bS21m


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


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


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


Mass: 20146.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P82663
#21: Protein 28S ribosomal protein S26, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYN8
#22: Protein 28S ribosomal protein S27, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q92552
#23: Protein 28S ribosomal protein S28, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2Q9
#24: Protein 28S ribosomal protein S29, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P51398
#25: Protein 28S ribosomal protein S31, mitochondrial / S31mt / Imogen 38 / Mitochondrial small ribosomal subunit protein mS31


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


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


Mass: 25695.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P82930
#28: Protein 28S ribosomal protein S35, mitochondrial / 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 / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P82673

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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 / Details: cell / Source: (natural) Homo sapiens (human) / 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 / Details: cell / Source: (natural) Homo sapiens (human) / 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 / Details: cell / Source: (natural) Homo sapiens (human) / 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
Details: Natural variant Thr68Ile and Phe263Leu / Source: (gene. exp.) Homo sapiens (human) / Description: cell / Gene: MTIF3, DC38 / Production host: Homo sapiens (human) / References: UniProt: Q9H2K0

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Non-polymers , 10 types, 3176 molecules

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


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


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-5I0 / [(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium / hydrated form of streptomycin


Mass: 602.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44N7O13 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: K
#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: Mg
#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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#41: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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


Mass: 18.015 Da / Num. of mol.: 3085 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Small subunit of human mitochondrial ribosome in complex with initiation factor 3RIBOSOME#1-#320MULTIPLE SOURCES
2Small subunit of human mitochondrial ribosome in complexCOMPLEX#1-#311NATURAL
3Translation initiation factor IF-3, mitochondrialCOMPLEX#321RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.20 Mpotassium chlorideKCl1
25.0 mMmagnesium acetateMg(CH3COO)21
325 mMHEPES-KOH buffer pH 7.51
40.05 % (w/v)n-dodecyl-beta-D-maltopyranosideC24H46O111
50.25 mM5'-guanylyl imidodiphosphateC10H17N6O13P31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

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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: 4000 nm / Nominal defocus min: 500 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: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 31773
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.8model fitting
9RELION3initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2487123
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 885199 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6RW4

6rw4


Accession code: 6RW4 / Source name: PDB / Type: experimental model

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