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Entry
Database: PDB / ID: 6gaz
TitleUnique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 28S ribosomal subunit.
Components
  • (Mitochondrial ribosomal protein ...) x 25
  • 12S ribosomal RNA, mitochondrial
  • 28S ribosomal protein S18b, mitochondrialRibosome
  • Aurora kinase A interacting protein 1
  • Death associated protein 3
  • MT-CO3 mRNA, mitochondrial
  • Mitoribosomal protein ms28, mrps28
  • P-site fMet-tRNAMet, mitochondrial
  • Translation initiation factor IF-2, mitochondrial
  • bS16m, MRPS16
  • mS31, MRPS31
  • unassigned secondary structure elements
KeywordsRIBOSOME / translation initiation / initiation factor IF2 / mitochondria / membrane targeting
Function / homology
Function and homology information


Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / : / translation factor activity, RNA binding / ribosome disassembly ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / : / translation factor activity, RNA binding / ribosome disassembly / mitochondrial ribosome assembly / Mitochondrial translation initiation / mitochondrial small ribosomal subunit / regulation of translational initiation / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / organelle membrane / translation initiation factor activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / GTP binding / nucleolus / mitochondrion / extracellular space / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Gonadotropin-releasing hormone / Gonadoliberin / Gonadotropin-releasing hormone / Gonadotropin-releasing hormones signature. / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 ...Gonadotropin-releasing hormone / Gonadoliberin / Gonadotropin-releasing hormone / Gonadotropin-releasing hormones signature. / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 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 S22 / Mitochondrial ribosomal protein S23 / 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 / 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 / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / 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 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 S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal S11, conserved site / Ribosomal protein S17/S11 / Ribosomal_S15 / Ribosomal protein S15
Similarity search - Domain/homology
N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m ...N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial / Small ribosomal subunit protein uS7m / Mitochondrial ribosomal protein S11 / 28S ribosomal protein S21, mitochondrial / Mitochondrial ribosomal protein S23 / 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S22 / Progonadoliberin / Small ribosomal subunit protein mS38 / Small ribosomal subunit protein uS15m / Uncharacterized protein / 28S ribosomal protein S17, mitochondrial / Small ribosomal subunit protein uS10m / 28S ribosomal protein S2, mitochondrial / Small ribosomal subunit protein mS33 / 28S ribosomal protein S35, mitochondrial isoform 1 / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / Mitochondrial ribosomal protein S6 / Mitochondrial ribosomal protein S27 / Large ribosomal subunit protein bL19m / Small ribosomal subunit protein mS29 / 28S ribosomal protein S9, mitochondrial / Small ribosomal subunit protein mS39 / Translation initiation factor IF-2, mitochondrial / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKummer, E. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 1196-2014 Switzerland
Swiss National Science Foundation310030B_163478 Switzerland
Swiss National Science Foundation138262 Switzerland
CitationJournal: Nature / Year: 2018
Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.
Authors: Eva Kummer / Marc Leibundgut / Oliver Rackham / Richard G Lee / Daniel Boehringer / Aleksandra Filipovska / Nenad Ban /
Abstract: Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The ...Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals. Furthermore, only one type of methionyl transfer RNA (tRNA) is used for both initiation and elongation, necessitating that the initiation factor specifically recognizes the formylated version of tRNA (fMet-tRNA). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Assembly

Deposited unit
BC: Translation initiation factor IF-2, mitochondrial
BT: Mitochondrial ribosomal protein L19
AA: 12S ribosomal RNA, mitochondrial
AB: Mitochondrial ribosomal protein S2
AC: Mitochondrial ribosomal protein S24
AE: Mitochondrial ribosomal protein S5
AF: Mitochondrial ribosomal protein S6
AG: Mitochondrial ribosomal protein S7
AI: Mitochondrial ribosomal protein S9
AJ: Mitochondrial ribosomal protein S10
AK: Mitochondrial ribosomal protein S11
AL: Mitochondrial ribosomal protein S12
AN: Mitochondrial ribosomal protein S14
AO: Mitochondrial ribosomal protein S15
AP: bS16m, MRPS16
AQ: Mitochondrial ribosomal protein S17
AR: Mitochondrial ribosomal protein S18C
AU: Mitochondrial ribosomal protein S21
AV: P-site fMet-tRNAMet, mitochondrial
AX: MT-CO3 mRNA, mitochondrial
AZ: unassigned secondary structure elements
Aa: Mitochondrial ribosomal protein S22
Ab: Mitochondrial ribosomal protein S23
Ac: Mitochondrial ribosomal protein S25
Ad: Mitochondrial ribosomal protein S26
Ae: Mitochondrial ribosomal protein S27
Af: Mitoribosomal protein ms28, mrps28
Ag: Death associated protein 3
Ah: mS31, MRPS31
Ai: Mitochondrial ribosomal protein S33
Aj: Mitochondrial ribosomal protein S34
Ak: Mitochondrial ribosomal protein S35
Am: Mitochondrial ribosomal protein S37
An: Aurora kinase A interacting protein 1
Ao: Mitochondrial ribosomal protein S39
Ap: 28S ribosomal protein S18b, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,334,800155
Polymers1,330,44136
Non-polymers4,359119
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 7 molecules BCAPAfAgAhAnAp

#1: Protein Translation initiation factor IF-2, mitochondrial / IF2(mt)


Mass: 72811.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mitochondria / Source: (gene. exp.) Homo sapiens (human) / Gene: MTIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46199
#15: Protein bS16m, MRPS16


Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver
#27: Protein Mitoribosomal protein ms28, mrps28


Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL56
#28: Protein Death associated protein 3


Mass: 45582.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LS10
#29: Protein mS31, MRPS31


Mass: 44091.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#34: Protein Aurora kinase A interacting protein 1


Mass: 22843.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287B3R8
#36: Protein 28S ribosomal protein S18b, mitochondrial / Ribosome / S18mt-b / 28S ribosomal protein S18-2 / mitochondrial / MRP-S18-2


Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: Q767K8

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Mitochondrial ribosomal protein ... , 25 types, 25 molecules BTABACAEAFAGAIAJAKALANAOAQARAUAaAbAcAdAeAiAjAkAmAo

#2: Protein Mitochondrial ribosomal protein L19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LNJ0
#4: Protein Mitochondrial ribosomal protein S2


Mass: 31731.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1S001
#5: Protein Mitochondrial ribosomal protein S24


Mass: 18935.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287ANU4
#6: Protein Mitochondrial ribosomal protein S5


Mass: 48213.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SU66
#7: Protein Mitochondrial ribosomal protein S6 / Mitoribosomal protein bs6m / mrps6


Mass: 14283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LEJ9
#8: Protein Mitochondrial ribosomal protein S7


Mass: 28150.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZJ25
#9: Protein Mitochondrial ribosomal protein S9


Mass: 45604.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LU08
#10: Protein Mitochondrial ribosomal protein S10


Mass: 23192.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RUU2
#11: Protein Mitochondrial ribosomal protein S11


Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZJJ6
#12: Protein Mitochondrial ribosomal protein S12 / Mitoribosomal protein us12m / mrps12


Mass: 15257.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL52
#13: Protein Mitochondrial ribosomal protein S14 / Mitoribosomal protein us14m / mrps14


Mass: 15120.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL53
#14: Protein Mitochondrial ribosomal protein S15


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BMP0
#16: Protein Mitochondrial ribosomal protein S17


Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RIU0
#17: Protein Mitochondrial ribosomal protein S18C / Mitoribosomal protein bs18m / mrps18c


Mass: 16211.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL54
#18: Protein Mitochondrial ribosomal protein S21


Mass: 10682.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZNB3
#22: Protein Mitochondrial ribosomal protein S22


Mass: 43234.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AQT5
#23: Protein Mitochondrial ribosomal protein S23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287AEW3
#24: Protein Mitochondrial ribosomal protein S25 / Mitoribosomal protein ms25 / mrps25


Mass: 19954.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL55
#25: Protein Mitochondrial ribosomal protein S26


Mass: 23637.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287AY01
#26: Protein Mitochondrial ribosomal protein S27


Mass: 45244.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LK09
#30: Protein Mitochondrial ribosomal protein S33


Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1S8G3
#31: Protein Mitochondrial ribosomal protein S34


Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RG19
#32: Protein Mitochondrial ribosomal protein S35


Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SG95
#33: Protein Mitochondrial ribosomal protein S37


Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SU49
#35: Protein Mitochondrial ribosomal protein S39


Mass: 76473.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: K7GKS8

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RNA chain , 3 types, 3 molecules AAAVAX

#3: RNA chain 12S ribosomal RNA, mitochondrial /


Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: GenBank: 11055671
#19: RNA chain P-site fMet-tRNAMet, mitochondrial


Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mitochondrial / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970
#20: RNA chain MT-CO3 mRNA, mitochondrial


Mass: 63946.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mitochondrial / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970

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Protein/peptide , 1 types, 1 molecules AZ

#21: Protein/peptide unassigned secondary structure elements


Mass: 1297.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned secondary structure elements have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver

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Non-polymers , 8 types, 124 molecules

#37: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 111 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#40: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#41: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#42: Chemical ChemComp-FME / N-FORMYLMETHIONINE / N-Formylmethionine


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S
#43: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#44: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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
1mammalian mitochondrial translation initiation complexRIBOSOME#1-#360MULTIPLE SOURCES
2Porcine RibosomeRIBOSOME#1-#361NATURAL
3Translation initiation factor IF-2, mitochondrialCOMPLEX#11RECOMBINANT
4Nucleic acidsNucleic acidCOMPLEX#19-#201RECOMBINANT
Molecular weightValue: 2.85 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24synthetic construct (others)32630
Buffer solutionpH: 7.6
SpecimenConc.: 0.171 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELDBright-field microscopy
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 13936
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1EMAN1.9particle selection
4RELION2.1CTF correction
7Cootmodel fitting
8Omodel fitting
9UCSF Chimeramodel fitting
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
14RELION2.13D reconstruction
21PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1366787
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139206 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 73.8 / Protocol: OTHER / Space: RECIPROCAL

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  • 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

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