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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 / homologyMRPS27/PTCD2 / Ribosomal protein S23/S25, mitochondrial / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Thioredoxin-like superfamily / Ribosomal protein S6 superfamily / Mitochondrial ribosome subunit S26 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Mitochondrial 28S ribosomal protein S34 ...MRPS27/PTCD2 / Ribosomal protein S23/S25, mitochondrial / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Thioredoxin-like superfamily / Ribosomal protein S6 superfamily / Mitochondrial ribosome subunit S26 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / Mitochondrial 28S ribosomal protein S34 / Ribosomal protein S10 domain / P-loop containing nucleoside triphosphate hydrolase / 28S ribosomal protein S24, mitochondrial / 28S ribosomal protein S26 / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S11 superfamily / Translation initiation factor IF- 2, domain 3 / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S23/Rsm25, mitochondrial / Ribosomal protein S28, mitochondrial / Ribosomal protein S22, mitochondrial / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein S24/S35, mitochondrial, conserved domain / 28S ribosomal protein S27, mitochondrial / Ribosomal protein S18, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Translation initiation factor IF-2, domain 3 superfamily / Pentatricopeptide repeat domain-containing protein 3 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S21 / Mitochondrial ribosomal protein S23 / Mitochondrial ribosomal protein MRP-S35 / Mitochondrial 28S ribosomal protein S22 / Mitochondrial ribosomal death-associated protein 3 / Mitochondrial ribosomal subunit protein / Mitochondrial 28S ribosomal protein S27 / Mitochondrial ribosomal subunit S27 / Mitochondrial domain of unknown function (DUF1713) / CHCH domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S6 / Ribosomal protein L19 / Ribosomal protein S18 / Ribosomal protein S21 superfamily / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Elongation factor Tu GTP binding domain / 28S ribosomal protein S17, mitochondrial / Ribosomal protein L19 superfamily / Translation initiation factor IF- 2 / Translation elongation factor EF1B/ribosomal protein S6 / Pentatricopeptide repeat domain / Ribosomal protein S12 signature. / Ribosomal protein S9 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S5, N-terminal / Ribosomal protein S5/S7 / Translation initiation factor aIF-2, bacterial-like / Mitochondrial ribosome subunit S24 / Mitochondrial 28S ribosomal protein S34 / Ribosomal protein S11 signature. / Ribosomal protein S18 signature. / Ribosomal protein S5 / Ribosomal protein S9 signature. / Ribosomal protein S5 signature. / Ribosomal protein S2 signature 1. / Initiation factor 2 signature. / S5 double stranded RNA-binding domain profile. / Pentatricopeptide (PPR) repeat profile. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Mitochondrial translation initiation / Mitochondrial translation elongation / Mitochondrial translation termination / Transcription factor, GTP-binding domain / Ribosomal protein S17/S11 / Ribosomal protein S14 / Ribosomal protein S12, bacterial-type / Ribosomal protein S27/S33, mitochondrial / Domain of unknown function DUF1713 / Nucleic acid-binding, OB-fold / Tetratricopeptide-like helical domain superfamily / CHCH / Cysteine alpha-hairpin motif superfamily / S15/NS1, RNA-binding / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily
Function and homology information
Specimen sourceHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsKummer, E. / Leibundgut, M. / Boehringer, D. / Ban, N.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2018 / Release: Aug 8, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 8, 2018Structure modelrepositoryInitial release
1.1Aug 22, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
Polyers1,330,44136
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/peptide , 8 types, 8 molecules BCAPAZAfAgAhAnAp

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


Mass: 72811.219 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (gene. exp.) Homo sapiens (human) / Details: mitochondriaMitochondrion / Gene: MTIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46199
#15: Protein/peptide bS16m, MRPS16


Mass: 15182.668 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver
#21: Protein/peptide unassigned secondary structure elements


Mass: 1297.416 Da / Num. of mol.: 1
Details: Unassigned secondary structure elements have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver
#27: Protein/peptide Mitoribosomal protein ms28, mrps28


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


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


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


Mass: 22843.941 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287B3R8
#36: Protein/peptide 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: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: Q767K8

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

#2: Protein/peptide Mitochondrial ribosomal protein L19


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 76473.766 Da / Num. of mol.: 1
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: (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: (synth.) Homo sapiens (human) / Details: mitochondrialMitochondrion / References: GenBank: 1208989970
#20: RNA chain MT-CO3 mRNA, mitochondrial


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

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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 / Formula: C10H16N5O13P3S
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#40: Chemical ChemComp-SPM / SPERMINE


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


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc
#42: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Mass: 177.221 Da / Num. of mol.: 1 / Formula: C6H11NO3S / N-Formylmethionine
#43: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#44: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1mammalian mitochondrial translation initiation complexRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,360MULTIPLE SOURCES
2Porcine RibosomeRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,361NATURAL
3Translation initiation factor IF-2, mitochondrialCOMPLEX11RECOMBINANT
4Nucleic acidsCOMPLEX19,201RECOMBINANT
Molecular weightValue: 2.85 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129823Sus scrofa (pig)
239606Homo sapiens (human)
349606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
13562Escherichia coli (E. coli)
2432630synthetic construct (others)
Buffer solutionpH: 7.6
SpecimenConc.: 0.171 mg/ml
Details: contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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) / Number 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 selectionNumber of particles selected: 1366787
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 139206 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 73.8 / Ref protocol: OTHER / Ref space: RECIPROCAL

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