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- PDB-6gaw: Unique features of mammalian mitochondrial translation initiation... -

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Basic information

Entry
Database: PDB / ID: 6gaw
TitleUnique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the complete 55S ribosome.
Components
  • (28S ribosomal protein ...) x 7
  • (39S ribosomal protein ...) x 11
  • (Mitochondrial ribosomal protein ...) x 35
  • (unassigned secondary structure ...) x 2
  • 12S ribosomal RNA, mitochondrial
  • 16S ribosomal RNA, mitochondrial
  • Aurora kinase A interacting protein 1
  • Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
  • Death associated protein 3
  • ICT1
  • MT-CO3 mRNA, mitochondrial
  • P-site fMet-tRNAMet, mitochondrial
  • Pentatricopeptide repeat domain-containing protein 3, mitochondrial
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein
  • Translation initiation factor IF-2, mitochondrial
  • Uncharacterized protein
  • bL32m
  • bL33m
  • bS16m
  • bS21m
  • mL42
  • mL43
  • mL45
  • mL50
  • mL53
  • mL54
  • mL64Microsoft Macro Assembler
  • mL65
  • mS27
  • mS31
  • mS33
  • tRNA-Phe, mitochondrial
  • uL14m
  • uL22m
  • uL23m
  • uL30m
  • uS17m
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 translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation initiation / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / regulation of translational initiation / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / organelle membrane / RNA processing / rescue of stalled ribosome / translation initiation factor activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / synapse / apoptotic process / GTP binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / 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 / 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 L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Tim44-like domain / Ribosomal protein L7/L12 dimerisation domain / Tim44 / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L49/IMG2 / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / : / : / : ...GUANOSINE-5'-MONOPHOSPHATE / N-FORMYLMETHIONINE / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SPERMINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein uL3m / Small ribosomal subunit protein uS7m / Mitochondrial ribosomal protein S11 / Large ribosomal subunit protein mL62 / 28S ribosomal protein S21, mitochondrial / Mitochondrial ribosomal protein L18 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL28m / 39S ribosomal protein L20, mitochondrial isoform 1 / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein mL64 / 39S ribosomal protein L23, mitochondrial / Large ribosomal subunit protein bL34m / Ribosomal protein / Mitochondrial ribosomal protein S23 / 28S ribosomal protein S24, mitochondrial / Mitochondrial ribosomal protein S22 / Mitochondrial ribosomal protein L12 / Mitochondrial ribosomal protein L41 / Progonadoliberin / Small ribosomal subunit protein mS38 / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein mL37 / Small ribosomal subunit protein uS15m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L57 / Large ribosomal subunit protein mL42 / 39S ribosomal protein L48, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Mitochondrial ribosomal protein S17 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein S18A / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein uL11m / Small ribosomal subunit protein uS10m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / 28S ribosomal protein S2, mitochondrial / Mitochondrial ribosomal protein L4 / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / 28S ribosomal protein S35, mitochondrial isoform 1 / Large ribosomal subunit protein uL29m / Mitochondrial ribosomal protein L39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein uL30m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / 39S ribosomal protein L48, mitochondrial / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein mL50 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein S6 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Small ribosomal subunit protein mS29 / Large ribosomal subunit protein bL32m / 28S ribosomal protein S9, mitochondrial / Small ribosomal subunit protein mS39 / 39S ribosomal protein L13, mitochondrial / 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: 3.2 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 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
CL: Mitochondrial ribosomal protein L12
DL: Mitochondrial ribosomal protein L12
EL: Mitochondrial ribosomal protein L12
FL: Mitochondrial ribosomal protein L12
GL: Mitochondrial ribosomal protein L12
HL: Mitochondrial ribosomal protein L12
B0: Mitochondrial ribosomal protein L27
B1: Mitochondrial ribosomal protein L28
B2: Mitochondrial ribosomal protein L47
B3: uL30m
B4: 39S ribosomal protein L55, mitochondrial
B5: bL32m
B6: bL33m
B7: Mitochondrial ribosomal protein L34
B8: Mitochondrial ribosomal protein L35
B9: Ribosomal protein
BA: 16S ribosomal RNA, mitochondrial
BB: tRNA-Phe, mitochondrial
BC: Translation initiation factor IF-2, mitochondrial
BD: 39S ribosomal protein L2, mitochondrial
BE: ICT1
BF: Mitochondrial ribosomal protein L4
BI: Mitochondrial ribosomal protein L9
BJ: Mitochondrial ribosomal protein L10
BK: Mitochondrial ribosomal protein L11
BL: Mitochondrial ribosomal protein L12
BN: 39S ribosomal protein L13, mitochondrial
BO: uL14m
BP: 39S ribosomal protein L15, mitochondrial
BQ: 39S ribosomal protein L16, mitochondrial
BR: 39S ribosomal protein L17, mitochondrial
BS: Mitochondrial ribosomal protein L18
BT: Mitochondrial ribosomal protein L19
BU: Mitochondrial ribosomal protein L20
BV: Mitochondrial ribosomal protein L21
BW: uL22m
BX: uL23m
BY: 39S ribosomal protein L24, mitochondrial
Ba: Mitochondrial ribosomal protein L37
Bb: Mitochondrial ribosomal protein L38
Bc: Mitochondrial ribosomal protein L39
Bd: 39S ribosomal protein L40, mitochondrial isoform 1
Be: Mitochondrial ribosomal protein L41
Bf: mL42
Bg: mL43
Bh: 39S ribosomal protein L44, mitochondrial
Bi: mL45
Bj: Mitochondrial ribosomal protein L46
Bk: Mitochondrial ribosomal protein L48
Bl: 39S ribosomal protein L49, mitochondrial
Bm: mL50
Bn: Mitochondrial ribosomal protein L51
Bo: 39S ribosomal protein L52, mitochondrial
Bp: mL53
Bq: mL54
Bt: Mitochondrial ribosomal protein L57
Bu: Peptidyl-tRNA hydrolase ICT1, mitochondrial
Bv: mL64
Bw: mL65
Bx: Mitochondrial ribosomal protein S18A
Bz: unassigned secondary structure elements
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: 28S ribosomal protein S9, mitochondrial
AJ: Mitochondrial ribosomal protein S10
AK: 28S ribosomal protein S11, mitochondrial
AL: Mitochondrial ribosomal protein S12
AN: Mitochondrial ribosomal protein S14
AO: Uncharacterized protein
AP: bS16m
AQ: uS17m
AR: Mitochondrial ribosomal protein S18C
AU: bS21m
AV: P-site fMet-tRNAMet, mitochondrial
AX: MT-CO3 mRNA, mitochondrial
AZ: unassigned secondary structure elements
Aa: Mitochondrial ribosomal protein S22
Ab: 28S ribosomal protein S23, mitochondrial
Ac: Mitochondrial ribosomal protein S25
Ad: Mitochondrial ribosomal protein S26
Ae: mS27
Af: 28S ribosomal protein S28, mitochondrial
Ag: Death associated protein 3
Ah: mS31
Ai: mS33
Aj: 28S ribosomal protein S34, mitochondrial
Ak: 28S ribosomal protein S35, mitochondrial
Am: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
An: Aurora kinase A interacting protein 1
Ao: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Ap: 28S ribosomal protein S18b, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,207,140436
Polymers3,196,22895
Non-polymers10,912341
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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Mitochondrial ribosomal protein ... , 35 types, 41 molecules CLDLELFLGLHLBLB0B1B2B7B8BFBIBJBKBSBTBUBVBaBbBcBeBjBkBnBtBxAB...

#1: Protein
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 7 / 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: A0A287ARV8
#2: Protein Mitochondrial ribosomal protein L27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RT79
#3: Protein Mitochondrial ribosomal protein L28 /


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZTW8
#4: Protein Mitochondrial ribosomal protein L47


Mass: 30085.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC7
#9: Protein Mitochondrial ribosomal protein L34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287A119
#10: Protein Mitochondrial ribosomal protein L35


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SVC5
#17: Protein Mitochondrial ribosomal protein L4


Mass: 33251.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B9C4, UniProt: F1S3J8*PLUS
#18: Protein Mitochondrial ribosomal protein L9


Mass: 30373.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LR45
#19: Protein Mitochondrial ribosomal protein L10


Mass: 29449.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RWJ0
#20: Protein Mitochondrial ribosomal protein L11


Mass: 20809.271 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: F1RU54
#26: Protein Mitochondrial ribosomal protein L18


Mass: 20582.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNK1
#27: 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) / References: UniProt: I3LNJ0
#28: Protein Mitochondrial ribosomal protein L20


Mass: 17554.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZU56
#29: Protein Mitochondrial ribosomal protein L21


Mass: 23154.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RY70
#33: Protein Mitochondrial ribosomal protein L37 /


Mass: 47917.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BIV6
#34: Protein Mitochondrial ribosomal protein L38


Mass: 44656.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RW03
#35: Protein Mitochondrial ribosomal protein L39


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHP6
#37: Protein Mitochondrial ribosomal protein L41


Mass: 15073.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287AWS0
#42: Protein Mitochondrial ribosomal protein L46


Mass: 32215.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SRT0
#43: Protein Mitochondrial ribosomal protein L48


Mass: 23749.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SUS9, UniProt: A0A480J9Z6*PLUS
#46: Protein Mitochondrial ribosomal protein L51


Mass: 15249.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BE26
#50: Protein Mitochondrial ribosomal protein L57


Mass: 12001.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BP93
#54: Protein Mitochondrial ribosomal protein S18A


Mass: 22273.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRH6
#57: 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) / References: UniProt: F1S001
#58: 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) / References: UniProt: A0A287ANU4
#59: 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
#60: 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) / References: UniProt: I3LEJ9
#61: 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) / References: UniProt: A0A286ZJ25
#63: 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) / References: UniProt: F1RUU2
#65: 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) / References: UniProt: A0A0M3KL52
#66: 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) / References: UniProt: A0A0M3KL53
#70: 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) / References: UniProt: A0A0M3KL54
#75: 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
#77: 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
#78: 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

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Protein , 29 types, 29 molecules B3B5B6B9BCBEBOBWBXBfBgBiBmBpBqBuBvBwAOAPAQAUAeAgAhAiAmAnAo

#5: Protein uL30m


Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1STE5
#7: Protein bL32m


Mass: 21537.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LTC4
#8: Protein bL33m


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZU68
#11: Protein Ribosomal protein /


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287A731
#14: Protein Translation initiation factor IF-2, mitochondrial / IF2(mt)


Mass: 72321.781 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
#16: Protein ICT1 / Mitochondrial ribosomal protein L3


Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A140UHW4
#22: Protein uL14m


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMZ6, UniProt: F1RQV7*PLUS
#30: Protein uL22m


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RQC9
#31: Protein uL23m


Mass: 17643.205 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: A0A286ZZC6
#38: Protein mL42


Mass: 16680.178 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) / References: UniProt: A0A287BQA1
#39: Protein mL43


Mass: 17728.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8U4
#41: Protein mL45


Mass: 35331.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM5
#45: Protein mL50


Mass: 18351.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9H6
#48: Protein mL53


Mass: 12029.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#49: Protein mL54


Mass: 15957.357 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) / References: UniProt: I3LN63
#51: Protein Peptidyl-tRNA hydrolase ICT1, mitochondrial


Mass: 23545.873 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: A0A286ZJR2
#52: Protein mL64 / Microsoft Macro Assembler


Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6
#53: Protein mL65


Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#67: Protein Uncharacterized protein


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMP0
#68: Protein bS16m


Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#69: Protein uS17m


Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RIU0
#71: Protein bS21m


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
#79: Protein mS27


Mass: 51945.984 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)
#81: 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
#82: Protein mS31


Mass: 44091.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#83: Protein mS33


Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8G3
#86: Protein Coiled-coil-helix-coiled-coil-helix domain-containing protein 1


Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SU49
#87: 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) / References: UniProt: A0A287B3R8
#88: Protein Pentatricopeptide repeat domain-containing protein 3, mitochondrial


Mass: 78518.156 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) / References: UniProt: K7GKS8

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39S ribosomal protein ... , 11 types, 11 molecules B4BDBNBPBQBRBYBdBhBlBo

#6: Protein 39S ribosomal protein L55, mitochondrial / Ribosome


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9J0
#15: Protein 39S ribosomal protein L2, mitochondrial / Ribosome


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRN2
#21: Protein 39S ribosomal protein L13, mitochondrial / Ribosome


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GP19
#23: Protein 39S ribosomal protein L15, mitochondrial / Ribosome


Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RSH0
#24: Protein 39S ribosomal protein L16, mitochondrial / Ribosome


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI89
#25: Protein 39S ribosomal protein L17, mitochondrial / Ribosome


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4
#32: Protein 39S ribosomal protein L24, mitochondrial / Ribosome


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RHJ1
#36: Protein 39S ribosomal protein L40, mitochondrial isoform 1 / Ribosome


Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98
#40: Protein 39S ribosomal protein L44, mitochondrial / Ribosome


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SR64
#44: Protein 39S ribosomal protein L49, mitochondrial / Ribosome / Mrpl34


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0R4J8D6
#47: Protein 39S ribosomal protein L52, mitochondrial / Ribosome


Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7

-
RNA chain , 5 types, 5 molecules BABBAAAVAX

#12: RNA chain 16S ribosomal RNA, mitochondrial /


Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: GenBank: 33320725
#13: RNA chain tRNA-Phe, mitochondrial


Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CCA end is added post-transcriptionally. / Source: (natural) Sus scrofa (pig) / Organ: liver / References: GenBank: 76262549
#56: 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) / References: GenBank: 11055671
#72: RNA chain P-site fMet-tRNAMet, mitochondrial


Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1390216722
#73: RNA chain MT-CO3 mRNA, mitochondrial


Mass: 63946.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1388777935

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Unassigned secondary structure ... , 2 types, 2 molecules BzAZ

#55: Protein unassigned secondary structure elements


Mass: 5846.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Unassigned secondary structure elements built as poly-alanine.
Source: (natural) Sus scrofa (pig)
#74: 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 built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver

-
28S ribosomal protein ... , 7 types, 7 molecules AIAKAbAfAjAkAp

#62: Protein 28S ribosomal protein S9, mitochondrial / Ribosome


Mass: 45604.570 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) / References: UniProt: I3LU08
#64: Protein 28S ribosomal protein S11, mitochondrial / Ribosome


Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJJ6
#76: Protein 28S ribosomal protein S23, mitochondrial / Ribosome


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEW3
#80: Protein 28S ribosomal protein S28, mitochondrial / Ribosome / 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
#84: Protein 28S ribosomal protein S34, mitochondrial / Ribosome


Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RG19
#85: Protein 28S ribosomal protein S35, mitochondrial / Ribosome


Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SG95
#89: 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) / References: UniProt: Q767K8

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Non-polymers , 9 types, 346 molecules

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


Mass: 24.305 Da / Num. of mol.: 326 / Source method: obtained synthetically / Formula: Mg
#91: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#92: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#93: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#94: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#95: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#96: 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
#97: 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
#98: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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

ComponentName: mammalian mitochondrial translation initiation complex
Type: RIBOSOME / Entity ID: #1-#89 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.85 MDa / Experimental value: NO
Source (natural)Organism: sus sucorfa (pig)
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

-
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

-
Processing

EM software
IDNameVersionCategory
4RELION2.1CTF correction
7Cootmodel fitting
8Omodel fitting
9UCSF Chimeramodel fitting
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
14RELION2.13D reconstruction
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1366787
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 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: 66.8 / Protocol: OTHER / Space: RECIPROCAL

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