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- PDB-6gb2: Unique features of mammalian mitochondrial translation initiation... -

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Entry
Database: PDB / ID: 6gb2
TitleUnique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit.
Components
  • ('Mitochondrial ribosomal protein ...) x 3
  • (Mitochondrial ribosomal protein ...) x 42
  • 16S ribosomal RNA, mitochondrial
  • CP tRNAPhe, mitochondrial
  • ICT1
  • Mrpl34
  • P-site fMet-tRNAMet, mitochondrial
  • Ribosomal protein
  • Translation initiation factor IF-2, mitochondrial
  • Uncharacterized protein
  • mL53, MRPL53
  • mL65, MRPS30
  • unassigned secondary structure elements
KeywordsRIBOSOME / translation initiation / initiation factor IF2 / mitochondria / membrane targeting
Function / homologyMitoribosomal protein mL52 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Thioredoxin-like superfamily / Ribosomal protein L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L22/L17 superfamily / PEBP-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain superfamily ...Mitoribosomal protein mL52 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Thioredoxin-like superfamily / Ribosomal protein L17 superfamily / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L22/L17 superfamily / PEBP-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S18 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal L18e/L15P superfamily / Translation initiation factor IF-2, domain 3 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L35 superfamily / MRP-L47 superfamily, mitochondrial / Ribosomal protein L33 superfamily / 39S ribosomal protein L40, mitochondrial / Elongation factor Tu GTP binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L7/L12, oligomerisation domain superfamily / L21-like superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L4 domain superfamily / Ribosomal protein L51, mitochondrial / Ribosomal protein L9, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L18e/L15P / Ribosomal protein L35 / Ribosomal protein L46, N-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Translation initiation factor IF- 2, domain 3 / Ribosomal protein L28/L24 / Ribosomal protein L36 superfamily / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S10 domain / Mitochondrial ribosomal protein L48 / Ribosomal protein L21-like / Ribosomal protein L15 / NTF2-like domain superfamily / Mitochondrial ribosomal protein L46 NUDIX / 39S ribosomal protein L52, mitochondrial / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L22p/L17e / Ribosomal protein L23 / Ribosomal protein L35, mitochondrial / 39S mitochondrial ribosomal protein L46 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L27 / Mitochondrial ribosomal protein L28 / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial 28S ribosomal protein S32 / Mitochondrial ribosomal subunit / Ribosomal subunit 39S / Translation-initiation factor 2 / Mitochondrial large subunit ribosomal protein (Img2) / Mitochondrial ribosome protein 63 / Ribosomal protein L7/L12 dimerisation domain / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L24 signature. / Initiation factor 2 signature. / Double stranded RNA-binding domain (dsRBD) profile. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Mitochondrial translation initiation / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Tim44-like domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L4/L1 family / Ribosomal protein L30p/L7e / Ribosomal protein S10p/S20e / Ribosomal protein L36 / Ribosomal protein L20 / Ribosomal protein L10 / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / RF-1 domain / Ribosomal protein L7/L12 C-terminal domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal Proteins L2, C-terminal domain / Ribosomal prokaryotic L21 protein / Ribosomal L28 family / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L27 protein / Ribosomal protein S18 / Phosphatidylethanolamine-binding protein / Ribosomal protein L17 / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35
Function and homology information
Specimen sourceHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 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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Structure visualization

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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: 'Mitochondrial ribosomal protein L30
B4: 'Mitochondrial ribosomal protein L55
B5: Mitochondrial ribosomal protein L32
B6: Mitochondrial ribosomal protein L33
B7: Mitochondrial ribosomal protein L34
B8: Mitochondrial ribosomal protein L35
B9: Ribosomal protein
BA: 16S ribosomal RNA, mitochondrial
BB: CP tRNAPhe, mitochondrial
BC: Translation initiation factor IF-2, mitochondrial
BD: Mitochondrial ribosomal protein L2
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: Mitochondrial ribosomal protein L13
BO: Mitochondrial ribosomal protein L14
BP: Mitochondrial ribosomal protein L15
BQ: Mitochondrial ribosomal protein L16
BR: Mitochondrial ribosomal protein L17
BS: Mitochondrial ribosomal protein L18
BT: Mitochondrial ribosomal protein L19
BU: Mitochondrial ribosomal protein L20
BV: Mitochondrial ribosomal protein L21
BW: Mitochondrial ribosomal protein L22
BX: Mitochondrial ribosomal protein L23
BY: Mitochondrial ribosomal protein L24
Ba: Mitochondrial ribosomal protein L37
Bb: Mitochondrial ribosomal protein L38
Bc: Mitochondrial ribosomal protein L39
Bd: Mitochondrial ribosomal protein L40
Be: Mitochondrial ribosomal protein L41
Bf: Mitochondrial ribosomal protein L42
Bg: Mitochondrial ribosomal protein L43
Bh: Mitochondrial ribosomal protein L44
Bi: Mitochondrial ribosomal protein L45
Bj: Mitochondrial ribosomal protein L46
Bk: Mitochondrial ribosomal protein L48
Bl: Mrpl34
Bm: Mitochondrial ribosomal protein L50
Bn: Mitochondrial ribosomal protein L51
Bo: Mitochondrial ribosomal protein L52
Bp: mL53, MRPL53
Bq: Uncharacterized protein
Bt: Mitochondrial ribosomal protein L57
Bu: Mitochondrial ribosomal protein L58
Bv: 'Mitochondrial ribosomal protein L59
Bw: mL65, MRPS30
Bx: Mitochondrial ribosomal protein S18A
Bz: unassigned secondary structure elements
AV: P-site fMet-tRNAMet, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,993,750288
Polyers1,986,43362
Non-polymers7,317226
Water362
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)387750
ΔGint (kcal/M)-4335
Surface area (Å2)580140
MethodPISA

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Components

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Mitochondrial ribosomal protein ... , 42 types, 48 molecules CLDLELFLGLHLBLB0B1B2B5B6B7B8BDBFBIBJBKBNBOBPBQBRBSBTBUBVBWBX...

#1: Protein/peptide
Mitochondrial ribosomal protein L12


Mass: 21268.975 Da / Num. of mol.: 7
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287ARV8
#2: Protein/peptide Mitochondrial ribosomal protein L27


Mass: 15943.688 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RT79
#3: Protein/peptide Mitochondrial ribosomal protein L28


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


Mass: 30085.088 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SGC7
#7: Protein/peptide Mitochondrial ribosomal protein L32 / bL32m


Mass: 21537.930 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver
#8: Protein/peptide Mitochondrial ribosomal protein L33


Mass: 7508.097 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZU68
#9: Protein/peptide Mitochondrial ribosomal protein L34


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


Mass: 21548.543 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SVC5
#15: Protein/peptide Mitochondrial ribosomal protein L2


Mass: 33270.934 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRN2
#17: Protein/peptide Mitochondrial ribosomal protein L4


Mass: 33251.469 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B9C4
#18: Protein/peptide Mitochondrial ribosomal protein L9


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


Mass: 29449.689 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWJ0
#20: Protein/peptide Mitochondrial ribosomal protein L11


Mass: 20809.271 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / References: UniProt: F1RU54
#21: Protein/peptide Mitochondrial ribosomal protein L13 / uL13m


Mass: 20633.801 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#22: Protein/peptide Mitochondrial ribosomal protein L14 / uL14m


Mass: 15955.632 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver
#23: Protein/peptide Mitochondrial ribosomal protein L15


Mass: 33481.723 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RSH0
#24: Protein/peptide Mitochondrial ribosomal protein L16


Mass: 28680.531 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI89
#25: Protein/peptide Mitochondrial ribosomal protein L17


Mass: 19268.178 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4
#26: Protein/peptide Mitochondrial ribosomal protein L18


Mass: 20582.568 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNK1
#27: Protein/peptide Mitochondrial ribosomal protein L19


Mass: 33441.539 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver
#28: Protein/peptide Mitochondrial ribosomal protein L20


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


Mass: 23154.861 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RY70
#30: Protein/peptide Mitochondrial ribosomal protein L22


Mass: 24313.357 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RQC9
#31: Protein/peptide Mitochondrial ribosomal protein L23


Mass: 17643.205 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZZC6
#32: Protein/peptide Mitochondrial ribosomal protein L24


Mass: 24893.529 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RHJ1
#33: Protein/peptide Mitochondrial ribosomal protein L37


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


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


Mass: 38523.422 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHP6
#36: Protein/peptide Mitochondrial ribosomal protein L40


Mass: 24075.658 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98
#37: Protein/peptide Mitochondrial ribosomal protein L41


Mass: 15073.404 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AWS0
#38: Protein/peptide Mitochondrial ribosomal protein L42


Mass: 16680.178 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BQA1
#39: Protein/peptide Mitochondrial ribosomal protein L43


Mass: 17728.109 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8U4
#40: Protein/peptide Mitochondrial ribosomal protein L44


Mass: 37527.195 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SR64
#41: Protein/peptide Mitochondrial ribosomal protein L45


Mass: 35331.805 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM5
#42: Protein/peptide Mitochondrial ribosomal protein L46


Mass: 32215.998 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRT0
#43: Protein/peptide Mitochondrial ribosomal protein L48


Mass: 23749.512 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1SUS9
#45: Protein/peptide Mitochondrial ribosomal protein L50


Mass: 18351.000 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3L9H6
#46: Protein/peptide Mitochondrial ribosomal protein L51


Mass: 15249.048 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BE26
#47: Protein/peptide Mitochondrial ribosomal protein L52


Mass: 13813.705 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7
#50: Protein/peptide Mitochondrial ribosomal protein L57


Mass: 12001.915 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287BP93
#51: Protein/peptide Mitochondrial ribosomal protein L58


Mass: 23545.873 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A286ZJR2
#54: Protein/peptide Mitochondrial ribosomal protein S18A


Mass: 22273.084 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRH6

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'Mitochondrial ribosomal protein ... , 3 types, 3 molecules B3B4Bv

#5: Protein/peptide 'Mitochondrial ribosomal protein L30


Mass: 18585.840 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1STE5
#6: Protein/peptide 'Mitochondrial ribosomal protein L55


Mass: 15156.537 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9J0
#52: Protein/peptide 'Mitochondrial ribosomal protein L59


Mass: 25815.031 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6

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Protein/peptide , 8 types, 8 molecules B9BCBEBlBpBqBwBz

#11: Protein/peptide Ribosomal protein /


Mass: 10841.016 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287A731
#14: 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: mitochondrialMitochondrion / Gene: MTIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46199
#16: Protein/peptide ICT1 / Mitochondrial ribosomal protein L3


Mass: 38427.199 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#44: Protein/peptide Mrpl34


Mass: 18957.779 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0R4J8D6
#48: Protein/peptide mL53, MRPL53


Mass: 12015.747 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: liver
#49: Protein/peptide Uncharacterized protein


Mass: 15957.357 Da / Num. of mol.: 1
Details: Unassigned residues have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LN63
#53: Protein/peptide mL65, MRPS30


Mass: 49100.504 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#55: Protein/peptide unassigned secondary structure elements


Mass: 5846.387 Da / Num. of mol.: 1
Details: Unassigned secondary structure elements have been built as poly-alanine.
Source: (natural) Sus scrofa (pig) / Organ: liver

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RNA chain , 3 types, 3 molecules BABBAV

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


Mass: 504852.031 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: GenBank: 33320725
#13: RNA chain CP tRNAPhe, mitochondrial


Mass: 23402.018 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: GenBank: 76262549
#56: RNA chain P-site fMet-tRNAMet, mitochondrial


Mass: 22664.498 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970

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Non-polymers , 8 types, 228 molecules

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


Mass: 24.305 Da / Num. of mol.: 216 / Formula: Mg / Magnesium
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc
#59: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Formula: C10H14N5O8P / Guanosine monophosphate
#60: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Formula: C10H26N4 / Spermine
#61: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3S
#62: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#63: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Mass: 177.221 Da / Num. of mol.: 1 / Formula: C6H11NO3S / N-Formylmethionine
#64: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 complexRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,560MULTIPLE SOURCES
2mammalian mitochondrial ribosomeRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,551NATURAL
3Translation initiation factor IF-2, mitochondrialCOMPLEX141RECOMBINANT
4tRNACOMPLEX561RECOMBINANT
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
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1366787
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 75666 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 56.9 / Ref protocol: OTHER / Ref space: RECIPROCAL

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