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- PDB-8apo: Structure of the mitochondrial ribosome from Polytomella magna wi... -

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Basic information

Entry
Database: PDB / ID: 8apo
TitleStructure of the mitochondrial ribosome from Polytomella magna with tRNAs bound to the A and P sites
Components
  • (Unknown) x 11
  • A-site tRNA anticodon loop
  • P-site tRNA anticodon loop
  • bL17m
  • bL19m
  • bL20m
  • bL21m
  • bL24m
  • bL25m
  • bL27m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL34m
  • bL35m
  • bL36m
  • bS16m
  • bS18m
  • bS19m
  • bS1m
  • bS21m
  • mL105
  • mL116
  • mL118
  • mL120
  • mL121
  • mL122
  • mL123
  • mL124
  • mL125
  • mL126
  • mL127
  • mL128
  • mL129
  • mL40
  • mL41
  • mL43
  • mL46
  • mL63
  • mL64Microsoft Macro Assembler
  • mL87
  • mRNAMessenger RNA
  • mS106
  • mS107
  • mS108
  • mS109
  • mS110
  • mS111
  • mS112
  • mS113
  • mS114
  • mS115
  • mS116
  • mS23
  • mS26
  • mS29
  • mS31
  • mS33
  • mS34
  • mS35
  • mS37
  • mS38
  • mS45
  • mt-5S
  • mtLSU-1
  • mtLSU-2
  • mtLSU-3
  • mtLSU-4
  • mtLSU-5
  • mtLSU-6
  • mtLSU-7
  • mtLSU-8
  • mtSSU-1
  • mtSSU-2
  • mtSSU-3
  • mtSSU-4
  • uL13m
  • uL14m
  • uL15m
  • uL16m
  • uL18m
  • uL22m
  • uL23m
  • uL29m
  • uL2m
  • uL30m
  • uL3m
  • uL4m
  • uL5m
  • uL6m
  • uL9m
  • uS10m
  • uS11m
  • uS12m
  • uS13m
  • uS14m
  • uS15m
  • uS17m
  • uS2m
  • uS3m
  • uS3m-2
  • uS4m
  • uS4m-2
  • uS5m
  • uS6m
  • uS7m
  • uS7m-2
  • uS8m
  • uS9m
KeywordsRIBOSOME / mitoribosome / mitochondria / polytomella / fragmentation / rrna / evolution / translation
Function / homologyADENOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPolytomella magna (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTobiasson, V. / Berzina, I. / Amunts, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2022
Title: Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
Authors: Victor Tobiasson / Ieva Berzina / Alexey Amunts /
Abstract: Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å ...Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.
History
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jan 10, 2024Group: Atomic model / Polymer sequence / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: mtLSU-1
A2: mtLSU-2
A3: mtLSU-3
A4: mtLSU-4
A5: mtLSU-5
A6: mtLSU-6
A7: mtLSU-7
A8: mtLSU-8
A9: mt-5S
Aa: uL2m
Ab: uL3m
Ac: uL4m
Ad: uL5m
Ae: uL6m
Af: uL9m
Ah: uL13m
Ai: uL14m
Aj: uL15m
Ak: uL16m
Al: bL17m
Am: uL18m
An: bL19m
Ao: bL20m
Ap: bL21m
Aq: uL22m
Ar: uL23m
As: bL24m
At: bL25m
Au: bL27m
Av: bL28m
Aw: uL29m
Ax: uL30m
Ay: bL31m
Az: bL32m
AA: bL33m
AB: bL34m
AC: bL35m
AD: bL36m
AE: mL40
AF: mL41
AG: mL43
AH: mL46
AI: mL63
AJ: mL64
AK: mL87
AL: mL116
AM: mL116
AN: mL116
AO: mL118
Xa: mL120
Xb: mL121
Xc: mL122
Xd: mL123
Xe: mL124
Xf: mL125
Xg: mL126
Xh: mL127
Xi: mL128
Xj: mL129
B1: mtSSU-1
B2: mtSSU-2
B3: mtSSU-3
B4: mtSSU-4
Ba: bS1m
Bb: uS2m
Bc: uS3m
Bd: uS4m
Be: uS5m
Bf: uS6m
Bg: uS7m
Bh: uS8m
Bi: uS9m
Bj: uS10m
Bk: uS11m
Bl: uS12m
Bm: uS13m
Bn: uS14m
Bo: uS15m
Bp: bS16m
Bq: uS17m
Br: bS18m
Bs: bS19m
Bt: bS21m
Bu: mS23
Bv: mS26
Bw: mS29
Bx: mS31
By: mS33
Bz: mS34
BA: mS35
BB: mS37
BC: mS38
BD: mS45
BE: mS106
BF: mS107
Ya: uS4m-2
Yb: mS108
Yc: mS109
Yd: mS110
Ye: uS3m-2
Yf: mS111
Yg: mS112
Yh: mS113
Yi: mS114
Yj: mS115
Yk: mS116
Yl: uS7m-2
C1: P-site tRNA anticodon loop
C2: A-site tRNA anticodon loop
C3: mRNA
Ub: mL105
Ua: Unknown
Ud: Unknown
Ue: Unknown
Uf: Unknown
Ug: Unknown
Uh: Unknown
Ui: Unknown
Uj: Unknown
Uk: Unknown
Ul: Unknown
Um: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,867,516266
Polymers2,863,048122
Non-polymers4,468144
Water9,080504
1


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

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Components

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RNA chain , 16 types, 16 molecules A1A2A3A4A5A6A7A8A9B1B2B3B4C1C2C3

#1: RNA chain mtLSU-1


Mass: 35302.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616
#2: RNA chain mtLSU-2


Mass: 26056.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616
#3: RNA chain mtLSU-3


Mass: 66621.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#4: RNA chain mtLSU-4


Mass: 23661.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#5: RNA chain mtLSU-5


Mass: 43735.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#6: RNA chain mtLSU-6


Mass: 35225.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#7: RNA chain mtLSU-7


Mass: 171975.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#8: RNA chain mtLSU-8


Mass: 112621.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#9: RNA chain mt-5S


Mass: 22130.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#58: RNA chain mtSSU-1


Mass: 32708.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616
#59: RNA chain mtSSU-2


Mass: 67696.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#60: RNA chain mtSSU-3


Mass: 122239.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant) / References: GenBank: 485474616
#61: RNA chain mtSSU-4


Mass: 108517.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#106: RNA chain P-site tRNA anticodon loop


Mass: 7324.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#107: RNA chain A-site tRNA anticodon loop


Mass: 6689.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#108: RNA chain mRNA / Messenger RNA


Mass: 2551.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)

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Protein , 89 types, 91 molecules AaAbAcAdAeAfAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzACAEAFAGAH...

#10: Protein uL2m


Mass: 33873.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#11: Protein uL3m


Mass: 34287.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#12: Protein uL4m


Mass: 33741.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#13: Protein uL5m


Mass: 21894.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#14: Protein uL6m


Mass: 27446.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#15: Protein uL9m


Mass: 6163.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#16: Protein uL13m


Mass: 21549.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#17: Protein uL14m


Mass: 13522.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#18: Protein uL15m


Mass: 22826.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#19: Protein uL16m


Mass: 19334.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#20: Protein bL17m


Mass: 20047.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#21: Protein uL18m


Mass: 12928.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#22: Protein bL19m


Mass: 19849.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#23: Protein bL20m


Mass: 13695.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#24: Protein bL21m


Mass: 22296.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#25: Protein uL22m


Mass: 21768.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#26: Protein uL23m


Mass: 18235.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#27: Protein bL24m


Mass: 13088.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#28: Protein bL25m


Mass: 28550.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#29: Protein bL27m


Mass: 16266.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#30: Protein bL28m


Mass: 15075.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#31: Protein uL29m


Mass: 14509.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#32: Protein uL30m


Mass: 20863.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#33: Protein bL31m


Mass: 8388.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#34: Protein bL32m


Mass: 6690.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#37: Protein bL35m


Mass: 16673.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#39: Protein mL40


Mass: 10895.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#40: Protein mL41


Mass: 10819.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#41: Protein mL43


Mass: 14180.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#42: Protein mL46


Mass: 20078.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#43: Protein mL63


Mass: 7181.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#44: Protein mL64 / Microsoft Macro Assembler


Mass: 14227.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#45: Protein mL87


Mass: 16437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#46: Protein mL116


Mass: 46617.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#47: Protein mL118


Mass: 40870.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#48: Protein mL120


Mass: 22283.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#49: Protein mL121


Mass: 27805.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#50: Protein mL122


Mass: 7019.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#51: Protein mL123


Mass: 45953.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#52: Protein mL124


Mass: 52212.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#53: Protein mL125


Mass: 22855.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#54: Protein mL126


Mass: 44063.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#55: Protein mL127


Mass: 16291.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#57: Protein mL129


Mass: 8260.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#62: Protein bS1m


Mass: 27631.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#63: Protein uS2m


Mass: 26625.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#64: Protein uS3m


Mass: 31441.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#65: Protein uS4m


Mass: 25534.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#66: Protein uS5m


Mass: 25956.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#67: Protein uS6m


Mass: 13776.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#68: Protein uS7m


Mass: 12740.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#69: Protein uS8m


Mass: 43012.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#70: Protein uS9m


Mass: 32274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#71: Protein uS10m


Mass: 45092.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#72: Protein uS11m


Mass: 12426.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#73: Protein uS12m


Mass: 13729.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#74: Protein uS13m


Mass: 12807.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#75: Protein uS14m


Mass: 13921.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#76: Protein uS15m


Mass: 18048.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#77: Protein bS16m


Mass: 14298.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#78: Protein uS17m


Mass: 15002.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#79: Protein bS18m


Mass: 10606.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#80: Protein bS19m


Mass: 10384.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#81: Protein bS21m


Mass: 8829.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#82: Protein mS23


Mass: 19393.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#83: Protein mS26


Mass: 19292.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#84: Protein mS29


Mass: 39282.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#85: Protein mS31


Mass: 66912.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#86: Protein mS33


Mass: 9022.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#87: Protein mS34


Mass: 14053.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#88: Protein mS35


Mass: 19588.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#89: Protein mS37


Mass: 9493.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#91: Protein mS45


Mass: 30779.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#92: Protein mS106


Mass: 18551.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#93: Protein mS107


Mass: 42316.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#94: Protein uS4m-2


Mass: 20395.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#96: Protein mS109


Mass: 18394.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#97: Protein mS110


Mass: 11167.972 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#98: Protein uS3m-2


Mass: 12220.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#99: Protein mS111


Mass: 17507.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#100: Protein mS112


Mass: 7917.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#101: Protein mS113


Mass: 7505.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#102: Protein mS114


Mass: 15270.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#103: Protein mS115


Mass: 40611.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#104: Protein mS116


Mass: 10018.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#105: Protein uS7m-2


Mass: 9622.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#109: Protein mL105


Mass: 15669.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#113: Protein Unknown


Mass: 6230.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#114: Protein Unknown


Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)

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Protein/peptide , 15 types, 15 molecules AAABADXiBCYbUaUdUeUhUiUjUkUlUm

#35: Protein/peptide bL33m


Mass: 5921.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#36: Protein/peptide bL34m


Mass: 6149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#38: Protein/peptide bL36m


Mass: 5495.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#56: Protein/peptide mL128


Mass: 2949.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#90: Protein/peptide mS38


Mass: 4004.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#95: Protein/peptide mS108


Mass: 5864.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#110: Protein/peptide Unknown


Mass: 2813.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#111: Protein/peptide Unknown


Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#112: Protein/peptide Unknown


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#115: Protein/peptide Unknown


Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#116: Protein/peptide Unknown


Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#117: Protein/peptide Unknown


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#118: Protein/peptide Unknown


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#119: Protein/peptide Unknown


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)
#120: Protein/peptide Unknown


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella magna (plant)

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Non-polymers , 5 types, 648 molecules

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


Mass: 24.305 Da / Num. of mol.: 112 / Source method: obtained synthetically / Formula: Mg
#122: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: K
#123: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#124: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#125: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mitochondrial ribosome from Polytomella magna in complex with A and P site tRNA as well as mRNA
Type: RIBOSOME / Entity ID: #1-#120 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Polytomella magna (plant)
Buffer solutionpH: 7.45
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
25 mMMagnesium ChlorideMgCl21
350 mMPotassium ChlorideKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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 / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 45850
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1RELION3.0.1particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.9.5model fitting
9RELION3.0.1initial Euler assignment
10RELION3.0.1final Euler assignment
11RELION3.0.1classification
12RELION3.0.13D reconstruction
13Rosettamodel refinement
14PHENIX3874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2999000
3D reconstructionResolution: 3.2 Å / Resolution method: OTHER / Num. of particles: 76000 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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