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- PDB-5aj4: Structure of the 55S mammalian mitoribosome. -

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Basic information

Entry
Database: PDB / ID: 5aj4
TitleStructure of the 55S mammalian mitoribosome.
Components
  • (MITORIBOSOMAL ...Mitochondrial ribosome) x 82
  • (UNASSIGNED HELICES) x 2
  • 28S RIBOSOMAL PROTEIN S18B, MITOCHONDRIALRibosome
  • MRNAMessenger RNA
  • P-SITE AND A-SITE TRNA
  • UNASSIGNED SECONDARY STRUCTURE ELEMENTS
KeywordsRIBOSOME / TRANSLATION / MITOCHONDRIA / MAMMALIAN 55S MITORIBOSOME / MAMMALIAN 55S MITOCHONDRIAL RIBOSOME / 28S SMALL SUBUNIT / 39S LARGE SUBUNIT / MRNA / TRNA / PTC / DECODING CENTER / CRYO- EM / SINGLE PARTICLE ANALYSIS
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial ribosome assembly / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial ribosome assembly / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / organelle membrane / RNA processing / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / 5S rRNA binding / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coiled-coil domain-containing protein 142 / Coiled-coil protein 142 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 ...Coiled-coil domain-containing protein 142 / Coiled-coil protein 142 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / 40S ribosomal protein rpS2 (S5p), N-terminal / Pentatricopeptide repeat domain / 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 / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / MRPL44, double-stranded RNA binding domain / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / CHCH / CHCH domain / : / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L15, bacterial-type / Ribosomal protein S18 / 50S ribosomal protein uL4 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / : / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein S2
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / 28S ribosomal protein S17, mitochondrial / : / : / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein bL17m / 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 / : / 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 mS26 / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / 39S ribosomal protein L18, mitochondrial isoform 1 / 28S ribosomal protein S35, mitochondrial isoform 1 / Coiled-coil domain containing 142 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / : / Mitochondrial ribosomal protein S24 / Large ribosomal subunit protein uL30m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / : / Large ribosomal subunit protein bL35m / : / Large ribosomal subunit protein mL50 / : / Large ribosomal subunit protein bL19m / : / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS40 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein bL34m
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGreber, B.J. / Bieri, P. / Leibundgut, M. / Leitner, A. / Aebersold, R. / Boehringer, D. / Ban, N.
CitationJournal: Science / Year: 2015
Title: Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Authors: Basil J Greber / Philipp Bieri / Marc Leibundgut / Alexander Leitner / Ruedi Aebersold / Daniel Boehringer / Nenad Ban /
Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of ...Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.
History
DepositionFeb 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references / Other / Structure summary
Revision 1.2May 25, 2016Group: Source and taxonomy
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Apr 4, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_nat / struct_ref_seq
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.2Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_conn.pdbx_leaving_atom_flag
Remark 700SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
AA: MITORIBOSOMAL 12S Ribosomal RNA
AB: MITORIBOSOMAL PROTEIN US2M, MRPS2
AC: MITORIBOSOMAL PROTEIN US3M, MRPS24
AE: MITORIBOSOMAL PROTEIN US5M, MRPS5
AF: MITORIBOSOMAL PROTEIN BS6M, MRPS6
AG: MITORIBOSOMAL PROTEIN US7M, MRPS7
AI: MITORIBOSOMAL PROTEIN US9M, MRPS9
AJ: MITORIBOSOMAL PROTEIN US10M, MRPS10
AK: MITORIBOSOMAL PROTEIN US11M, MRPS11
AL: MITORIBOSOMAL PROTEIN US12M, MRPS12
AN: MITORIBOSOMAL PROTEIN US14M, MRPS14
AO: MITORIBOSOMAL PROTEIN US15M, MRPS15
AP: MITORIBOSOMAL PROTEIN BS16M, MRPS16
AQ: MITORIBOSOMAL PROTEIN US17M, MRPS17
AR: MITORIBOSOMAL PROTEIN BS18M, MRPS18C
AU: MITORIBOSOMAL PROTEIN BS21M, MRPS21
AV: P-SITE AND A-SITE TRNA
AX: MRNA
AY: P-SITE AND A-SITE TRNA
Aa: MITORIBOSOMAL PROTEIN MS22, MRPS22
Ab: MITORIBOSOMAL PROTEIN MS23, MRPS23
Ac: MITORIBOSOMAL PROTEIN MS25, MRPS25
Ad: MITORIBOSOMAL PROTEIN MS26, MRPS26
Ae: MITORIBOSOMAL PROTEIN MS27, MRPS27
Af: MITORIBOSOMAL PROTEIN MS28, MRPS28
Ag: MITORIBOSOMAL PROTEIN MS29, MRPS29
Ah: MITORIBOSOMAL PROTEIN MS31, MRPS31
Ai: MITORIBOSOMAL PROTEIN MS33, MRPS33
Aj: MITORIBOSOMAL PROTEIN MS34, MRPS34
Ak: MITORIBOSOMAL PROTEIN MS35, MRPS35
Am: MITORIBOSOMAL PROTEIN MS37, MRPS37
An: MITORIBOSOMAL PROTEIN MS38, MRPS38
Ao: MITORIBOSOMAL PROTEIN MS39, MRPS39
Ap: 28S RIBOSOMAL PROTEIN S18B, MITOCHONDRIAL
As: UNASSIGNED HELICES
Az: UNASSIGNED HELICES
B0: MITORIBOSOMAL PROTEIN BL27M, MRPL27
B1: MITORIBOSOMAL PROTEIN BL28M, MRPL28
B2: MITORIBOSOMAL PROTEIN UL29M, MRPL47
B3: MITORIBOSOMAL PROTEIN UL30M, MRPL30
B4: MITORIBOSOMAL PROTEIN BL31M, MRPL55
B5: MITORIBOSOMAL PROTEIN BL32M, MRPL32
B6: MITORIBOSOMAL PROTEIN BL33M, MRPL33
B7: MITORIBOSOMAL PROTEIN BL34M, MRPL34
B8: MITORIBOSOMAL PROTEIN BL35M, MRPL35
B9: MITORIBOSOMAL PROTEIN BL36M, MRPL36
BA: MITORIBOSOMAL 16S Ribosomal RNA
BB: MITORIBOSOMAL CP TRNA
BD: MITORIBOSOMAL PROTEIN UL2M, MRPL2
BE: MITORIBOSOMAL PROTEIN UL3M, MRPL3
BF: MITORIBOSOMAL PROTEIN UL4M, MRPL4
BI: MITORIBOSOMAL PROTEIN BL9M, MRPL9
BJ: MITORIBOSOMAL PROTEIN UL10M, MRPL10
BK: MITORIBOSOMAL PROTEIN UL11M, MRPL11
BN: MITORIBOSOMAL PROTEIN UL13M, MRPL13
BO: MITORIBOSOMAL PROTEIN UL14M, MRPL14
BP: MITORIBOSOMAL PROTEIN UL15M, MRPL15
BQ: MITORIBOSOMAL PROTEIN UL16M, MRPL16
BR: MITORIBOSOMAL PROTEIN BL17M, MRPL17
BS: MITORIBOSOMAL PROTEIN UL18M, MRPL18
BT: MITORIBOSOMAL PROTEIN BL19M, MRPL19
BU: MITORIBOSOMAL PROTEIN BL20M, MRPL20
BV: MITORIBOSOMAL PROTEIN BL21M, MRPL21
BW: MITORIBOSOMAL PROTEIN UL22M, MRPL22
BX: MITORIBOSOMAL PROTEIN UL23M, MRPL23
BY: MITORIBOSOMAL PROTEIN UL24M, MRPL24
Ba: MITORIBOSOMAL PROTEIN ML37, MRPL37
Bb: MITORIBOSOMAL PROTEIN ML38, MRPL38
Bc: MITORIBOSOMAL PROTEIN ML39, MRPL39
Bd: MITORIBOSOMAL PROTEIN ML40, MRPL40
Be: MITORIBOSOMAL PROTEIN ML41, MRPL41
Bf: MITORIBOSOMAL PROTEIN ML42, MRPL42
Bg: MITORIBOSOMAL PROTEIN ML43, MRPL43
Bh: MITORIBOSOMAL PROTEIN ML44, MRPL44
Bi: MITORIBOSOMAL PROTEIN ML45, MRPL45
Bj: MITORIBOSOMAL PROTEIN ML46, MRPL46
Bk: MITORIBOSOMAL PROTEIN ML48, MRPL48
Bl: MITORIBOSOMAL PROTEIN ML49, MRPL49
Bm: MITORIBOSOMAL PROTEIN ML50, MRPL50
Bn: MITORIBOSOMAL PROTEIN ML51, MRPL51
Bo: MITORIBOSOMAL PROTEIN ML52, MRPL52
Bp: MITORIBOSOMAL PROTEIN ML53, MRPL53
Bq: MITORIBOSOMAL PROTEIN ML54, MRPL54
Bt: MITORIBOSOMAL PROTEIN ML63, MRPL57
Bu: MITORIBOSOMAL PROTEIN ML62, MRPL58
Bv: MITORIBOSOMAL PROTEIN ML64, MRPL59
Bw: MITORIBOSOMAL PROTEIN ML65, MRPS30
Bx: MITORIBOSOMAL PROTEIN ML66, MRPS18A
Bz: UNASSIGNED SECONDARY STRUCTURE ELEMENTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,758,859447
Polymers2,749,49389
Non-polymers9,367358
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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MITORIBOSOMAL ... , 82 types, 82 molecules AAABACAEAFAGAIAJAKALANAOAPAQARAUAaAbAcAdAeAfAgAhAiAjAkAmAnAo...

#1: RNA chain MITORIBOSOMAL 12S Ribosomal RNA


Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: GenBank: 223972359
#2: Protein MITORIBOSOMAL PROTEIN US2M, MRPS2


Mass: 24986.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S001
#3: Protein MITORIBOSOMAL PROTEIN US3M, MRPS24


Mass: 15238.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1ST79
#4: Protein MITORIBOSOMAL PROTEIN US5M, MRPS5


Mass: 37306.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SU66
#5: Protein MITORIBOSOMAL PROTEIN BS6M, MRPS6


Mass: 14283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS18M / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#6: Protein MITORIBOSOMAL PROTEIN US7M, MRPS7


Mass: 24523.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RVX4
#7: Protein MITORIBOSOMAL PROTEIN US9M, MRPS9


Mass: 35515.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#8: Protein MITORIBOSOMAL PROTEIN US10M, MRPS10


Mass: 23192.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#9: Protein MITORIBOSOMAL PROTEIN US11M, MRPS11


Mass: 14251.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SRT1
#10: Protein MITORIBOSOMAL PROTEIN US12M, MRPS12


Mass: 12030.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#11: Protein MITORIBOSOMAL PROTEIN US14M, MRPS14


Mass: 15120.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#12: Protein MITORIBOSOMAL PROTEIN US15M, MRPS15


Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#13: Protein MITORIBOSOMAL PROTEIN BS16M, MRPS16


Mass: 13273.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH MS25 / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SU70
#14: Protein MITORIBOSOMAL PROTEIN US17M, MRPS17


Mass: 12133.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RIU0
#15: Protein MITORIBOSOMAL PROTEIN BS18M, MRPS18C


Mass: 11224.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS6M / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#16: Protein MITORIBOSOMAL PROTEIN BS21M, MRPS21


Mass: 10551.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3L971
#19: Protein MITORIBOSOMAL PROTEIN MS22, MRPS22


Mass: 39258.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#20: Protein MITORIBOSOMAL PROTEIN MS23, MRPS23


Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#21: Protein MITORIBOSOMAL PROTEIN MS25, MRPS25


Mass: 19508.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH BS16M / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#22: Protein MITORIBOSOMAL PROTEIN MS26, MRPS26


Mass: 20854.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S8A5
#23: Protein MITORIBOSOMAL PROTEIN MS27, MRPS27


Mass: 28613.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PPR FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#24: Protein MITORIBOSOMAL PROTEIN MS28, MRPS28


Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OB-FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#25: Protein MITORIBOSOMAL PROTEIN MS29, MRPS29


Mass: 44924.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: AAA ATPASE-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#26: Protein MITORIBOSOMAL PROTEIN MS31, MRPS31


Mass: 12382.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RME2
#27: Protein MITORIBOSOMAL PROTEIN MS33, MRPS33


Mass: 11720.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S8G3
#28: Protein MITORIBOSOMAL PROTEIN MS34, MRPS34


Mass: 25681.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SH3-LIKE CORE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#29: Protein MITORIBOSOMAL PROTEIN MS35, MRPS35


Mass: 31653.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEPTIDYL TRNA HYDROLASE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SG95
#30: Protein MITORIBOSOMAL PROTEIN MS37, MRPS37


Mass: 13343.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SU49
#31: Protein MITORIBOSOMAL PROTEIN MS38, MRPS38


Mass: 9078.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#32: Protein MITORIBOSOMAL PROTEIN MS39, MRPS39


Mass: 48540.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PPR FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: K7GKS8
#36: Protein MITORIBOSOMAL PROTEIN BL27M, MRPL27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RT79
#37: Protein MITORIBOSOMAL PROTEIN BL28M, MRPL28


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RGV8, UniProt: A0A0R4J8D5*PLUS
#38: Protein MITORIBOSOMAL PROTEIN UL29M, MRPL47


Mass: 30085.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#39: Protein MITORIBOSOMAL PROTEIN UL30M, MRPL30


Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1STE5
#40: Protein MITORIBOSOMAL PROTEIN BL31M, MRPL55


Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LQ65
#41: Protein MITORIBOSOMAL PROTEIN BL32M, MRPL32


Mass: 21537.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LTC4
#42: Protein MITORIBOSOMAL PROTEIN BL33M, MRPL33


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#43: Protein MITORIBOSOMAL PROTEIN BL34M, MRPL34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: W5IDC1
#44: Protein MITORIBOSOMAL PROTEIN BL35M, MRPL35


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SVC5
#45: Protein MITORIBOSOMAL PROTEIN BL36M, MRPL36


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3LDE8
#46: RNA chain MITORIBOSOMAL 16S Ribosomal RNA


Mass: 504538.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#47: RNA chain MITORIBOSOMAL CP TRNA


Mass: 15180.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BUILT AS POLY-PURINE AND POLY-PYRIMIDINE / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#48: Protein MITORIBOSOMAL PROTEIN UL2M, MRPL2


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RRN2
#49: Protein MITORIBOSOMAL PROTEIN UL3M, MRPL3


Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#50: Protein MITORIBOSOMAL PROTEIN UL4M, MRPL4


Mass: 33251.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S3J8
#51: Protein MITORIBOSOMAL PROTEIN BL9M, MRPL9


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
#52: Protein MITORIBOSOMAL PROTEIN UL10M, MRPL10


Mass: 29449.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH PROTEIN ML66 / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RWJ0
#53: Protein MITORIBOSOMAL PROTEIN UL11M, MRPL11


Mass: 20809.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RU54
#54: Protein MITORIBOSOMAL PROTEIN UL13M, MRPL13


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S286
#55: Protein MITORIBOSOMAL PROTEIN UL14M, MRPL14


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RQV7
#56: Protein MITORIBOSOMAL PROTEIN UL15M, MRPL15


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
#57: Protein MITORIBOSOMAL PROTEIN UL16M, MRPL16


Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RI89
#58: Protein MITORIBOSOMAL PROTEIN BL17M, MRPL17


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RMQ4
#59: Protein MITORIBOSOMAL PROTEIN UL18M, MRPL18


Mass: 20582.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SB64, UniProt: A0A0R4J8D5*PLUS
#60: Protein MITORIBOSOMAL PROTEIN BL19M, MRPL19


Mass: 32957.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-TERMINAL RESIDUES 54-68 CONTACT THE 28S SUBUNIT FOOT AND ARE BUILT AS UNK
Source: (natural) SUS SCROFA (pig) / References: UniProt: I3LNJ0
#61: Protein MITORIBOSOMAL PROTEIN BL20M, MRPL20


Mass: 17554.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: F1RJD0
#62: Protein MITORIBOSOMAL PROTEIN BL21M, MRPL21


Mass: 23154.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: F1RY70
#63: Protein MITORIBOSOMAL PROTEIN UL22M, MRPL22


Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#64: Protein MITORIBOSOMAL PROTEIN UL23M, MRPL23


Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#65: Protein MITORIBOSOMAL PROTEIN UL24M, MRPL24


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: F1RHJ1
#66: Protein MITORIBOSOMAL PROTEIN ML37, MRPL37


Mass: 47935.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RESTRICTION ENDONUCLEASE-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#67: Protein MITORIBOSOMAL PROTEIN ML38, MRPL38


Mass: 44656.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEBP-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RW03
#68: Protein MITORIBOSOMAL PROTEIN ML39, MRPL39


Mass: 38523.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRNA SYNTHETASE DOMAIN LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#69: Protein MITORIBOSOMAL PROTEIN ML40, MRPL40


Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HOMOLOG TO YEAST ML40 / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RK59
#70: Protein MITORIBOSOMAL PROTEIN ML41, MRPL41


Mass: 15073.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HOMOLOG TO YEAST ML41 / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#71: Protein MITORIBOSOMAL PROTEIN ML42, MRPL42


Mass: 15908.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#72: Protein MITORIBOSOMAL PROTEIN ML43, MRPL43


Mass: 17728.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: THIOREDOXIN LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S8U4
#73: Protein MITORIBOSOMAL PROTEIN ML44, MRPL44


Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNASE III DOMAIN-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SR64
#74: Protein MITORIBOSOMAL PROTEIN ML45, MRPL45


Mass: 36119.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CYSTATIN-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#75: Protein MITORIBOSOMAL PROTEIN ML46, MRPL46


Mass: 32215.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NUDIX HYDROLASE-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SRT0
#76: Protein MITORIBOSOMAL PROTEIN ML48, MRPL48


Mass: 23749.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FERREDOXIN-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#77: Protein MITORIBOSOMAL PROTEIN ML49, MRPL49


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: EIF1-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#78: Protein MITORIBOSOMAL PROTEIN ML50, MRPL50


Mass: 18351.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACP-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: I3L9H6
#79: Protein MITORIBOSOMAL PROTEIN ML51, MRPL51


Mass: 15219.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STAR PROTEIN DIMERIZATION DOMAIN / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#80: Protein MITORIBOSOMAL PROTEIN ML52, MRPL52


Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1S9B7
#81: Protein MITORIBOSOMAL PROTEIN ML53, MRPL53


Mass: 12015.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: THIOREDOXIN-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1SLH8
#82: Protein MITORIBOSOMAL PROTEIN ML54, MRPL54


Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#83: Protein MITORIBOSOMAL PROTEIN ML63, MRPL57


Mass: 12001.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HOMEO-DOMAIN-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#84: Protein MITORIBOSOMAL PROTEIN ML62, MRPL58


Mass: 23281.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PEPTIDYL-TRNA HYDROLASE / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: W5IDC0
#85: Protein MITORIBOSOMAL PROTEIN ML64, MRPL59


Mass: 25347.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#86: Protein MITORIBOSOMAL PROTEIN ML65, MRPS30


Mass: 49071.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RESTRICTION ENDONUCLEASE-LIKE FOLD / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#87: Protein MITORIBOSOMAL PROTEIN ML66, MRPS18A


Mass: 22273.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZINC BINDING MOTIF WITH UL10 / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: F1RRH6

-
RNA chain , 2 types, 3 molecules AVAYAX

#17: RNA chain P-SITE AND A-SITE TRNA


Mass: 19163.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#18: RNA chain MRNA / Messenger RNA


Mass: 3545.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER

-
Protein , 2 types, 2 molecules ApBz

#33: Protein 28S RIBOSOMAL PROTEIN S18B, MITOCHONDRIAL / Ribosome


Mass: 22027.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER / References: UniProt: Q767K8
#88: Protein UNASSIGNED SECONDARY STRUCTURE ELEMENTS


Mass: 8017.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BUILT AS UNK / Source: (natural) SUS SCROFA (pig) / Organ: LIVER

-
Protein/peptide , 2 types, 2 molecules AsAz

#34: Protein/peptide UNASSIGNED HELICES


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
#35: Protein/peptide UNASSIGNED HELICES


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER

-
Non-polymers , 4 types, 698 molecules

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


Mass: 24.305 Da / Num. of mol.: 351 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#91: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#92: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsRESIDUES 251-266 OF US9M BUILT AS UNK RESIDUES 309-356 OF MS22 BUILT AS UNK PPR FOLD OF mS27 BUILT ...RESIDUES 251-266 OF US9M BUILT AS UNK RESIDUES 309-356 OF MS22 BUILT AS UNK PPR FOLD OF mS27 BUILT AS UNK RESIDUES 52-69 OF MS29 BUILT AS UNK RESIDUES 152-158 OF MS34 BUILT AS UNK N-TERMINAL SEQUENCE OF MS38 IS MISSING PPR FOLD OF MS39 BUILT AS UNK ALL RESIDUES OF CHAINS s,z (UNASSIGNED HELICES AND FOLDS) BUILT AS UNK MRNA BUILT AS POLY-PYRIMIDINE A- AND P-SITE tRNAs (CHAINS Y,V) BUILT AS POLY-PYRIMIDINE AND POLY-PURINE GENBANK REFERENCE FOR CHAIN F EW168165.2 GENBANK REFERENCE FOR CHAIN J AK233895.1 GENBANK REFERENCE FOR CHAIN N FD598185.1 GENBANK REFERENCE FOR CHAIN O AK343256.1 GENBANK REFERENCE FOR CHAIN a AK348087.1 GENBANK REFERENCE FOR CHAIN b XP_005669015.1 GENBANK REFERENCE FOR CHAIN f DN116920.1 GENBANK REFERENCE FOR CHAIN g XP_003361167.1 GENBANK REFERENCE FOR CHAIN j NP_001231761.1

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: SUS SCROFA 55S MITOCHONDRIAL RIBOSOME / Type: RIBOSOME
Details: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM.
Buffer solutionName: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT / pH: 7.4 / Details: 20 MM HEPES-KOH, 50 MM KCL, 40 MM MGCL2, 1 MM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Details: MIXTURE OF LIQUID ETHANE AND PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 30, 2014
Details: IMAGES WERE ACQUIRED IN 2 SESSIONS ON A FEI TITAN KRIOS IN MAY 2014.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3EMAN1.93D reconstruction
4RELION1.23D reconstruction
5RELION1.33D reconstruction
CTF correctionDetails: PER DETECTOR FRAME
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM LIKELIHOOD BASED REFINEMENT IMPLEMENTED IN RELION.
Resolution: 3.8 Å / Num. of particles: 60872 / Actual pixel size: 1.39 Å
Details: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION. THE COMBINED COORDINATES WERE REFINED IN RECIPROCAL SPACE USING PHENIX.REFINE AGAINST THE MLHL TARGET. ...Details: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION. THE COMBINED COORDINATES WERE REFINED IN RECIPROCAL SPACE USING PHENIX.REFINE AGAINST THE MLHL TARGET. FOR THIS, THE CRYO-EM MAPS (EMD-2914) WERE CONVERTED TO RECIPROCAL SPACE STRUCTURE FACTORS.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--HIGH RESOLUTION CRYO-EM
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43028 23144 178 118 66468

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