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- PDB-4ce4: 39S large subunit of the porcine mitochondrial ribosome -

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Basic information

Entry
Database: PDB / ID: 4ce4
Title39S large subunit of the porcine mitochondrial ribosome
Components
  • (UNASSIGNED HELICES) x 2
  • 16S Ribosomal RNA
  • ICT1
  • MRPL13
  • MRPL14
  • MRPL15
  • MRPL16
  • MRPL17
  • MRPL18
  • MRPL19
  • MRPL2
  • MRPL20
  • MRPL21
  • MRPL22
  • MRPL23
  • MRPL24
  • MRPL27
  • MRPL28
  • MRPL3
  • MRPL30
  • MRPL32
  • MRPL33
  • MRPL34
  • MRPL35
  • MRPL36
  • MRPL38
  • MRPL39
  • MRPL4
  • MRPL44
  • MRPL45
  • MRPL47
  • MRPL49
  • MRPL52
  • MRPL9
  • THIOREDOXIN FOLD
  • UNASSIGNED RNA
KeywordsRIBOSOME / MAMMALIAN MITOCHONDRIAL RIBOSOME / 39S LARGE RIBOSOMAL SUBUNIT / TRANSLATION / RIBOSOMAL PROTEINS / RRNA / POLYPEPTIDE EXIT SITE / MEMBRANE ASSOCIATION
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial translation ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial translational elongation / microprocessor complex / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial translation / organelle membrane / RNA processing / double-stranded RNA binding / large ribosomal subunit / 5S rRNA binding / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein ...Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / 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 / Beta-grasp domain superfamily / NTF2-like domain superfamily / 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 L22, bacterial/chloroplast-type / Ribosomal protein L35 / 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 / 50S ribosomal protein uL4 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L15 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L30p/L7e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein S11 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1 family / Zinc-binding ribosomal protein / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / 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 / : ...: / 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 / : / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein mL38 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein bL21m / : / Mitochondrial ribosomal protein L4 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL29m / Mitochondrial ribosomal protein L39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL35m / : / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / 39S ribosomal protein L22, mitochondrial / Mrpl23 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein bL34m
Similarity search - Component
Biological speciesSUS SCROFA DOMESTICA (domestic pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsGreber, B.J. / Boehringer, D. / Leitner, A. / Bieri, P. / Voigts-Hoffmann, F. / Erzberger, J.P. / Leibundgut, M. / Aebersold, R. / Ban, N.
CitationJournal: Nature / Year: 2014
Title: Architecture of the large subunit of the mammalian mitochondrial ribosome.
Authors: Basil J Greber / Daniel Boehringer / Alexander Leitner / Philipp Bieri / Felix Voigts-Hoffmann / Jan P Erzberger / Marc Leibundgut / Ruedi Aebersold / Nenad Ban /
Abstract: Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by ...Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.
History
DepositionNov 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Jan 29, 2014Group: Database references
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / em_image_scans / em_software / entity / 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 / _entity.pdbx_description / _entity.src_method
Revision 2.1Apr 10, 2019Group: Data collection / Database references / Category: pdbx_seq_map_depositor_info / struct_ref
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_ref.db_name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Movie
  • Deposited structure unit
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: MRPL27
1: MRPL28
2: MRPL47
3: MRPL30
5: MRPL32
6: MRPL33
7: MRPL34
8: MRPL35
9: MRPL36
A: 16S Ribosomal RNA
B: UNASSIGNED RNA
D: MRPL2
E: MRPL3
F: MRPL4
I: MRPL9
N: MRPL13
O: MRPL14
P: MRPL15
Q: MRPL16
R: MRPL17
S: MRPL18
T: MRPL19
U: MRPL20
V: MRPL21
W: MRPL22
X: MRPL23
Y: MRPL24
b: MRPL38
c: MRPL39
h: MRPL44
i: MRPL45
l: MRPL49
o: MRPL52
u: ICT1
v: UNASSIGNED HELICES
w: UNASSIGNED HELICES
x: THIOREDOXIN FOLD
z: UNASSIGNED HELICES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,307,23640
Polymers1,307,10538
Non-polymers1312
Water0
1


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

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Components

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Protein , 35 types, 36 molecules 012356789DEFINOPQRSTUVWXYbchil...

#1: Protein MRPL27


Mass: 15943.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RT79
#2: Protein MRPL28


Mass: 30148.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RGV8, UniProt: A0A0R4J8D5*PLUS
#3: Protein MRPL47


Mass: 30085.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1SGC7*PLUS
#4: Protein MRPL30


Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1STE5
#5: Protein MRPL32


Mass: 15932.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: I3LTC4
#6: Protein MRPL33


Mass: 7508.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion
#7: Protein MRPL34


Mass: 10871.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: W5IDC1*PLUS
#8: Protein MRPL35


Mass: 21548.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1SVC5
#9: Protein MRPL36


Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: I3LDE8
#12: Protein MRPL2


Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RRN2
#13: Protein MRPL3


Mass: 43708.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RX24
#14: Protein MRPL4


Mass: 24306.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1S3J8
#15: Protein MRPL9


Mass: 30373.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: I3LR45
#16: Protein MRPL13


Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1S286
#17: Protein MRPL14


Mass: 15955.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RQV7
#18: Protein MRPL15


Mass: 32471.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RSH0
#19: Protein MRPL16


Mass: 22745.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RI89
#20: Protein MRPL17


Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RMQ4
#21: Protein MRPL18


Mass: 20582.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1SB64, UniProt: A0A0R4J8D5*PLUS
#22: Protein MRPL19


Mass: 33441.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: I3LNJ0
#23: Protein MRPL20


Mass: 15563.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RJD0
#24: Protein MRPL21


Mass: 22894.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RY70
#25: Protein MRPL22


Mass: 15072.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: W5IDB8*PLUS
#26: Protein MRPL23


Mass: 9807.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: W5IDB9*PLUS
#27: Protein MRPL24


Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RHJ1
#28: Protein MRPL38


Mass: 44656.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1RW03
#29: Protein MRPL39


Mass: 33832.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1SHP6
#30: Protein MRPL44


Mass: 32637.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: F1SR64
#31: Protein MRPL45


Mass: 36119.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: I3LGM5*PLUS
#32: Protein MRPL49


Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: A0A0R4J8D5*PLUS
#33: Protein MRPL52


Mass: 4783.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion
#34: Protein ICT1


Mass: 23545.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: W5IDC0*PLUS
#35: Protein UNASSIGNED HELICES


Mass: 7762.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion
#36: Protein THIOREDOXIN FOLD


Mass: 7251.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion
#37: Protein UNASSIGNED HELICES


Mass: 36272.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion

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RNA chain , 2 types, 2 molecules AB

#10: RNA chain 16S Ribosomal RNA /


Mass: 501424.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / References: GenBank: 4220565
#11: RNA chain UNASSIGNED RNA


Mass: 5641.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA DOMESTICA (domestic pig) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion

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Non-polymers , 1 types, 2 molecules

#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsCHAINS I W X 7: ACCESSION CODE PROVIDED FOR MRNA SEQUENCE, PROTEIN SEQUENCE IS TRANSLATED MRNA. ...CHAINS I W X 7: ACCESSION CODE PROVIDED FOR MRNA SEQUENCE, PROTEIN SEQUENCE IS TRANSLATED MRNA. CHAINS B V W X Z: SEQUENCE UNASSIGNED. CHAIN 2 HAS AUTHOR PROVIDED GENBANK SEQUENCE XP_003132595.1 CHAIN 6 HAS AUTHOR PROVIDED GENBANK SEQUENCE XP_003125332.1 CHAIN 7 HAS AUTHOR PROVIDED GENBANK SEQUENCE AW415886.1 CHAIN C HAS AUTHOR PROVIDED GENBANK SEQUENCE XM_003132745.3 CHAIN I HAS AUTHOR PROVIDED GENBANK SEQUENCE AK350308.1 CHAIN L HAS AUTHOR PROVIDED GENBANK SEQUENCE NP_001231942.1 CHAIN O HAS AUTHOR PROVIDED GENBANK SEQUENCE NP_001172080.1 CHAIN U HAS AUTHOR PROVIDED GENBANK SEQUENCE NP_001231224.1 CHAIN W HAS AUTHOR PROVIDED GENBANK SEQUENCE AK392578.1 CHAIN X HAS AUTHOR PROVIDED GENBANK SEQUENCE AK392218.1

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 39S MITOCHONDRIAL RIBOSOMAL SUBUNIT / Type: RIBOSOME
Buffer solutionName: 20 MM HEPES-KOH PH 7.9, 100 MM KCL, 1 MM DTT, 20 MM MGCL2
pH: 7.9
Details: 20 MM HEPES-KOH PH 7.9, 100 MM KCL, 1 MM DTT, 20 MM MGCL2
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: MANUAL BLOTTING FOLLOWED BY MANUAL PLUNGING INTO LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: IMAGES COLLECTED ON A FEI TITAN KRIOS BETWEEN NOVEMBER 2012 AND JUNE 2013. CALIBRATED MAGNIFICATION 141510 FOR FALCON II DATA AND 99290 FOR FALCON I DATA.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 79 K / Tilt angle max: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Cootmodel fitting
3Omodel fitting
4UCSF Chimeramodel fitting
5IMAGIC53D reconstruction
6RELION3D reconstruction
7SPIDER3D reconstruction
CTF correctionDetails: PER DETECTOR FRAME
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: ANGULAR RECONSTITUTION FOR INITIAL MODEL GENERATION FOLLOWED BY REFINEMENT BY PROJECTION MATCHING
Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232181 / Actual pixel size: 1.41 Å
Details: RESOLUTION DETERMIED ACCORDING TO GOLD STANDARD FSC BY FSC EQUAL 0.143 CRITERION FROM TWO INDEPENDENTLY REFINED DATA HALF SETS
Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: REFINEMENT PROTOCOL--X-RAY STRUCTURES, HOMOLOGY MODELS
Atomic model building
IDPDB-ID 3D fitting-ID
13V2D

3v2d
PDB Unreleased entry

1
21R73

1r73

1
32QYQ

2qyq

1
41QF6

1qf6

1
51O0W

1o0w

1
62CW9

2cw9

1
72XZN

2xzn
PDB Unreleased entry

1
81J26

1j26

1
91S3A

1s3a

1
RefinementHighest resolution: 4.9 Å
Refinement stepCycle: LAST / Highest resolution: 4.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34467 31004 2 0 65473

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