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 / Small ribosomal subunit protein uS5m, 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 / 39S ribosomal protein L52, mitochondrial / : / Mitoribosomal protein mL52 / Ribosomal protein L35, mitochondrial / 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 L10 / Ribosomal protein L10P / 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, RNA binding domain / Ribosomal protein L11/L12 / 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 S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / 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 L32p / Ribosomal protein L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / : / 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 / Mitochondrial ribosomal protein S17 / : / : / 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 species
SUS SCROFA (pig)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
Journal: 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
Deposition
Feb 20, 2015
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Apr 22, 2015
Provider: repository / Type: Initial release
Revision 1.1
May 6, 2015
Group: Database references / Other / Structure summary
SHEET 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.
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
MITORIBOSOMALPROTEINUS2M, 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
MITORIBOSOMALPROTEINUS3M, 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
MITORIBOSOMALPROTEINUS5M, 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
MITORIBOSOMALPROTEINBS6M, 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
MITORIBOSOMALPROTEINUS7M, 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
MITORIBOSOMALPROTEINUS9M, 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
MITORIBOSOMALPROTEINUS10M, 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
MITORIBOSOMALPROTEINUS11M, 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
MITORIBOSOMALPROTEINUS12M, 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
MITORIBOSOMALPROTEINUS14M, 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
MITORIBOSOMALPROTEINUS15M, 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
MITORIBOSOMALPROTEINBS16M, 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
MITORIBOSOMALPROTEINUS17M, 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
MITORIBOSOMALPROTEINBS18M, 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
MITORIBOSOMALPROTEINBS21M, 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
MITORIBOSOMALPROTEINMS22, 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
MITORIBOSOMALPROTEINMS23, 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
MITORIBOSOMALPROTEINMS25, 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
MITORIBOSOMALPROTEINMS26, 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
MITORIBOSOMALPROTEINMS27, 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
MITORIBOSOMALPROTEINMS28, 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
MITORIBOSOMALPROTEINMS29, 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
MITORIBOSOMALPROTEINMS31, 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
MITORIBOSOMALPROTEINMS33, 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
MITORIBOSOMALPROTEINMS34, 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
MITORIBOSOMALPROTEINMS35, 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
MITORIBOSOMALPROTEINMS37, 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
MITORIBOSOMALPROTEINMS38, 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
MITORIBOSOMALPROTEINMS39, 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
MITORIBOSOMALPROTEINBL27M, 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
MITORIBOSOMALPROTEINBL28M, 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
MITORIBOSOMALPROTEINUL29M, 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
MITORIBOSOMALPROTEINUL30M, 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
MITORIBOSOMALPROTEINBL31M, 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
MITORIBOSOMALPROTEINBL32M, 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
MITORIBOSOMALPROTEINBL33M, 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
MITORIBOSOMALPROTEINBL34M, 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
MITORIBOSOMALPROTEINBL35M, 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
MITORIBOSOMALPROTEINBL36M, 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
MITORIBOSOMAL16SRibosomalRNA
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
MITORIBOSOMALCPTRNA
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
MITORIBOSOMALPROTEINUL2M, 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
MITORIBOSOMALPROTEINUL3M, 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
MITORIBOSOMALPROTEINUL4M, 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
MITORIBOSOMALPROTEINBL9M, 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
MITORIBOSOMALPROTEINUL10M, 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
MITORIBOSOMALPROTEINUL11M, 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
MITORIBOSOMALPROTEINUL13M, 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
MITORIBOSOMALPROTEINUL14M, 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
MITORIBOSOMALPROTEINUL15M, 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
MITORIBOSOMALPROTEINUL16M, 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
MITORIBOSOMALPROTEINBL17M, 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
MITORIBOSOMALPROTEINUL18M, 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
MITORIBOSOMALPROTEINBL19M, 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
MITORIBOSOMALPROTEINBL20M, 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
MITORIBOSOMALPROTEINBL21M, 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
MITORIBOSOMALPROTEINUL22M, MRPL22
Mass: 24313.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#64: Protein
MITORIBOSOMALPROTEINUL23M, MRPL23
Mass: 17643.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig)
#65: Protein
MITORIBOSOMALPROTEINUL24M, 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
MITORIBOSOMALPROTEINML37, 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
MITORIBOSOMALPROTEINML38, 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
MITORIBOSOMALPROTEINML39, 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
MITORIBOSOMALPROTEINML40, 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
MITORIBOSOMALPROTEINML41, 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
MITORIBOSOMALPROTEINML42, 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
MITORIBOSOMALPROTEINML43, 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
MITORIBOSOMALPROTEINML44, 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
MITORIBOSOMALPROTEINML45, 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
MITORIBOSOMALPROTEINML46, 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
MITORIBOSOMALPROTEINML48, 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
MITORIBOSOMALPROTEINML49, 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
MITORIBOSOMALPROTEINML50, 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
MITORIBOSOMALPROTEINML51, 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
MITORIBOSOMALPROTEINML52, 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
MITORIBOSOMALPROTEINML53, 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
MITORIBOSOMALPROTEINML54, 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
MITORIBOSOMALPROTEINML63, 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
MITORIBOSOMALPROTEINML62, 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
MITORIBOSOMALPROTEINML64, 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
MITORIBOSOMALPROTEINML65, 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
MITORIBOSOMALPROTEINML66, 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-SITEANDA-SITETRNA
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
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
28SRIBOSOMALPROTEINS18B, MITOCHONDRIAL
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
UNASSIGNEDSECONDARYSTRUCTUREELEMENTS
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
UNASSIGNEDHELICES
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
UNASSIGNEDHELICES
Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
RESIDUES 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
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Experimental details
-
Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
-
Sample preparation
Component
Name: SUS SCROFA 55S MITOCHONDRIAL RIBOSOME / Type: RIBOSOME Details: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM.
Buffer solution
Name: 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
Specimen
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support
Details: CARBON
Vitrification
Instrument: 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
Microscopy
Model: FEI TITAN KRIOS / Date: May 30, 2014 Details: IMAGES WERE ACQUIRED IN 2 SESSIONS ON A FEI TITAN KRIOS IN MAY 2014.
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holder
Temperature: 85 K
Image recording
Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelength
Relative weight: 1
-
Processing
EM software
ID
Name
Version
Category
1
CTFFIND
3
CTFcorrection
2
UCSF Chimera
modelfitting
3
EMAN
1.9
3Dreconstruction
4
RELION
1.2
3Dreconstruction
5
RELION
1.3
3Dreconstruction
CTF correction
Details: PER DETECTOR FRAME
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Method: 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 building
Protocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--HIGH RESOLUTION CRYO-EM
Refinement
Highest resolution: 3.8 Å
Refinement step
Cycle: LAST / Highest resolution: 3.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
43028
23144
178
118
66468
+
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