ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L19e, archaeal / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Ribosomal protein L2, archaeal-type / Helix-hairpin-helix domain / Ribosomal L15/L27a, N-terminal / Translation factors / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L18e Similarity search - Domain/homology
VIRGINIAMYCIN S1 / : / : / VIRGINIAMYCIN M1 / : / : / : / : / : / : ...VIRGINIAMYCIN S1 / : / : / VIRGINIAMYCIN M1 / : / : / : / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 Similarity search - Component
Biological species
HALOARCULA MARISMORTUI (Halophile) STREPTOMYCES VIRGINIAE (bacteria)
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KC" 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.
50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules 123ABCDEFHIJKLMNOPQRSTUVWXYZ
#2: Protein
50SRIBOSOMALPROTEINL37E
Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32410
#3: Protein/peptide
50SRIBOSOMALPROTEINL39E
Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22452
#4: Protein
50SRIBOSOMALPROTEINL44E
Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P32411
#7: Protein
50SRIBOSOMALPROTEINL2P
Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P20276
#8: Protein
50SRIBOSOMALPROTEINL3P
Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55378384, UniProt: P20279*PLUS
#9: Protein
50SRIBOSOMALPROTEINL4E
Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12735
#10: Protein
50SRIBOSOMALPROTEINL5P
Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14124
#11: Protein
50SRIBOSOMALPROTEINL6P
Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14135
#12: Protein
50SRIBOSOMALPROTEINL7AE
Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12743
#14: Protein
50SRIBOSOMALPROTEINL10E
Mass: 19942.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231756, UniProt: P60617*PLUS
#15: Protein
50SRIBOSOMALPROTEINL11P
Mass: 17097.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 132647, UniProt: P14122*PLUS
#16: Protein
50SRIBOSOMALPROTEINL13P
Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P29198
#17: Protein
50SRIBOSOMALPROTEINL14P
Mass: 14191.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P22450
#18: Protein
50SRIBOSOMALPROTEINL15P
Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12737
#19: Protein
50SRIBOSOMALPROTEINL15E
Mass: 22275.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231501, UniProt: P60618*PLUS
#20: Protein
50SRIBOSOMALPROTEINL18P
Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14123
#21: Protein
50SRIBOSOMALPROTEINL18E
Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12733
#22: Protein
50SRIBOSOMALPROTEINL19E
Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14119
#23: Protein
50SRIBOSOMALPROTEINL21E
Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12734
#24: Protein
50SRIBOSOMALPROTEINL22P
Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10970
#25: Protein
50SRIBOSOMALPROTEINL23P
Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12732
#26: Protein
50SRIBOSOMALPROTEINL24P
Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10972
#27: Protein
50SRIBOSOMALPROTEINL24E
Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14116
#28: Protein
50SRIBOSOMALPROTEINL29P
Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P10971
#29: Protein
50SRIBOSOMALPROTEINL30P
Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P14121
#30: Protein
50SRIBOSOMALPROTEINL31E
Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P18138
#31: Protein
50SRIBOSOMALPROTEINL32E
Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P12736
#32: Protein
50SRIBOSOMALPROTEINL37AE
Mass: 9409.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: GenBank: 55231162, UniProt: P60619*PLUS
-
VIRGINIAMYCIN ... / Protein , 2 types, 2 molecules 8G
#13: Protein
ACIDICRIBOSOMALPROTEINP0HOMOLOG
Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / References: UniProt: P15825
#5: Protein/peptide
VIRGINIAMYCINS1 / VIRGINIAMYCIN FACTOR S1 / VIRGINIAMYCIN S
Type: Cyclic peptide / Class: Antibiotic, Antimicrobial / Mass: 841.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: VIRGINIAMYCIN S1 IS A CYLIC HEPTAPEPTIDE. THE RING IS GENERATED BY LINKING RESIDUE 2 SIDE-CHAIN AND RESIDUE 7 MAIN-CHAIN. Source: (natural) STREPTOMYCES VIRGINIAE (bacteria) / References: NOR: NOR00679, VIRGINIAMYCIN S1
Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
-
Details
Sequence details
SEQUENCE REFERENCE FOR THE RIBOSOME: BALIGA, N.S., ET AL, (2004). GENOME SEQUENCE OF HALOARCULA ...SEQUENCE REFERENCE FOR THE RIBOSOME: BALIGA, N.S., ET AL, (2004). GENOME SEQUENCE OF HALOARCULA MARISMORTUI: A HALOPHILIC ARCHAEON FROM THE DEAD SEA. GENOME RES. 14, 2221-2234. DOI 10.1101/GR.2700304
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi