ribosome assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / negative regulation of translation / tRNA binding ...ribosome assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / RNA binding / metal ion binding Similarity search - Function
Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L13 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 ...Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal protein L13 / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L22/L17 / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L14/L23 / Ribosomal Protein L14 / Outer Surface Protein A; domain 3 / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / RRM (RNA recognition motif) domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11, C-terminal / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Nucleic acid-binding proteins / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L34 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal L28 family / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L30, bacterial-type / Ribosomal protein L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 Similarity search - Domain/homology
RNA (> 1000) / 50S ribosomal protein L16 / 50S ribosomal protein L25 / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 50S ribosomal protein L29 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L20 ...RNA (> 1000) / 50S ribosomal protein L16 / 50S ribosomal protein L25 / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 50S ribosomal protein L29 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L20 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 50S ribosomal protein L13 / 50S ribosomal protein L21 / 50S ribosomal protein L19 / 50S ribosomal protein L35 / RNA (> 100) / 50S ribosomal protein L7/L12 / 50S ribosomal protein L11 / 50S ribosomal protein L33 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L17 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 50S ribosomal protein L32 / RNA / RNA (> 10) / 50S ribosomal protein L27 Similarity search - Component
Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
#2: RNA chain
ribosomal5SRNA
Mass: 39276.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant)
+
50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWZ12345
#3: Protein
50SribosomalproteinL2 /
Mass: 29976.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ9
#4: Protein
50SribosomalproteinL3 /
Mass: 22477.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK2
#5: Protein
50SribosomalproteinL4 /
Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK1
#6: Protein
50SribosomalproteinL5 /
Mass: 20379.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ0
#7: Protein
50SribosomalproteinL6 /
Mass: 19613.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL3
#8: Protein
50SribosomalproteinL11 /
Mass: 14889.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS7
#9: Protein
50SribosomalproteinL13 /
Mass: 19223.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXY1
#10: Protein
50SribosomalproteinL14 /
Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ2
#11: Protein
50SribosomalproteinL15 /
Mass: 16894.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSK9
#12: Protein
50SribosomalproteinL16 /
Mass: 16257.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#13: Protein
50SribosomalproteinL17 /
Mass: 12926.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSJ5
#14: Protein
50SribosomalproteinL18 /
Mass: 12163.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL2
#15: Protein
50SribosomalproteinL19 /
Mass: 18347.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RWB4
#16: Protein
50SribosomalproteinL20 /
Mass: 13991.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW7
#17: Protein
50SribosomalproteinL21 /
Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY64
#18: Protein
50SribosomalproteinL22 /
Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7
#19: Protein
50SribosomalproteinL23 /
Mass: 10539.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK0
#20: Protein
50SribosomalproteinL24 /
Mass: 12384.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ1
#21: Protein
50SribosomalproteinL25 / / General stress protein CTC
Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88
#22: Protein
50SribosomalproteinL27 /
Mass: 9609.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY65
#23: Protein
50SribosomalproteinL28 /
Mass: 8982.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RRG8
#24: Protein
50SribosomalproteinL29 /
Mass: 7774.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ4
#25: Protein
50SribosomalproteinL30 /
Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL0
#26: Protein
50SribosomalproteinL32 /
Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228
#27: Protein
50SribosomalproteinL33 / / Coordinate model: Cα atoms only
Mass: 6374.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS4
#28: Protein/peptide
50SribosomalproteinL34 / / Coordinate model: Cα atoms only
Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSH2
#29: Protein
50SribosomalproteinL35 / / Coordinate model: Cα atoms only
Mass: 7448.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW6
#30: Protein/peptide
50SribosomalproteinL36 /
Mass: 4322.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSK0
#31: Protein
50SribosomalproteinL7/L12 / Ribosome / Coordinate model: Cα atoms only
Mass: 12642.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RST0
-
Details
Sequence details
THE SEQUENCE OF THE CHAIN X (RRNA-23S) MATCHES TO RESIDUES 2587937 - 2590816 IN GENEBANK WITH ...THE SEQUENCE OF THE CHAIN X (RRNA-23S) MATCHES TO RESIDUES 2587937 - 2590816 IN GENEBANK WITH ACCESSION 11612676. THE SEQUENCE OF THE CHAIN Y (RRNA-5S) MATCHES TO RESIDUES 254392 - 254514 IN GENEBANK WITH ACCESSION 11612676.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 7
-
Sample preparation
Crystal
Density Matthews: 4.38 Å3/Da / Density % sol: 71.92 %
Crystal grow
Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
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