negative regulation of translational elongation / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding ...negative regulation of translational elongation / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / defense response to Gram-positive bacterium / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function
Thiazolylpeptide-type bacteriocin precursor / 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 L13p; Chain: A; / Ribosomal protein L13 / Ribosomal protein L11/L12, C-terminal domain ...Thiazolylpeptide-type bacteriocin precursor / 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 L13p; Chain: A; / Ribosomal protein L13 / 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 L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / 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 L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / RRM (RNA recognition motif) domain / Ribosomal protein L11, bacterial-type / Nucleic acid-binding proteins / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Beta Complex / 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 L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 Similarity search - Domain/homology
Nosiheptide / Chem-NO1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Nosiheptide precursor / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 ...Nosiheptide / Chem-NO1 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Nosiheptide precursor / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 Similarity search - Component
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" 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 1234ABCDEFGHIJKLMNOPQRSTUVWY
#1: 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
#2: 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
#3: 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
#4: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#30: 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
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Protein/peptide , 1 types, 1 molecules 5
#5: Protein/peptide
NOSIHEPTIDE
Type: Thiopeptide / Class: Antibiotic / Mass: 1195.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND ...Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND CYS(8). THE OBSERVED C-TERMINAL AMINO GROUP NH2(13) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE Source: (natural) STREPTOMYCES ACTUOSUS (bacteria) / References: UniProt: C6FX52, Nosiheptide
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RNA chain , 2 types, 2 molecules XZ
#29: RNA chain
RIBOSOMAL23SRNA
Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513
#31: RNA chain
RIBOSOMAL5SRNA
Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: AE000513
Type: Thiopeptide / Class: Antibiotic / Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3 Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND ...Details: NOSIHEPTIDE IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FIVE THIAZOLES AND ONE 3-HYDROXYPYRIDINE RINGS. A MODIFIED INDOLE RING NO1(14) IS LINKED VIA THE SIDE CHAINS OF 3-HYDROXY 3GL(6) AND CYS(8). THE OBSERVED C-TERMINAL AMINO GROUP NH2(13) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE References: Nosiheptide
Mass: 24.305 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Mg
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Details
Compound details
Nosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, ...Nosiheptide is a member of a sulphur-rich heterocyclic peptides class. All share a macrocylic core, consisting of a nitrogen containing, six-membered ring central to dehydroamino acids and a subset of five member ring structures including thiazoles, thiazolines and oxazoles. The main characteristic of the nosiheptide structure is a general tendency to be more oxidized than the thiostrepton one. No thiazoline, or hydrogenated quinaldic precursor nor tetrahydropyridine rings are present in nosiheptide. All the corresponding rings are unsaturated. Nosiheptide possess an indolic acid ring system that is appended to the side chains of the Ser/Cys and a central 6-membered nitrogen heterocycle produced by cyclization between two corresponding dehydroalanine acids with incorporation of an adjacent carbonyl group. Thiazole formation is by nucleophilic addition of each Cys side chain to the proceeding carbonyl group followed by dehydration and dehydrogenation. HERE, NOSIHEPTIDE IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE ONE LIGAND (HET) NO1.
Nonpolymer details
THE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE ...THE CHIRALITY OF THE 4-HYDROXY GLUTAMIC ACID (3GL) IS NOT SATTELED. IN THE CURRENT ENTRY THE DIASTEREOMER IS SHOWN TO BE (2S,4S), WHILES CCDC 15794 NOSHEP10 ENTRY SHOWS IT TO BE (2S,4R) (DOI 10.1021/JA00461A039).
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 7
-
Sample preparation
Crystal
Density Matthews: 4 Å3/Da / Density % sol: 66 %
Crystal grow
Details: VAPOR DIFFUSION, HANGING DROP
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength
SYNCHROTRON
SLS
X06SA
1
1
SYNCHROTRON
ESRF
ID29
2
0.97
Detector
Type
ID
Detector
Date
MARRESEARCH
1
CCD
Feb 1, 2006
ADSC QUANTUM 315
2
CCD
Dec 3, 2007
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.97
1
Reflection
Resolution: 3.7→30 Å / Num. obs: 216249 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Rsym value: 0.14 / Net I/σ(I): 6.1
Reflection shell
Resolution: 3.7→3.76 Å / Mean I/σ(I) obs: 1.2 / Rsym value: 0.63 / % possible all: 75.2
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Processing
Software
Name
Classification
CNS
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
CNS
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZJR
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