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- PDB-7elw: Crystal structure of RNase L in complex with Myricetin -

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Basic information

Entry
Database: PDB / ID: 7elw
TitleCrystal structure of RNase L in complex with Myricetin
ComponentsRibonuclease L
KeywordsHYDROLASE / RNase L / Inhibitor / Myricetin
Function / homology
Function and homology information


regulation of RNA metabolic process / negative regulation of viral genome replication / RNA nuclease activity / mRNA processing / defense response to virus / protein kinase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
RNase L, RNase domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...RNase L, RNase domain / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-25L / Chem-MYC / PHOSPHATE ION / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsTang, J. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778808 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery
Authors: Tang, J. / Dong, B. / Liu, M. / Liu, S. / Niu, X. / Gaughan, C. / Asthana, A. / Zhou, H. / Xu, Z. / Zhang, G. / Silverman, R.H. / Huang, H.
History
DepositionApr 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Ribonuclease L
b: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,7187
Polymers162,6562
Non-polymers3,0635
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-8 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.608, 111.925, 264.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain a and ((resid 23 and (name N or name...
21(chain b and (resid 23 through 567 or (resid 571...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain a and ((resid 23 and (name N or name...aA238
12SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
13SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
14SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
15SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
16SERSERTHRTHR(chain a and ((resid 23 and (name N or name...aA22 - 7277 - 712
21LEULEUGLYGLY(chain b and (resid 23 through 567 or (resid 571...bB23 - 5678 - 552
22GLUGLUGLUGLU(chain b and (resid 23 through 567 or (resid 571...bB571556
23LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
24LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
25LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712
26LEULEUTHRTHR(chain b and (resid 23 through 567 or (resid 571...bB23 - 7278 - 712

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Components

#1: Protein Ribonuclease L


Mass: 81327.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: RNASEL / Production host: Escherichia coli (E. coli) / References: UniProt: A5H025
#2: Chemical ChemComp-25L / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate / 2'-5'-oligoadenylate trimer


Mass: 1165.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H40N15O25P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN


Mass: 318.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG4000, 100 mM Tris, 150 mM (NH4)2SO4 and 2 mM DTT Buffer, pH7.0
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 3.55→22.92 Å / Num. obs: 22127 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.993 / Net I/σ(I): 13.03
Reflection shellResolution: 3.55→3.676 Å / Num. unique obs: 2166 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M11

6m11


Resolution: 3.55→22.92 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1077 4.87 %
Rwork0.2405 21050 -
obs0.2425 22127 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.02 Å2 / Biso mean: 72.1738 Å2 / Biso min: 22.84 Å2
Refinement stepCycle: final / Resolution: 3.55→22.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 185 0 10909
Biso mean--62.68 --
Num. residues----1351
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11a4096X-RAY DIFFRACTION4.508TORSIONAL
12b4096X-RAY DIFFRACTION4.508TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.55-3.710.31971240.295126102734100
3.71-3.910.28441220.284725652687100
3.91-4.150.34161230.277626192742100
4.15-4.470.29471440.260625832727100
4.47-4.910.31191270.241226342761100
4.91-5.610.34791380.244426242762100
5.61-7.040.26261400.226926762816100
7.04-22.920.19241590.17022739289899
Refinement TLS params.Method: refined / Origin x: 8.4795 Å / Origin y: -26.2135 Å / Origin z: -43.204 Å
111213212223313233
T0.2068 Å2-0.1441 Å2-0.2878 Å2-0.295 Å2-0.1106 Å2--0.3566 Å2
L0.8509 °20.2377 °20.1298 °2-1.0824 °20.3077 °2--1.219 °2
S0.2691 Å °-0.0144 Å °0.265 Å °0.6116 Å °-0.0098 Å °0.1467 Å °0.2599 Å °0.1906 Å °0.0642 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1alla22 - 727
2X-RAY DIFFRACTION1alla801 - 802
3X-RAY DIFFRACTION1allb23 - 727
4X-RAY DIFFRACTION1allb801 - 802
5X-RAY DIFFRACTION1allA1

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