[English] 日本語
Yorodumi
- PDB-7elw: Crystal structure of RNase L in complex with Myricetin -

+
Open data


ID or keywords:

Loading...

-
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


RNA nuclease activity / mRNA processing / protein kinase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more