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- PDB-6m12: Crystal Structure of Rnase L in complex with SU11652 -

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Basic information

Entry
Database: PDB / ID: 6m12
TitleCrystal Structure of Rnase L in complex with SU11652
ComponentsRibonuclease L
KeywordsHYDROLASE / Inhibitor / Complex / RNase L / SU11652
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-J60 / PHOSPHATE ION / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTang, J. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Biochem.J. / Year: 2020
Title: Sunitinib inhibits RNase L by destabilizing its active dimer conformation.
Authors: Tang, J. / Wang, Y. / Zhou, H. / Ye, Y. / Talukdar, M. / Fu, Z. / Liu, Z. / Li, J. / Neculai, D. / Gao, J. / Huang, H.
History
DepositionFeb 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)165,9127
Polymers162,6562
Non-polymers3,2565
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-19 kcal/mol
Surface area58700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.710, 110.380, 262.590
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
11a
21b

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 726 / Label seq-ID: 9 - 711

Dom-IDAuth asym-IDLabel asym-ID
1aA
2bB

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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-J60 / 5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE


Mass: 414.928 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG4000, 100 mM Tris, 150 mM (NH4)2SO4, 2mM DTT, pH 7.5

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→57.3 Å / Num. obs: 67474 / % possible obs: 99.39 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.2967 / Num. unique obs: 3336 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O1P

4o1p


Resolution: 2.4→57.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.956 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 3336 4.9 %RANDOM
Rwork0.2306 ---
obs0.2323 64138 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 209.27 Å2 / Biso mean: 83.037 Å2 / Biso min: 36.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å20 Å2
2--2.14 Å20 Å2
3----5.86 Å2
Refinement stepCycle: final / Resolution: 2.4→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10860 0 197 0 11057
Biso mean--95.97 --
Num. residues----1365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911275
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210320
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9815257
X-RAY DIFFRACTIONr_angle_other_deg1.0813.00223964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12951357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38324.725563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.919151994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4641577
X-RAY DIFFRACTIONr_chiral_restr0.0910.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022223
Refine LS restraints NCS

Ens-ID: 1 / Number: 42666 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1a
2b
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 227 -
Rwork0.378 4702 -
all-4929 -
obs--99.9 %

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