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- PDB-4g8k: Intact sensor domain of human RNase L in the inactive signaling state -

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Basic information

Entry
Database: PDB / ID: 4g8k
TitleIntact sensor domain of human RNase L in the inactive signaling state
Components2-5A-dependent ribonuclease
KeywordsHYDROLASE / Ankyrin-repeat domain / single-stranded RNA
Function / homology
Function and homology information


OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / RNA processing / ribonucleoprotein complex binding / RNA endonuclease activity / regulation of mRNA stability / positive regulation of glucose import ...OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / RNA processing / ribonucleoprotein complex binding / RNA endonuclease activity / regulation of mRNA stability / positive regulation of glucose import / mRNA processing / rRNA processing / nuclear matrix / Interferon alpha/beta signaling / defense response to virus / rRNA binding / mitochondrial matrix / protein kinase activity / protein phosphorylation / positive regulation of transcription by RNA polymerase II / RNA binding / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
RNase L, RNase domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) ...RNase L, RNase domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHan, Y. / Whitney, G. / Donovan, J. / Korennykh, A.
CitationJournal: Cell Rep / Year: 2012
Title: Innate Immune Messenger 2-5A Tethers Human RNase L into Active High-Order Complexes.
Authors: Han, Y. / Whitney, G. / Donovan, J. / Korennykh, A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-5A-dependent ribonuclease
B: 2-5A-dependent ribonuclease


Theoretical massNumber of molelcules
Total (without water)74,2892
Polymers74,2892
Non-polymers00
Water4,089227
1
A: 2-5A-dependent ribonuclease


Theoretical massNumber of molelcules
Total (without water)37,1441
Polymers37,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-5A-dependent ribonuclease


Theoretical massNumber of molelcules
Total (without water)37,1441
Polymers37,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 63.000, 241.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-5A-dependent ribonuclease / 2-5A-dependent RNase / Ribonuclease 4 / Ribonuclease L / RNase L


Mass: 37144.305 Da / Num. of mol.: 2 / Fragment: 2-5A-sensor domain (ANK domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEL, RNS4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05823, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 50 mM potassium acetate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.4→60.375 Å / Num. obs: 38136 / % possible obs: 99.1 % / Observed criterion σ(F): 2.87 / Observed criterion σ(I): 2.87
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.5199.1
2.5-2.7199.3
2.7-3199.9
3-51100
5-71100
7-101100
10-60198.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WDY

1wdy


Resolution: 2.4→60.375 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1906 5 %RANDOM
Rwork0.2172 ---
obs0.2189 38131 99.1 %-
all-38136 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.716 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1302 Å20 Å20 Å2
2--0.3176 Å2-0 Å2
3---4.8126 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 0 227 4795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024620
X-RAY DIFFRACTIONf_angle_d0.5936225
X-RAY DIFFRACTIONf_dihedral_angle_d19.6652897
X-RAY DIFFRACTIONf_chiral_restr0.045735
X-RAY DIFFRACTIONf_plane_restr0.002806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.26491220.26142325X-RAY DIFFRACTION92
2.46-2.52650.31891330.25182519X-RAY DIFFRACTION97
2.5265-2.60090.26231330.24752536X-RAY DIFFRACTION99
2.6009-2.68480.24541350.23462561X-RAY DIFFRACTION100
2.6848-2.78080.24051350.22982568X-RAY DIFFRACTION100
2.7808-2.89210.28431360.24112584X-RAY DIFFRACTION100
2.8921-3.02380.28971360.23392583X-RAY DIFFRACTION100
3.0238-3.18320.28541370.23822603X-RAY DIFFRACTION100
3.1832-3.38260.29151350.24052570X-RAY DIFFRACTION100
3.3826-3.64370.24751380.21832612X-RAY DIFFRACTION100
3.6437-4.01030.2391390.18872635X-RAY DIFFRACTION100
4.0103-4.59050.19531380.16752631X-RAY DIFFRACTION100
4.5905-5.78280.19571410.18322686X-RAY DIFFRACTION100
5.7828-60.39410.20951480.18652812X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3738-0.58230.77911.0588-0.62550.52650.1405-0.0321-0.0739-0.01150.00490.24830.03490.01930.00010.1660.0163-0.01230.0919-0.03770.1609-10.814115.2787-48.2648
21.01610.4418-0.6640.4005-0.5811.2069-0.1357-0.27340.0676-0.0969-0.0224-0.1141-0.005-0.1043-0.00410.2173-0.0221-0.00490.3856-0.00470.1333-24.016624.344-21.8106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 21:327
2X-RAY DIFFRACTION2CHAIN B AND RESID 24:328

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