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- PDB-4g8l: Active state of intact sensor domain of human RNase L with 2-5A bound -

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Basic information

Entry
Database: PDB / ID: 4g8l
TitleActive state of intact sensor domain of human RNase L with 2-5A bound
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 / nuclear matrix / rRNA processing / Interferon alpha/beta signaling / defense response to virus / rRNA binding / protein kinase activity / mitochondrial matrix / 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
Chem-25A / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: 2-5A-dependent ribonuclease
D: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,6008
Polymers148,5774
Non-polymers4,0234
Water00
1
A: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1502
Polymers37,1441
Non-polymers1,0061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1502
Polymers37,1441
Non-polymers1,0061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1502
Polymers37,1441
Non-polymers1,0061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1502
Polymers37,1441
Non-polymers1,0061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 164.110, 86.220
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESID 21:155 OR RESID 168:500 OR RESID 1996)
211chain B AND (RESID 21:155 OR RESID 168:500 OR RESID 1996)
311CHAIN C AND (RESID 21:155 OR RESID 168:500 OR RESID 1996)
411CHAIN D AND (RESID 21:155 OR RESID 168:500 OR RESID 1996)
112CHAIN A AND (RESID 1:20)
212CHAIN C AND (RESID 1:20)

NCS ensembles :
ID
1
2

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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.: 4 / 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: Chemical
ChemComp-25A / 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE


Mass: 1005.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H38N15O19P3

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 200 mM sodium acetate, 18% PEG 3350, 1.3M sodium citrate, 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: Mar 11, 2012
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: 2.8→39 Å / Num. obs: 42322 / % possible obs: 99.8 % / Observed criterion σ(F): 1.82 / Observed criterion σ(I): 1.82
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.9199.8
2.9-4199.8
4-6199.8
6-10199.9
10-10199.8
10-201100
20-301100
30-40195

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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 4G8K

4g8k


Resolution: 2.8→38.75 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2115 5.01 %RANDOM
Rwork0.2282 ---
obs0.2299 42245 99.74 %-
all-42322 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.122 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.769 Å20 Å2-10.7293 Å2
2---15.2196 Å2-0 Å2
3---29.2152 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9147 0 268 0 9415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069547
X-RAY DIFFRACTIONf_angle_d0.98512912
X-RAY DIFFRACTIONf_dihedral_angle_d23.0256086
X-RAY DIFFRACTIONf_chiral_restr0.0631523
X-RAY DIFFRACTIONf_plane_restr0.0041622
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2292X-RAY DIFFRACTIONPOSITIONAL
12B2292X-RAY DIFFRACTIONPOSITIONAL0.026
13C2288X-RAY DIFFRACTIONPOSITIONAL0.027
14D2292X-RAY DIFFRACTIONPOSITIONAL0.029
21A38X-RAY DIFFRACTIONPOSITIONAL
22C38X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86510.40741430.37182700X-RAY DIFFRACTION100
2.8651-2.93680.30691380.32422622X-RAY DIFFRACTION100
2.9368-3.01610.40741410.30412671X-RAY DIFFRACTION100
3.0161-3.10480.31751390.30442655X-RAY DIFFRACTION100
3.1048-3.2050.37011410.27562678X-RAY DIFFRACTION100
3.205-3.31950.28471430.26512694X-RAY DIFFRACTION100
3.3195-3.45230.31261390.23352648X-RAY DIFFRACTION100
3.4523-3.60930.25071400.22822654X-RAY DIFFRACTION100
3.6093-3.79950.22871400.20932663X-RAY DIFFRACTION100
3.7995-4.03730.26481420.21142690X-RAY DIFFRACTION100
4.0373-4.34860.21521410.18912670X-RAY DIFFRACTION100
4.3486-4.78550.23041430.18542709X-RAY DIFFRACTION100
4.7855-5.47640.23091400.19722665X-RAY DIFFRACTION100
5.4764-6.89330.25911430.21082704X-RAY DIFFRACTION100
6.8933-38.75380.16561420.17782707X-RAY DIFFRACTION99
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)
10.1926-0.1427-0.01590.2660.21720.2199-0.05160.1742-0.3087-0.09470.02380.04390.03450.1528-0.04810.2035-0.0198-0.029-0.0972-0.08920.25398.0005-29.068836.4262
20.0902-0.08570.09240.2246-0.11640.0262-0.04860.13030.3079-0.0317-0.0017-0.1314-0.00590.0388-0.00230.2132-0.0152-0.00870.09720.02470.25368.5849-65.460537.7839
30.85820.3250.05460.22450.09790.0274-0.09550.03130.4299-0.05230.09980.1047-0.0175-0.02880.20690.10270.06490.02370.347-0.22460.106416.3004-81.48435.6532
40.09380.02230.07630.1579-0.00030.044-0.08150.1134-0.3717-0.01150.0379-0.10620.0295-0.04470.00580.10030.0359-0.00180.32490.20710.405215.9787-44.95634.5239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 16:325
2X-RAY DIFFRACTION2CHAIN B AND RESID 21:325
3X-RAY DIFFRACTION3CHAIN C AND RESID 15:325
4X-RAY DIFFRACTION4CHAIN D AND RESID 21:325

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