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- PDB-4oau: Complete human RNase L in complex with biological activators. -

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Basic information

Entry
Database: PDB / ID: 4oau
TitleComplete human RNase L in complex with biological activators.
Components
  • 2-5A-dependent ribonuclease
  • RNA (5'-R(P*A*AP*A)-2')
KeywordsHYDROLASE/RNA / RNase L / RNASEL / 2-5A / 2' / 5'-oligoadenylate / interferon / KEN / pseudokinase / kinase / inflammation / Ire1 / RIDD / regulated RNA decay / splicing cleavage / HPC1 / hereditary prostate cancer 1 / RNase L kinase-homology and KEN domain-containing / innate immunity / interferon response / antiviral response / 2-5A (2' / 5'-linked oligoadenylate)and RNA / HYDROLASE-RNA complex
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 processing / RNA nuclease activity / 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 processing / RNA nuclease activity / 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 / 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 / KEN 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 / de novo design (two linked rop proteins) / Ankyrin repeat-containing domain ...RNase L, RNase domain / KEN 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 / de novo design (two linked rop 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHan, Y. / Donovan, J. / Rath, S. / Whitney, G. / Chitrakar, A. / Korennykh, A.
CitationJournal: Science / Year: 2014
Title: Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response.
Authors: Han, Y. / Donovan, J. / Rath, S. / Whitney, G. / Chitrakar, A. / Korennykh, A.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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
C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8355
Polymers80,3592
Non-polymers4763
Water2,504139
1
C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules

C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,67010
Polymers160,7184
Non-polymers9526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12060 Å2
ΔGint-55 kcal/mol
Surface area60980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.130, 116.600, 162.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 79416.344 Da / Num. of mol.: 1 / Fragment: UNP residues 21-719 / Mutation: H672N
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: RNA chain RNA (5'-R(P*A*AP*A)-2')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl 2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio ...Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl 2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio 1:1.5:1.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→53.442 Å / Num. all: 28957 / Num. obs: 28947 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.442 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1798 5 %RANDOM
Rwork0.2113 ---
obs0.2133 -99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→53.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 67 29 139 5774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035747
X-RAY DIFFRACTIONf_angle_d0.7887761
X-RAY DIFFRACTIONf_dihedral_angle_d20.9913594
X-RAY DIFFRACTIONf_chiral_restr0.061853
X-RAY DIFFRACTIONf_plane_restr0.003990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.3431370.32472594X-RAY DIFFRACTION100
2.6703-2.74890.34571360.32392583X-RAY DIFFRACTION100
2.7489-2.83760.3751350.31242574X-RAY DIFFRACTION100
2.8376-2.9390.32921360.29192585X-RAY DIFFRACTION100
2.939-3.05670.32351380.27152604X-RAY DIFFRACTION100
3.0567-3.19580.30341360.24632600X-RAY DIFFRACTION100
3.1958-3.36420.30361380.24022611X-RAY DIFFRACTION100
3.3642-3.5750.25421360.2012594X-RAY DIFFRACTION100
3.575-3.85090.25151390.18682630X-RAY DIFFRACTION100
3.8509-4.23830.20841380.17772626X-RAY DIFFRACTION100
4.2383-4.85130.22581400.15882651X-RAY DIFFRACTION100
4.8513-6.11070.21381420.20112691X-RAY DIFFRACTION100
6.1107-53.45350.20731470.19192801X-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)
11.95280.0566-2.24910.512-0.23713.6844-0.07120.18310.0541-0.07230.05370.09610.0847-0.31130.030.4256-0.0337-0.08390.44070.04310.3948-2.1477-7.8617-17.183
29.03260.2735-0.86277.21871.49754.65730.0714-0.1739-0.0632-0.0653-0.36490.16080.4149-0.22580.23160.73260.05370.00380.4646-0.03310.3941-2.0124-32.987112.3325
34.9714-1.28531.36037.7501-0.83342.37040.01-0.2132-0.82290.4748-0.0342-0.65030.50470.3231-0.01181.10170.18080.06590.4811-0.01220.781512.0602-55.022713.8441
43.47940.77860.06110.63380.24912.3859-0.3026-0.0162-0.4112-0.11380.18450.59860.5937-0.0360.25771.83470.16140.21950.58530.02841.55899.1432-86.22069.0501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain C and (resid 25:330)
5X-RAY DIFFRACTION1chain A and (resid 1:3)
2X-RAY DIFFRACTION2chain C and resid 331:437
3X-RAY DIFFRACTION3chain C and (resid 438:584 or resid 801 or resid 802:803)
4X-RAY DIFFRACTION4chain C and resid 585:719

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