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- PDB-4oav: Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AM... -

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Basic information

Entry
Database: PDB / ID: 4oav
TitleComplete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate.
Components
  • PROTEIN (RNase L)
  • RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
KeywordsHYDROLASE/RNA / HPC1 / 2-5A / 2' / 5'-oligoadenylate / interferon / dsRNA / kinase / RNase / RIDD / Ire1 / RNA decay / RNase L protein kinase / pseudokinase / KEN-domain containing / Regulated RNA decay / innate immune response / antiviral response / dsRNA response / 5'-linked oligoadenylates / 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 nuclease activity / ribonucleoprotein complex binding / RNA processing / regulation of mRNA stability / RNA endonuclease activity / positive regulation of D-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 / ribonucleoprotein complex binding / RNA processing / regulation of mRNA stability / RNA endonuclease activity / positive regulation of D-glucose import / nuclear matrix / mRNA processing / rRNA processing / Interferon alpha/beta signaling / defense response to virus / protein kinase activity / rRNA binding / 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 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-PUP / RNA / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_sheet.number_strands / _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
B: PROTEIN (RNase L)
A: RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
D: PROTEIN (RNase L)
C: RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,46611
Polymers161,8384
Non-polymers1,6287
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-92 kcal/mol
Surface area58100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 160.700, 230.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 4 molecules BDAC

#1: Protein PROTEIN (RNase L)


Mass: 79416.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05823
#2: RNA chain RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')


Mass: 1502.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis

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Non-polymers , 4 types, 918 molecules

#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PUP / (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate


Mass: 520.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
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 MgCl2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio 1: ...Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl2, 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, 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 CHANNEL11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→46.7 Å / Num. all: 128179 / Num. obs: 128124 / % possible obs: 100 % / 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
Starting model: PDB ENTRY 4G8L

4g8l


Resolution: 2.1→46.622 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 6405 5 %RANDOM
Rwork0.198 ---
obs0.1995 128099 99.95 %-
all-128124 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10751 202 99 911 11963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411270
X-RAY DIFFRACTIONf_angle_d0.92215244
X-RAY DIFFRACTIONf_dihedral_angle_d20.8446924
X-RAY DIFFRACTIONf_chiral_restr0.0721677
X-RAY DIFFRACTIONf_plane_restr0.0031913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.31672080.2853945X-RAY DIFFRACTION100
2.1239-2.14890.30212130.2774042X-RAY DIFFRACTION100
2.1489-2.17510.31632110.26684037X-RAY DIFFRACTION100
2.1751-2.20260.32332080.26563935X-RAY DIFFRACTION100
2.2026-2.23160.30622130.25514047X-RAY DIFFRACTION100
2.2316-2.26210.29832130.24854046X-RAY DIFFRACTION100
2.2621-2.29450.29632080.2443949X-RAY DIFFRACTION100
2.2945-2.32870.29282120.23344034X-RAY DIFFRACTION100
2.3287-2.36510.28472120.24224028X-RAY DIFFRACTION100
2.3651-2.40390.28022110.23784016X-RAY DIFFRACTION100
2.4039-2.44530.28652120.23044036X-RAY DIFFRACTION100
2.4453-2.48980.29522100.22194003X-RAY DIFFRACTION100
2.4898-2.53770.25682140.22394049X-RAY DIFFRACTION100
2.5377-2.58950.26152110.22024020X-RAY DIFFRACTION100
2.5895-2.64580.28312120.21374021X-RAY DIFFRACTION100
2.6458-2.70730.22582120.21434025X-RAY DIFFRACTION100
2.7073-2.7750.2572130.21394045X-RAY DIFFRACTION100
2.775-2.850.25762110.21544024X-RAY DIFFRACTION100
2.85-2.93390.27832160.20984091X-RAY DIFFRACTION100
2.9339-3.02850.25532100.20654006X-RAY DIFFRACTION100
3.0285-3.13680.24822140.20744060X-RAY DIFFRACTION100
3.1368-3.26230.21732160.20514101X-RAY DIFFRACTION100
3.2623-3.41080.23392130.19744038X-RAY DIFFRACTION100
3.4108-3.59050.19382140.18384076X-RAY DIFFRACTION100
3.5905-3.81540.222150.1794089X-RAY DIFFRACTION100
3.8154-4.10980.19012160.16674101X-RAY DIFFRACTION100
4.1098-4.52310.1712180.1594146X-RAY DIFFRACTION100
4.5231-5.17680.16472170.15724124X-RAY DIFFRACTION100
5.1768-6.51940.2222220.19194200X-RAY DIFFRACTION100
6.5194-46.63340.1932300.17954360X-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)
10.60280.86110.04143.5428-0.38070.4215-0.0289-0.061-0.0636-0.01470.08630.00970.03040.0136-0.05180.3120.04320.0330.3882-0.00130.324913.7076-15.3912107.7443
24.44690.99711.60022.7710.69833.0227-0.04730.0927-0.0024-0.18120.1201-0.0492-0.00360.0369-0.0710.4404-0.0663-0.00180.3465-0.01610.254512.642711.977982.3975
32.64270.36381.01751.9443-0.26626.8643-0.06770.3197-0.0116-0.21030.09090.0373-0.1989-0.3621-0.01840.5571-0.0869-0.03380.5361-0.01080.33020.243812.684960.0183
43.5898-0.7616-0.97333.02210.06596.75730.1404-0.0528-0.0525-0.059-0.1885-0.0311-0.0845-0.16450.02760.5925-0.1224-0.04960.58130.03410.33325.68718.688928.5636
50.70050.81440.16962.35190.34710.3027-0.0653-0.08990.0798-0.03380.0370.2134-0.0027-0.04850.02650.28990.0243-0.02210.3556-0.0340.31118.512815.3748107.172
64.13730.4143-1.62772.7522-1.10783.1384-0.03680.0804-0.0942-0.03040.16710.1632-0.0859-0.1928-0.12270.4674-0.08090.00450.3717-0.02540.288311.5027-12.495682.5443
73.68310.0325-1.78122.05370.02687.18150.01080.2434-0.0347-0.1650.0291-0.07850.17920.3085-0.00750.4993-0.07660.0180.4342-0.02950.310126.5704-13.254361.88
83.3502-0.52850.63783.89420.34917.73830.02750.3432-0.0897-0.4595-0.07220.01590.30680.1460.04140.6183-0.04640.04470.69510.0080.320726.5898-9.153229.9256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )C1 - 6
2X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )C7
3X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )D26 - 327
4X-RAY DIFFRACTION2( CHAIN D AND RESID 336:436 )D336 - 436
5X-RAY DIFFRACTION3( CHAIN D AND ( RESID 437:586 OR RESID 1001:1003 ) )D437 - 586
6X-RAY DIFFRACTION3( CHAIN D AND ( RESID 437:586 OR RESID 1001:1003 ) )D1001 - 1003
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 587:719 OR RESID 1004:1004 ) )D587 - 719
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 587:719 OR RESID 1004:1004 ) )D1004
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )A1 - 6
10X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )A7
11X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )B24 - 327
12X-RAY DIFFRACTION6( CHAIN B AND RESID 336:436 )B336 - 436
13X-RAY DIFFRACTION7( CHAIN B AND ( RESID 437:586 OR RESID 801:803 ) )B437 - 586
14X-RAY DIFFRACTION7( CHAIN B AND ( RESID 437:586 OR RESID 801:803 ) )B801 - 803
15X-RAY DIFFRACTION8( CHAIN B AND ( RESID 587:717 OR RESID 1012:1014 ) )B587 - 717
16X-RAY DIFFRACTION8( CHAIN B AND ( RESID 587:717 OR RESID 1012:1014 ) )B1012 - 1014

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