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- PDB-4o1p: Crystal Structure of RNase L in complex with 2-5A and AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4o1p
TitleCrystal Structure of RNase L in complex with 2-5A and AMP-PNP
ComponentsRibonuclease L
KeywordsTRANSFERASE / HYDROLASE / ankyrin repeat-kinase-RNAse / RNA cleavage / 2-5A
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 / 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 ...RNase L, RNase domain / KEN domain / 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
Chem-25L / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribonuclease L
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.5 Å
AuthorsHuang, H. / Zeqiraj, E. / Ceccarelli, D.F. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2014
Title: Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity.
Authors: Huang, H. / Zeqiraj, E. / Dong, B. / Jha, B.K. / Duffy, N.M. / Orlicky, S. / Thevakumaran, N. / Talukdar, M. / Pillon, M.C. / Ceccarelli, D.F. / Wan, L.C. / Juang, Y.C. / Mao, D.Y. / ...Authors: Huang, H. / Zeqiraj, E. / Dong, B. / Jha, B.K. / Duffy, N.M. / Orlicky, S. / Thevakumaran, N. / Talukdar, M. / Pillon, M.C. / Ceccarelli, D.F. / Wan, L.C. / Juang, Y.C. / Mao, D.Y. / Gaughan, C. / Brinton, M.A. / Perelygin, A.A. / Kourinov, I. / Guarne, A. / Silverman, R.H. / Sicheri, F.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _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_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 / _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
A: Ribonuclease L
B: Ribonuclease L
C: Ribonuclease L
D: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,19320
Polymers325,3114
Non-polymers6,88216
Water18,5551030
1
A: Ribonuclease L
B: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,09610
Polymers162,6562
Non-polymers3,4418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint13 kcal/mol
Surface area58630 Å2
MethodPISA
2
C: Ribonuclease L
D: Ribonuclease L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,09610
Polymers162,6562
Non-polymers3,4418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint13 kcal/mol
Surface area58570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.197, 267.392, 110.210
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 22 - 729 / Label seq-ID: 7 - 714

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ribonuclease L /


Mass: 81327.836 Da / Num. of mol.: 4 / Fragment: UNP residues 21-732
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 4 / Source method: obtained synthetically / Formula: C30H40N15O25P5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1030 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5 mM MgCl2, 5 mM DTT, 18% PEG2000, 100 mM NaCl, and 100 mM SPG buffer, pH 7. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.773
11h,-k,-l20.227
ReflectionResolution: 2.5→59.2 Å / Num. obs: 106347 / % possible obs: 95.7 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.8
Reflection shellResolution: 2.504→2.569 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.6 / Num. unique all: 7277 / % possible all: 88.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 4G8K

4g8k


Resolution: 2.5→59.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.961 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 1.6 / ESU R: 0.133 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23107 5725 5.1 %RANDOM
Rwork0.19568 ---
obs0.1975 106347 95.67 %-
all-111125 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.977 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å21.86 Å2
2---18.36 Å20 Å2
3---15.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21367 0 432 1030 22829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01922220
X-RAY DIFFRACTIONr_bond_other_d0.0030.0220975
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.98230092
X-RAY DIFFRACTIONr_angle_other_deg0.8323.00148204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39452666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04424.7121112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.195153934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.38615152
X-RAY DIFFRACTIONr_chiral_restr0.0730.23322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225018
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025114
X-RAY DIFFRACTIONr_mcbond_it2.6955.10210724
X-RAY DIFFRACTIONr_mcbond_other2.6925.10110723
X-RAY DIFFRACTIONr_mcangle_it4.3577.63813370
X-RAY DIFFRACTIONr_mcangle_other4.3577.63813371
X-RAY DIFFRACTIONr_scbond_it2.7895.33611496
X-RAY DIFFRACTIONr_scbond_other2.7885.33611490
X-RAY DIFFRACTIONr_scangle_other4.6167.88516713
X-RAY DIFFRACTIONr_long_range_B_refined9.06947.46693506
X-RAY DIFFRACTIONr_long_range_B_other9.06547.47993190
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A427870.04
12B427870.04
21A430520.03
22C430520.03
31A425260.04
32D425260.04
41B429760.02
42C429760.02
51B428440.03
52D428440.03
61C426870.03
62D426870.03
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 403 -
Rwork0.273 7277 -
obs--88.4 %

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