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- PDB-4rpt: The 1.35A structure of a viral RNase L antagonist reveals basis f... -

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Basic information

Entry
Database: PDB / ID: 4rpt
TitleThe 1.35A structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and enzyme activity.
ComponentsCapping enzyme protein
KeywordsVIRAL PROTEIN / 2H phosphodiesterase
Function / homology
Function and homology information


: / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / RNA binding
Similarity search - Function
Protein VP3, rotavirus / Rotavirus VP3 protein / Viral protein 3 containing mRNA (guanine-N(7)-)-methyltransferase family profile.
Similarity search - Domain/homology
MALONATE ION / Protein VP3
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsHu, L. / Prasad, B.V.V.
CitationJournal: J.Virol. / Year: 2015
Title: Structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral RNase L antagonist.
Authors: Ogden, K.M. / Hu, L. / Jha, B.K. / Sankaran, B. / Weiss, S.R. / Silverman, R.H. / Patton, J.T. / Prasad, B.V.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Capping enzyme protein
B: Capping enzyme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8616
Polymers33,5332
Non-polymers3284
Water5,909328
1
A: Capping enzyme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9313
Polymers16,7661
Non-polymers1642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Capping enzyme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9313
Polymers16,7661
Non-polymers1642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-2 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.240, 68.370, 52.420
Angle α, β, γ (deg.)90.00, 106.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capping enzyme protein / Capping protein VP3 / VP3


Mass: 16766.479 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 694-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Strain: RRV / Production host: Escherichia coli (E. coli) / References: UniProt: B3F2X4
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / pH: 4
Details: 14% PEG3350, 0.2 M sodium malonate, pH 4, 1 M NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2014
RadiationMonochromator: SI(220) ASYMMETRIC CUT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.35→31.86 Å / Num. obs: 56612 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.039 / Rsym value: 0.044 / Net I/σ(I): 19.2
Reflection shellResolution: 1.35→1.42 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.528 / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.35→31.86 Å / SU ML: 0.16 / σ(F): 2 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 2846 5.03 %
Rwork0.191 --
obs0.192 56597 95 %
all-56638 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 22 328 2683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072407
X-RAY DIFFRACTIONf_angle_d1.2643239
X-RAY DIFFRACTIONf_dihedral_angle_d12.246897
X-RAY DIFFRACTIONf_chiral_restr0.05361
X-RAY DIFFRACTIONf_plane_restr0.007399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.33041720.31143441X-RAY DIFFRACTION93
1.3653-1.38140.33431930.29433522X-RAY DIFFRACTION94
1.3814-1.39830.32351620.27593413X-RAY DIFFRACTION93
1.3983-1.4160.27481770.26823565X-RAY DIFFRACTION94
1.416-1.43460.27381840.26013454X-RAY DIFFRACTION93
1.4346-1.45420.27772120.25613483X-RAY DIFFRACTION95
1.4542-1.4750.2781490.25463539X-RAY DIFFRACTION94
1.475-1.4970.22942090.2473536X-RAY DIFFRACTION95
1.497-1.52040.28381940.23633442X-RAY DIFFRACTION94
1.5204-1.54530.27141560.22813600X-RAY DIFFRACTION95
1.5453-1.5720.23972080.21533452X-RAY DIFFRACTION95
1.572-1.60060.24311650.21643603X-RAY DIFFRACTION95
1.6006-1.63140.24932060.21393502X-RAY DIFFRACTION96
1.6314-1.66470.24022010.20763576X-RAY DIFFRACTION96
1.6647-1.70090.24181820.20333532X-RAY DIFFRACTION95
1.7009-1.74040.27141790.20013570X-RAY DIFFRACTION96
1.7404-1.78390.22461400.20723622X-RAY DIFFRACTION96
1.7839-1.83220.24211670.20353615X-RAY DIFFRACTION96
1.8322-1.88610.21571750.2133573X-RAY DIFFRACTION96
1.8861-1.94690.22952000.20793589X-RAY DIFFRACTION96
1.9469-2.01650.26062120.19773576X-RAY DIFFRACTION97
2.0165-2.09720.19982210.1793596X-RAY DIFFRACTION97
2.0972-2.19270.16761940.17993564X-RAY DIFFRACTION97
2.1927-2.30820.21241870.17513561X-RAY DIFFRACTION97
2.3082-2.45280.20231890.1843600X-RAY DIFFRACTION96
2.4528-2.64210.21052090.19183580X-RAY DIFFRACTION96
2.6421-2.90780.192020.18933566X-RAY DIFFRACTION96
2.9078-3.32820.19012190.17373399X-RAY DIFFRACTION93
3.3282-4.19170.16952100.16423652X-RAY DIFFRACTION99
4.1917-31.86950.15011510.16143499X-RAY DIFFRACTION93

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