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- PDB-8x3v: Crystal structure of 2C from encephalomyocarditis virus bound with ATP -

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Basic information

Entry
Database: PDB / ID: 8x3v
TitleCrystal structure of 2C from encephalomyocarditis virus bound with ATP
ComponentsProtein 2C
KeywordsHYDROLASE / helicase / ATPase / RNA-binding
Function / homology
Function and homology information


host cell nucleolus / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity ...host cell nucleolus / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA helicase / symbiont entry into host cell / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Genome polyprotein
Similarity search - Component
Biological speciesEncephalomyocarditis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, H. / Zhao, H. / Dong, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: To Be Published
Title: Crystal structure of 2C from encephalomyocarditis virus bound with ATP
Authors: Zhang, H. / Zhao, H. / Dong, Y.H.
History
DepositionNov 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein 2C
B: Protein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6883
Polymers48,1812
Non-polymers5071
Water00
1
A: Protein 2C
B: Protein 2C
hetero molecules

A: Protein 2C
B: Protein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3766
Polymers96,3624
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.000, 171.000, 77.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Protein 2C / C / P2C


Mass: 24090.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalomyocarditis virus / Production host: Escherichia coli (E. coli) / References: UniProt: P03304, RNA helicase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.2 M Sodium citrate tribasic, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 15238 / % possible obs: 99.9 % / Redundancy: 38.5 % / Biso Wilson estimate: 76.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.189 / Net I/σ(I): 21.2
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 38.9 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1108 / CC1/2: 0.78 / Rrim(I) all: 0.866 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.36 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1524 10.01 %
Rwork0.224 --
obs0.229 15230 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 31 0 3266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013360
X-RAY DIFFRACTIONf_angle_d1.1384568
X-RAY DIFFRACTIONf_dihedral_angle_d16.771235
X-RAY DIFFRACTIONf_chiral_restr0.06527
X-RAY DIFFRACTIONf_plane_restr0.011595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.3621360.32121221X-RAY DIFFRACTION100
2.99-3.10.38571350.30661215X-RAY DIFFRACTION100
3.1-3.220.44031350.33911216X-RAY DIFFRACTION100
3.22-3.370.29321360.28171226X-RAY DIFFRACTION100
3.37-3.550.29981350.24751220X-RAY DIFFRACTION100
3.55-3.770.29941370.23291230X-RAY DIFFRACTION100
3.77-4.060.28351380.23391241X-RAY DIFFRACTION100
4.06-4.470.24441380.18261240X-RAY DIFFRACTION100
4.47-5.110.24911400.18751259X-RAY DIFFRACTION100
5.11-6.440.27631420.23431279X-RAY DIFFRACTION100
6.44-49.360.21671520.19071359X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -40.5829 Å / Origin y: 49.2852 Å / Origin z: -8.3053 Å
111213212223313233
T0.4571 Å2-0.0136 Å20.0442 Å2-0.4434 Å20.057 Å2--0.3978 Å2
L1.5474 °20.6599 °20.2188 °2-1.1153 °20.0609 °2--0.6508 °2
S0.0157 Å °0.0331 Å °-0.1677 Å °-0.1287 Å °-0.0422 Å °-0.1093 Å °0.2269 Å °0.1919 Å °0 Å °
Refinement TLS groupSelection details: all

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