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- PDB-5z3q: Crystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (... -

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Basic information

Entry
Database: PDB / ID: 5z3q
TitleCrystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (2.55 Angstrom)
ComponentsPV-2C
KeywordsVIRAL PROTEIN / ATPase
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsGuan, H. / Tian, J. / Zhang, C. / Qin, B. / Cui, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81572005 China
CitationJournal: PLoS Pathog. / Year: 2018
Title: Crystal structure of a soluble fragment of poliovirus 2CATPase
Authors: Guan, H. / Tian, J. / Zhang, C. / Qin, B. / Cui, S.
History
DepositionJan 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PV-2C
A: PV-2C
D: PV-2C
C: PV-2C
E: PV-2C
H: PV-2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,60815
Polymers141,9316
Non-polymers6779
Water3,927218
1
B: PV-2C
D: PV-2C
C: PV-2C
E: PV-2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,07210
Polymers94,6204
Non-polymers4526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-50 kcal/mol
Surface area38900 Å2
MethodPISA
2
A: PV-2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8153
Polymers23,6551
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area10920 Å2
MethodPISA
3
H: PV-2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7212
Polymers23,6551
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-28 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.698, 84.073, 172.562
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PV-2C


Mass: 23655.119 Da / Num. of mol.: 6 / Fragment: UNP residues 1243-1456 / Mutation: E207A, K209A,R149A
Source method: isolated from a genetically manipulated source
Details: synthetic / Source: (gene. exp.) Human poliovirus 1 Mahoney / Strain: Mahoney / Plasmid: pET 28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: P03300, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MgCl2 0.2M, MES 0.1M pH 6.5, 3%(v/v) PGE4000, Polypropylene glycol P 400 (9.2% v/v) , 0.5mM TECP HCl
PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2017
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.545→43.809 Å / Num. obs: 95988 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.42 % / CC1/2: 0.993 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.132 / Net I/av σ(I): 7.38 / Net I/σ(I): 7.56
Reflection shellResolution: 2.545→2.574 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 15058 / CC1/2: 0.468 / Rrim(I) all: 1.029 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQ1

5gq1


Resolution: 2.545→40.618 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2522 5.13 %0.2642
Rwork0.202 ---
obs0.2052 49190 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.545→40.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8353 0 21 218 8592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188481
X-RAY DIFFRACTIONf_angle_d1.47111423
X-RAY DIFFRACTIONf_dihedral_angle_d14.8995273
X-RAY DIFFRACTIONf_chiral_restr0.0661299
X-RAY DIFFRACTIONf_plane_restr0.011494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5451-2.59410.34631140.30592349X-RAY DIFFRACTION90
2.5941-2.6470.34111550.28172585X-RAY DIFFRACTION100
2.647-2.70450.311250.27312600X-RAY DIFFRACTION100
2.7045-2.76740.35941360.27212613X-RAY DIFFRACTION100
2.7674-2.83660.3041540.26432562X-RAY DIFFRACTION100
2.8366-2.91330.3581460.25692602X-RAY DIFFRACTION100
2.9133-2.9990.33051290.26742603X-RAY DIFFRACTION100
2.999-3.09580.35721240.26922648X-RAY DIFFRACTION100
3.0958-3.20640.38221400.24682561X-RAY DIFFRACTION100
3.2064-3.33470.29171320.22772584X-RAY DIFFRACTION100
3.3347-3.48640.28591540.2252620X-RAY DIFFRACTION100
3.4864-3.67010.27621740.20442574X-RAY DIFFRACTION100
3.6701-3.89990.27961420.19092574X-RAY DIFFRACTION100
3.8999-4.20070.2191370.172622X-RAY DIFFRACTION100
4.2007-4.62290.20331470.15072608X-RAY DIFFRACTION100
4.6229-5.29060.20561500.15392631X-RAY DIFFRACTION100
5.2906-6.66080.28581240.19562645X-RAY DIFFRACTION100
6.6608-40.62350.21641390.18262687X-RAY DIFFRACTION99

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