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- PDB-7ztw: Crystal Structure of Human Parechovirus 1 2A protein -

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Basic information

Entry
Database: PDB / ID: 7ztw
TitleCrystal Structure of Human Parechovirus 1 2A protein
ComponentsProtein 2A
KeywordsVIRAL PROTEIN / 2A protein / unknown function / NlpC/P60 protein
Function / homology
Function and homology information


host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral ...Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesHuman parechovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
Authorsvon Castelmur, E. / Perrakis, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Human Parechovirus 1 2A protein
Authors: von Castelmur, E. / Perrakis, A.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,1987
Polymers68,0934
Non-polymers1053
Water3,081171
1
A: Protein 2A
B: Protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0703
Polymers34,0472
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-54 kcal/mol
Surface area13710 Å2
MethodPISA
2
C: Protein 2A
D: Protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1294
Polymers34,0472
Non-polymers822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-54 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.548, 127.805, 54.282
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein 2A / P2A


Mass: 17023.285 Da / Num. of mol.: 4 / Mutation: I918M
Source method: isolated from a genetically manipulated source
Details: SPYGQQPQNRMMKLAYLDRGFYKHYGIIVGDHVYQLDSDDIFKTALTGKAKFTKTKLTSDWVIEEECELDYFRIKYLESA VDSEHIFSVDKNCETIAKDIFGTHTLSQHQAIGLVGTILLTAGLMSTIKTPVNAVTIKEFFNHAIDGDEQ
Source: (gene. exp.) Human parechovirus 1 / Strain: Harris / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66578
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl 0.2M Na acetate 10% glycerol 28% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→42.6 Å / Num. obs: 42961 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.053 / Net I/σ(I): 10.4
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2808 / CC1/2: 0.865 / Rpim(I) all: 0.579 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→42.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.31 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 2113 4.9 %RANDOM
Rwork0.1841 ---
obs0.1867 40816 99.19 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 107.92 Å2 / Biso mean: 42.421 Å2 / Biso min: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å2-0 Å20.04 Å2
2---1.86 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.93→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 6 171 4707
Biso mean--40.69 39.83 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194625
X-RAY DIFFRACTIONr_bond_other_d0.0020.024419
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9446243
X-RAY DIFFRACTIONr_angle_other_deg0.866310190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09924.857210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5251512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021054
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 159 -
Rwork0.315 2953 -
all-3112 -
obs--98.36 %
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)
10.8394-0.0664-0.5931.2940.10322.4190.0579-0.05630.08220.01260.0956-0.1763-0.05820.2026-0.15350.111-0.00360.00840.1265-0.03620.0358-0.940327.347425.5077
20.81330.2251-0.250.74120.22913.53190.0797-0.09130.06280.0594-0.04450.0544-0.2052-0.4894-0.03520.10290.03430.0130.1609-0.00420.0073-18.736928.338142.7251
30.45330.17230.29020.5895-0.3361.93380.03950.0091-0.0187-0.1312-0.0003-0.13710.15950.0726-0.03920.30180.02440.0690.0948-0.00220.0517-1.9189-4.756416.6063
40.478-0.3466-0.22420.52260.11153.13370.08310.082-0.06080.0124-0.01980.09340.2025-0.5603-0.06330.25-0.04890.04290.1680.00830.0309-16.131-4.0751-3.3137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 146
2X-RAY DIFFRACTION2B5 - 146
3X-RAY DIFFRACTION3C6 - 146
4X-RAY DIFFRACTION4D6 - 146

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