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- PDB-7lw2: Crystal structure of EV-D68 2A protease N84T mutant -

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Basic information

Entry
Database: PDB / ID: 7lw2
TitleCrystal structure of EV-D68 2A protease N84T mutant
ComponentsProtease 2A
KeywordsHYDROLASE / metal ion binding / viral process / Enterovirus EV-D68 / protease / catalytic activity / ion binding / structural molecule activity / modulation of process of other organism / interaction with host / cellular process / gene expression / regulation of biological process / biological regulation / VIRAL PROTEIN
Function / homology
Function and homology information


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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
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) / Picornavirales 3C/3C-like protease domain ...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) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Biological speciesHuman enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsLiu, C. / Lee, M.-Y. / Liu, W. / Wang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH-NIAID-R01AI147325 United States
CitationJournal: To Be Published
Title: Crystal structure of EV-D68 2A protease C107A mutant
Authors: Liu, C. / Lee, M.-Y. / Ma, C. / Liu, W. / Wang, J.
History
DepositionFeb 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Protease 2A
A: Protease 2A
B: Protease 2A
C: Protease 2A
D: Protease 2A
F: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59712
Polymers96,2056
Non-polymers3926
Water63135
1
E: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1002
Polymers16,0341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.255, 119.255, 80.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 6 or (resid 7...
d_2ens_1(chain "B" and (resid 1 through 6 or (resid 7...
d_3ens_1(chain "C" and (resid 1 through 6 or (resid 7...
d_4ens_1(chain "D" and (resid 1 through 6 or (resid 7...
d_5ens_1(chain "E" and (resid 1 through 6 or (resid 7...
d_6ens_1(chain "F" and (resid 1 through 8 or (resid 9...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 1 - 141 / Label seq-ID: 1 - 141

Dom-IDAuth asym-IDLabel asym-ID
d_1AB
d_2BC
d_3CD
d_4DE
d_5EA
d_6FF

NCS oper:
IDCodeMatrixVector
1given(0.509196085845, 0.467540650725, 0.722582234822), (-0.546428223048, -0.473027319246, 0.691130488622), (0.664932735859, -0.746760266194, 0.0146137475207)41.5529680283, -47.2377771778, 21.6351175526
2given(0.563646246078, 0.371297901708, -0.737862302513), (-0.572280921003, -0.468618020795, -0.672972286236), (-0.59564876961, 0.801582820907, -0.05164808311)44.6191844808, -39.9362663136, 9.24542606988
3given(-0.49600564576, 0.475915660166, -0.726280031244), (0.452095043574, -0.572565483628, -0.683943593094), (-0.741342343962, -0.667587485928, 0.0688366013265)63.2650256441, -31.7878664794, 25.0129656002
4given(-0.994190861711, 0.106561960218, 0.0151353601115), (0.104929733213, 0.99091365557, -0.0841420126434), (-0.0239641728204, -0.0820650707574, -0.996338819169)5.48744824206, 1.03085553629, 25.998998044
5given(-0.501354762764, 0.536907545772, 0.67850842968), (0.512850153786, -0.447185842796, 0.732809348852), (0.696870232981, 0.715370609751, -0.0511543652921)29.8486137877, -60.8756817892, 5.38733750315

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Components

#1: Protein
Protease 2A / P2A


Mass: 16034.170 Da / Num. of mol.: 6 / Mutation: N84T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68 / Plasmid: pE-SUMOstar / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A097BW19, picornain 2A
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Sodium Cacodylate, 10%(v/v) 2-propanol, 0.005 M Magnesium Chloride, 0.005 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.28361 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28361 Å / Relative weight: 1
ReflectionResolution: 2.57→44.43 Å / Num. obs: 36120 / % possible obs: 99.94 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03151 / Rpim(I) all: 0.03151 / Rrim(I) all: 0.04457 / Net I/σ(I): 16.31
Reflection shellResolution: 2.57→2.66 Å / Rmerge(I) obs: 0.698 / Num. unique obs: 3599 / CC1/2: 0.371 / Rpim(I) all: 0.698 / Rrim(I) all: 0.987

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Processing

Software
NameVersionClassification
PHENIXdev_3893refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JRE

7jre


Resolution: 2.57→44.43 Å / Cross valid method: FREE R-VALUE / σ(F): 98.71 / Phase error: 26.8634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2423 1984 5.49 %
Rwork0.2155 34132 -
obs0.2245 36116 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.96 Å2
Refinement stepCycle: LAST / Resolution: 2.57→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 6 35 6169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626284
X-RAY DIFFRACTIONf_angle_d0.82638569
X-RAY DIFFRACTIONf_chiral_restr0.0613928
X-RAY DIFFRACTIONf_plane_restr0.00551136
X-RAY DIFFRACTIONf_dihedral_angle_d16.75642095
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.724767668577
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS0.868368065037
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS0.743859797063
ens_1d_5BX-RAY DIFFRACTIONTorsion NCS0.698649250735
ens_1d_6BX-RAY DIFFRACTIONTorsion NCS0.740148417889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.630.32481460.31862409X-RAY DIFFRACTION93.7
2.63-2.70.38061430.32522424X-RAY DIFFRACTION94.43
2.71-2.780.3041460.31052425X-RAY DIFFRACTION94.32
2.78-2.870.36251420.29882409X-RAY DIFFRACTION94.43
2.87-2.980.2951420.28512421X-RAY DIFFRACTION94.46
2.98-3.10.32741360.26742426X-RAY DIFFRACTION94.69
3.1-3.240.27361420.25882451X-RAY DIFFRACTION94.52
3.24-3.410.26861380.24642410X-RAY DIFFRACTION94.58
3.41-3.620.32781390.24732442X-RAY DIFFRACTION94.61
3.62-3.90.24671440.22352426X-RAY DIFFRACTION94.4
3.9-4.290.22411430.20332442X-RAY DIFFRACTION94.47
4.29-4.910.18381420.17662446X-RAY DIFFRACTION94.51
4.91-6.190.21031370.19362479X-RAY DIFFRACTION94.76
6.19-44.430.26561440.21682522X-RAY DIFFRACTION94.49

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