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- PDB-7mg0: Crystal structure of EV-D68 2A protease -

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Basic information

Entry
Database: PDB / ID: 7mg0
TitleCrystal structure of EV-D68 2A protease
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 / : ...: / 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 / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / 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: 3.5 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
Authors: Liu, C. / Lee, M.-Y. / Ma, C. / Liu, W. / Wang, J.
History
DepositionApr 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)96,67512
Polymers96,2836
Non-polymers3926
Water21612
1
E: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1132
Polymers16,0471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.157, 118.157, 81.735
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 2 through 48 or (resid 49...
d_2ens_1(chain "B" and (resid 2 through 3 or (resid 4...
d_3ens_1(chain "C" and (resid 2 through 17 or (resid 18...
d_4ens_1(chain "D" and (resid 2 through 3 or (resid 4...
d_5ens_1(chain "E" and (resid 2 through 3 or (resid 4...
d_6ens_1(chain "F" and (resid 2 through 17 or (resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROTRPB2 - 139
d_21ens_1PROTRPC2 - 139
d_31ens_1PROTRPD1 - 138
d_41ens_1PROTRPE1 - 138
d_51ens_1PROTRPA2 - 139
d_61ens_1PROTRPF2 - 139

NCS oper:
IDCodeMatrixVector
1given(-0.00369224734723, -0.999992399666, 0.00125216642677), (-0.999974322413, 0.00368448413948, -0.006146469744), (0.00614180944143, -0.00127482856077, -0.999980326301)0.405630936505, 0.187696125136, 27.690362625
2given(-0.556579922681, 0.484072611166, -0.675198116694), (0.487566732026, -0.467719950524, -0.737235871146), (-0.672679322924, -0.739534823387, 0.0243058328096)49.5513508834, -40.477810963, 2.68332458553
3given(-0.484528201256, -0.499696327462, 0.718008358244), (-0.471440374206, -0.542233454364, -0.695504748033), (0.736869320678, -0.675489793623, 0.0271503766957)29.017428448, -57.0423705154, -58.6887214625
4given(-0.504351264118, 0.468015966723, 0.725665802746), (0.547921120369, -0.476067217798, 0.687853509107), (0.667392124793, 0.7445274065, -0.0163307297357)41.3904015527, -48.7484924792, 25.2788569709
5given(0.463958255934, 0.543293742555, 0.699696109787), (0.497265717739, 0.493945089103, -0.713263664372), (-0.733123142939, 0.678859453975, -0.0409914507672)57.7193853345, -29.5192303799, 86.3738630792

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Components

#1: Protein
Protease 2A


Mass: 16047.170 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Sodium Cacodylate pH 6.0, 0.005 M Magnesium Chloride, 0.002 M Calcium Chloride, 15% v/v 2-Propanol, 0.001 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.88 Å / Num. obs: 14387 / % possible obs: 99.92 % / Redundancy: 3.9 % / CC1/2: 0.988 / Net I/σ(I): 25.4
Reflection shellResolution: 3.2→3.66 Å / Num. unique obs: 931 / CC1/2: 0.477

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Processing

Software
NameVersionClassification
PHENIXdev_4189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LW2

7lw2


Resolution: 3.5→47.88 Å / Cross valid method: FREE R-VALUE / σ(F): 261.21 / Phase error: 30.2922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2851 1446 10.05 %
Rwork0.2376 12941 -
obs0.2432 14387 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.15 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 6 12 5998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326120
X-RAY DIFFRACTIONf_angle_d0.70728349
X-RAY DIFFRACTIONf_chiral_restr0.0511929
X-RAY DIFFRACTIONf_plane_restr0.00531107
X-RAY DIFFRACTIONf_dihedral_angle_d4.0028901
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS1.02761498346
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS1.35664026154
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS1.11112326469
ens_1d_5BX-RAY DIFFRACTIONTorsion NCS1.20279814465
ens_1d_6BX-RAY DIFFRACTIONTorsion NCS1.19641182729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.620.29771410.3021257X-RAY DIFFRACTION89.85
3.63-3.770.3381420.2781296X-RAY DIFFRACTION90.13
3.77-3.940.29811470.26861289X-RAY DIFFRACTION89.76
3.94-4.150.34381430.25051265X-RAY DIFFRACTION89.84
4.15-4.410.25171450.23321304X-RAY DIFFRACTION89.99
4.41-4.750.29671430.21731285X-RAY DIFFRACTION89.92
4.75-5.230.28561430.21731292X-RAY DIFFRACTION90.03
5.23-5.980.30051460.24221308X-RAY DIFFRACTION89.96
5.98-7.530.28911450.22281302X-RAY DIFFRACTION89.98
7.53-47.880.26351510.23491343X-RAY DIFFRACTION89.89

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