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- PDB-7jre: Crystal structure of EV-D68 2A protease C107A mutant -

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Basic information

Entry
Database: PDB / ID: 7jre
TitleCrystal structure of EV-D68 2A protease C107A mutant
ComponentsProtease 2A
KeywordsVIRAL PROTEIN / HYDROLASE / 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
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: 2.5 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 C107A mutant
Authors: Liu, C. / Lee, M.-Y. / Ma, C. / Liu, W. / Wang, J.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: 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
A: Protease 2A
B: Protease 2A
C: Protease 2A
D: Protease 2A
E: Protease 2A
F: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,48312
Polymers96,0916
Non-polymers3926
Water1,06359
1
A: Protease 2A
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1614
Polymers32,0302
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-17 kcal/mol
Surface area12900 Å2
MethodPISA
2
C: Protease 2A
D: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1614
Polymers32,0302
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-20 kcal/mol
Surface area13130 Å2
MethodPISA
3
E: Protease 2A
F: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1614
Polymers32,0302
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-19 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.772, 118.772, 80.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Space group name HallP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 4 and (name N or name...
d_2ens_1(chain "B" and (resid 4 through 12 or (resid 13...
d_3ens_1(chain "C" and ((resid 4 and (name N or name...
d_4ens_1(chain "D" and ((resid 4 and (name N or name...
d_5ens_1(chain "E" and ((resid 4 and (name N or name...
d_6ens_1(chain "F" and ((resid 4 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PHETRPA2 - 137
d_21ens_1PHETRPC2 - 137
d_31ens_1PHETRPE2 - 137
d_41ens_1PHETRPG1 - 136
d_51ens_1PHETRPI4 - 139
d_61ens_1PHETRPK1 - 136

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Components

#1: Protein
Protease 2A


Mass: 16015.104 Da / Num. of mol.: 6 / Mutation: C107A
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 / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.86 Å3/Da / Density % sol: 57 % / Description: square shaped three dementional crystal
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.37
ReflectionResolution: 2.5→47.76 Å / Num. obs: 38883 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Rrim(I) all: 0.062 / Net I/σ(I): 21
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3875 / CC1/2: 0.835 / Rpim(I) all: 0.213 / Rrim(I) all: 0.302 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIXdev_3893refinement
XDSdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hrv

2hrv


Resolution: 2.5→47.76 Å / Cross valid method: FREE R-VALUE / σ(F): 131.3 / Phase error: 35.4303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 1979 5.09 %
Rwork0.2192 36904 -
obs0.226 38883 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.77 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 6 59 6215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646312
X-RAY DIFFRACTIONf_angle_d0.77248607
X-RAY DIFFRACTIONf_chiral_restr0.052929
X-RAY DIFFRACTIONf_plane_restr0.00651129
X-RAY DIFFRACTIONf_dihedral_angle_d17.03042122
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.27864451658
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.01796671694
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.06568107605
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.33728407831
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.33502131434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.34731360.32892629X-RAY DIFFRACTION95.08
2.56-2.630.36061600.32542603X-RAY DIFFRACTION94.21
2.63-2.710.33851300.31842607X-RAY DIFFRACTION95.22
2.71-2.80.30771290.30512637X-RAY DIFFRACTION95.34
2.8-2.90.31361640.29062623X-RAY DIFFRACTION94.12
2.9-3.010.29281400.27962608X-RAY DIFFRACTION94.91
3.01-3.150.30691260.26462620X-RAY DIFFRACTION95.31
3.15-3.320.29291420.25752647X-RAY DIFFRACTION94.91
3.32-3.520.28381270.24242645X-RAY DIFFRACTION95.38
3.52-3.80.2351740.22962605X-RAY DIFFRACTION93.64
3.8-4.180.20961380.20752627X-RAY DIFFRACTION94.97
4.18-4.780.21571260.17812676X-RAY DIFFRACTION95.33
4.78-6.020.19711470.18882640X-RAY DIFFRACTION94.56
6.02-47.760.22521400.20722737X-RAY DIFFRACTION95.13

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