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- PDB-9fgo: Crystal structure of Enterovirus 71 2A protease mutant C110A cont... -

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Basic information

Entry
Database: PDB / ID: 9fgo
TitleCrystal structure of Enterovirus 71 2A protease mutant C110A containing VP1-2A junction in the active site
ComponentsPolyprotein
KeywordsVIRAL PROTEIN / 2A Protease
Function / homology
Function and homology information


viral process / peptidase activity / host cell cytoplasm / proteolysis / cytoplasm
Similarity search - Function
Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsNi, X. / Koekemoer, L. / Williams, E.P. / Wang, S. / Wright, N.D. / Godoy, A.S. / Aschenbrenner, J.C. / Balcomb, B.H. / Lithgo, R.M. / Marples, P.G. ...Ni, X. / Koekemoer, L. / Williams, E.P. / Wang, S. / Wright, N.D. / Godoy, A.S. / Aschenbrenner, J.C. / Balcomb, B.H. / Lithgo, R.M. / Marples, P.G. / Fairhead, M. / Thompson, W. / Kirkegaard, K. / Fearon, D. / Walsh, M.A. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: To Be Published
Title: Crystal structure of Enterovirus 71 2A protease mutant C110A containing VP1-2A junction in the active site
Authors: Ni, X. / Koekemoer, L. / Williams, E.P. / Wang, S. / Wright, N.D. / Godoy, A.S. / Aschenbrenner, J.C. / Balcomb, B.H. / Lithgo, R.M. / Marples, P.G. / Fairhead, M. / Thompson, W. / ...Authors: Ni, X. / Koekemoer, L. / Williams, E.P. / Wang, S. / Wright, N.D. / Godoy, A.S. / Aschenbrenner, J.C. / Balcomb, B.H. / Lithgo, R.M. / Marples, P.G. / Fairhead, M. / Thompson, W. / Kirkegaard, K. / Fearon, D. / Walsh, M.A. / von Delft, F.
History
DepositionMay 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2416
Polymers17,0341
Non-polymers2075
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-30 kcal/mol
Surface area7340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.544, 61.544, 78.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Polyprotein


Mass: 17034.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli (E. coli) / References: UniProt: E5L2F2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1M Sodium chloride, 15% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.43→28.69 Å / Num. obs: 31516 / % possible obs: 99.8 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.013 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 30.2
Reflection shellResolution: 1.43→1.45 Å / % possible obs: 96.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.726 / Num. measured all: 12681 / Num. unique obs: 1500 / CC1/2: 0.843 / Rpim(I) all: 0.262 / Rrim(I) all: 0.773 / Χ2: 1.06 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→28.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.473 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16478 1443 4.6 %RANDOM
Rwork0.1514 ---
obs0.15203 30029 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.43→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 5 152 1303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171080
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.6261671
X-RAY DIFFRACTIONr_angle_other_deg1.5341.5712506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09421.56264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41415187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.089158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.211.142614
X-RAY DIFFRACTIONr_mcbond_other1.1951.137613
X-RAY DIFFRACTIONr_mcangle_it1.8621.712771
X-RAY DIFFRACTIONr_mcangle_other1.8661.718772
X-RAY DIFFRACTIONr_scbond_it1.9281.301605
X-RAY DIFFRACTIONr_scbond_other1.9221.293603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6721.889893
X-RAY DIFFRACTIONr_long_range_B_refined4.75614.8391357
X-RAY DIFFRACTIONr_long_range_B_other4.58813.8221320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.464 Å
RfactorNum. reflection% reflection
Rfree0.218 92 -
Rwork0.204 2183 -
obs--97.85 %
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)
11.4820.0708-0.62140.88410.11692.2437-0.0771-0.0614-0.06650.0416-0.02760.08870.1434-0.21770.10470.0573-0.0150.00310.0742-0.00860.063-32.87728.3079-5.2159
20.87470.09730.16620.6379-0.19160.9727-0.0594-0.0151-0.02370.01370.0356-0.06330.03020.05520.02380.0631-0.0024-0.00440.0527-0.00990.055-20.26696.6979-8.0181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 47
2X-RAY DIFFRACTION2A48 - 144

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