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- PDB-3w95: Crystal structure of 2A proteinase (C110A) from enterovirus 71 -

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Basic information

Entry
Database: PDB / ID: 3w95
TitleCrystal structure of 2A proteinase (C110A) from enterovirus 71
ComponentsGenome polyprotein
KeywordsHYDROLASE / chymotrypsin-fold six-stranded beta-barrel catalytic triad Zinc-coordination / chymotrypsin-fold six-stranded beta-barrel catalytic triad
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / 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 / entry receptor-mediated virion attachment to host cell / RNA helicase activity / DNA replication / 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 / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMu, Z. / Gao, X. / Cui, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal Structure of 2A Proteinase from Hand, Foot and Mouth Disease Virus
Authors: Mu, Z. / Wang, B. / Zhang, X. / Gao, X. / Qin, B. / Zhao, Z. / Cui, S.
History
DepositionMar 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9302
Polymers18,8651
Non-polymers651
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.5238, 92.5238, 36.1267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Genome polyprotein / Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Virion protein 4 / Protein VP2 / P1B / Virion protein 2 ...Protein VP0 / VP4-VP2 / Protein VP4 / P1A / Virion protein 4 / Protein VP2 / P1B / Virion protein 2 / Protein VP3 / P1C / Virion protein 3 / Protein VP1 / P1D / Virion protein 1 / Picornain 2A / P2A / Protein 2A / Protein 2B / P2B / Protein 2C / P2C / Protein 3A / P3A / Protein 3B / P3B / VPg / Picornain 3C / Protease 3C / P3C / RNA-directed RNA polymerase 3D-POL / P3D-POL


Mass: 18864.982 Da / Num. of mol.: 1 / Fragment: UNP residues 863-1012 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Strain: 7423/MS/87 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q66479*PLUS, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KC875402 FOR THIS SEQUENCE. AT THE RESIDUE 110 ...AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KC875402 FOR THIS SEQUENCE. AT THE RESIDUE 110 (CHAIN A), THE ENGINEERED MUTATION HAS BEEN CAUSED.

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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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.2M Magnesium chloride, 0.1M Tris-Hcl, 1%(v/v) PEG4000, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 12, 2013 / Details: VariMax
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→29.26 Å / Num. obs: 13786 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.77 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.279 / Num. unique all: 13786 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HRV

2hrv


Resolution: 1.85→29.259 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 685 4.98 %RANDOM
Rwork0.2173 ---
obs0.2189 13744 98.7 %-
all-13786 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.835 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2426 Å20 Å2-0 Å2
2--2.2426 Å2-0 Å2
3----4.4852 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 1 206 1363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071191
X-RAY DIFFRACTIONf_angle_d1.011617
X-RAY DIFFRACTIONf_dihedral_angle_d13.988421
X-RAY DIFFRACTIONf_chiral_restr0.063170
X-RAY DIFFRACTIONf_plane_restr0.004213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.99290.36191330.34742456X-RAY DIFFRACTION95
1.9929-2.19340.29761480.24522572X-RAY DIFFRACTION100
2.1934-2.51070.31811140.24122607X-RAY DIFFRACTION99
2.5107-3.16260.23071400.19872645X-RAY DIFFRACTION100
3.1626-29.26220.20751500.1912779X-RAY DIFFRACTION100

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