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- PDB-2a4o: Dual modes of modification of Hepatitis A virus 3C protease by a ... -

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Basic information

Entry
Database: PDB / ID: 2a4o
TitleDual modes of modification of Hepatitis A virus 3C protease by a serine derived beta-lactone: selective crytstallization and high resolution structure of the His102 adduct
ComponentsProbable protein P3CProbability
KeywordsHYDROLASE / beta barrel
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Mainly Beta
Similarity search - Domain/homology
ACETYL GROUP / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / PHENYLALANINE AMIDE / VALINE / Genome polyprotein
Similarity search - Component
Biological speciesHuman hepatitis A virus Hu/Northern Africa/MBB/1978
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G.
CitationJournal: J.MOL.BIOL. / Year: 2005
Title: Dual Modes of Modification of Hepatitis A Virus 3C Protease by a Serine-derived beta-Lactone: Selective Crystallization and Formation of a Functional Catalytic Triad in the Active Site
Authors: Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G.
History
DepositionJun 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Probable protein P3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6685
Polymers24,1201
Non-polymers5494
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 56.072, 81.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is likely to be a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable protein P3C / Probability / 3C protease


Mass: 24119.771 Da / Num. of mol.: 1 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human hepatitis A virus Hu/Northern Africa/MBB/1978
Genus: Hepatovirus / Species: Hepatitis A virusHepatitis A / Strain: MBB / Gene: 3C / Plasmid: pHAV-3CEX / Production host: Escherichia coli (E. coli) / Strain (production host): D1210 / References: UniProt: P13901, picornain 3C

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-BBL / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE


Mass: 223.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO4
#3: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#5: Chemical ChemComp-NFA / PHENYLALANINE AMIDE


Type: L-peptide linking / Mass: 164.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, Glycerol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115889 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2004
RadiationMonochromator: dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115889 Å / Relative weight: 1
ReflectionResolution: 1.55→46.19 Å / Num. obs: 29065 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.55→1.63 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4088 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.89 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19759 1425 4.9 %RANDOM
Rwork0.17808 ---
all0.17905 28861 --
obs0.17905 27436 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 0 258 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221706
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9742301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49124.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.542157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021259
X-RAY DIFFRACTIONr_nbd_refined0.2050.2838
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.229
X-RAY DIFFRACTIONr_mcbond_it1.0681.51083
X-RAY DIFFRACTIONr_mcangle_it1.56221714
X-RAY DIFFRACTIONr_scbond_it2.2063695
X-RAY DIFFRACTIONr_scangle_it3.384.5587
X-RAY DIFFRACTIONr_rigid_bond_restr1.34731778
X-RAY DIFFRACTIONr_sphericity_free2.9683290
X-RAY DIFFRACTIONr_sphericity_bonded2.57531672
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 105 -
Rwork0.285 1907 -
obs--94.86 %

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