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- PDB-1z8r: 2A cysteine proteinase from human coxsackievirus B4 (strain JVB /... -

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Entry
Database: PDB / ID: 1z8r
Title2A cysteine proteinase from human coxsackievirus B4 (strain JVB / Benschoten / New York / 51)
ComponentsCoxsackievirus B4 polyprotein
KeywordsHYDROLASE / beta barrel coordinated zinc ion
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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. / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman coxsackievirus B4
MethodSOLUTION NMR / torsion angle dynamics, cartesian slow-cool annealing energy minimisation
AuthorsBaxter, N.J. / Roetzer, A. / Liebig, H.D. / Sedelnikova, S.E. / Hounslow, A.M. / Skern, T. / Waltho, J.P.
CitationJournal: J.Virol. / Year: 2006
Title: Structure and dynamics of coxsackievirus B4 2A proteinase, an enyzme involved in the etiology of heart disease.
Authors: Baxter, N.J. / Roetzer, A. / Liebig, H.D. / Sedelnikova, S.E. / Hounslow, A.M. / Skern, T. / Waltho, J.P.
History
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_nmr_software.name / _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_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coxsackievirus B4 polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,4271
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Coxsackievirus B4 polyprotein


Mass: 18426.523 Da / Num. of mol.: 1 / Fragment: Picornain 2A / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus B4 / Genus: Enterovirus / Species: Human enterovirus B / Gene: picornain 2A / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: P08292, picornain 2A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: simultaneously acquired 15N- and 13C-edited 3D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25 mM U-15N 2A proteinase 10 mM DTT 90% H2O, 10% D2O90% H2O/10% D2O
20.25 mM U-15N U-13C 2A proteinase 10 mM DTT 90% H2O, 10% D2O90% H2O/10% D2O
30.50 mM U-15N U-13C 2A proteinase 10 mM DTT 90% H2O, 10% D2O90% H2O/10% D2O
40.25 mM U-15N U-13C 2A proteinase 10 mM DTT 100% D2O100% D2O
50.55 mM biosynthetically directed fractional 10%-13C 2A proteinase 10 mM DTT 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM potassium phosphate 7.6 ambient 303 K
250 mM potassium phosphate 7.6 ambient 303 K
350 mM potassium phosphate 7.6 ambient 303 K
450 mM potassium phosphate 7.6 ambient 303 K
550 mM potassium phosphate 7.6 ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Felix2000Accelrys Inc, San Diego, CAprocessing
Felix2000Accelrys Inc, San Diego, CAdata analysis
CNS1.1Brunger, et al.structure solution
CNS1.1Brunger, et al.refinement
RefinementMethod: torsion angle dynamics, cartesian slow-cool annealing energy minimisation
Software ordinal: 1
Details: total of 1905 experimentally determined restraints, 1577 NOE-derived distance restraints, 168 dihedral angle restraints, 112 hydrogen bond distance restraints, 4 zinc-protein bond ...Details: total of 1905 experimentally determined restraints, 1577 NOE-derived distance restraints, 168 dihedral angle restraints, 112 hydrogen bond distance restraints, 4 zinc-protein bond restraints, 16 zinc-protein angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 17

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