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- PDB-2bai: The Zinc finger domain of Mengovirus Leader polypeptide -

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Basic information

Entry
Database: PDB / ID: 2bai
TitleThe Zinc finger domain of Mengovirus Leader polypeptide
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Zinc finger domain / virus / viruses / cardiovirus / mengovirus / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Leader peptide, picornavirus / Viral leader polypeptide zinc finger / Virion protein N terminal domain / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMengo virus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCornilescu, C.C. / Porter, F.W. / Qin, Z. / Lee, M.S. / Palmenberg, A.C. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Febs Lett. / Year: 2008
Title: NMR structure of the mengovirus Leader protein zinc-finger domain.
Authors: Cornilescu, C.C. / Porter, F.W. / Zhao, K.Q. / Palmenberg, A.C. / Markley, J.L.
History
DepositionOct 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7902
Polymers3,7241
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Genome polyprotein / MENGOVIRUS LEADER POLYPEPTIDE


Mass: 3724.245 Da / Num. of mol.: 1 / Fragment: zinc finger domain, residues 1-32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengo virus / Genus: Cardiovirus / Species: Encephalomyocarditis virus / Production host: Escherichia coli (E. coli) / References: UniProt: P32540
#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 experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HCCHTOCSY
141HNCA
151H(CCO)NH
161C(CO)NH

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Sample preparation

DetailsContents: 1mM NC-labeled mengol, 50mM NaPi, 93% H2O, 7% D2O / Solvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 50mM / pH: 6.5 / Pressure: ambient / Temperature: 298 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
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeFrank Delaglioprocessing
PIPP/STAPPDan Garrettdata analysis
CYANA2Guentertstructure solution
CYANA2Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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