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- PDB-2bl6: Solution structure of the Zn complex of EIAV NCp11(22-58) peptide... -

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Basic information

Entry
Database: PDB / ID: 2bl6
TitleSolution structure of the Zn complex of EIAV NCp11(22-58) peptide, including two CCHC Zn-binding motifs.
ComponentsNUCLEOCAPSID PROTEIN P11Capsid
KeywordsNUCLEOCAPSID PROTEIN / LENTIVIRUS / POLYPROTEIN / CORE PROTEIN / RETROVIRUS ZINC FINGER-LIKE DOMAINS
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
Gag protein p15 / Gag protein p15 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Gag protein p15 / Gag protein p15 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesEQUINE INFECTIOUS ANEMIA VIRUS
MethodSOLUTION NMR / SIMULATED ANNEALING-ENERGY MINIMIZATION
AuthorsAmodeo, P. / Castiglione-Morelli, M.A. / Ostuni, A. / Bavoso, A.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Features in Eiav Ncp11: A Lentivirus Nucleocapsid Protein with a Short Linker
Authors: Amodeo, P. / Castiglione-Morelli, M.A. / Ostuni, A. / Battistuzzi, G. / Bavoso, A.
History
DepositionMar 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN P11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2843
Polymers4,1531
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 150STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, FAVORABLE ENERGY, THE LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein/peptide NUCLEOCAPSID PROTEIN P11 / Capsid


Mass: 4152.872 Da / Num. of mol.: 1 / Fragment: RESIDUES 381-417 / Source method: obtained synthetically
Details: FRAGMENT 22-58 OF NCP11 CORRESPONDS TO 381-417 OF THE WHOLE EIAV GAG PROTEIN CONTAINS TWO ZN IONS IN TWO CCHC ZN-BINDING DOMAINS
Source: (synth.) EQUINE INFECTIOUS ANEMIA VIRUS / References: UniProt: P69732
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 210 mM / pH: 5.8 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
Amberstructure solution
RefinementMethod: SIMULATED ANNEALING-ENERGY MINIMIZATION / Software ordinal: 1
Details: SIMULATED ANNEALING FOLLOWED BY ENERGY MINIMIZATION, BOTH PERFORMED WITH A GBSA IMPLICIT SOLVENT APPROACH
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, FAVORABLE ENERGY, THE LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 150 / Conformers submitted total number: 30

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