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Yorodumi- PDB-2bl6: Solution structure of the Zn complex of EIAV NCp11(22-58) peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bl6 | ||||||
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Title | Solution structure of the Zn complex of EIAV NCp11(22-58) peptide, including two CCHC Zn-binding motifs. | ||||||
Components | NUCLEOCAPSID PROTEIN P11 | ||||||
Keywords | NUCLEOCAPSID PROTEIN / LENTIVIRUS / POLYPROTEIN / CORE PROTEIN / RETROVIRUS ZINC FINGER-LIKE DOMAINS | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / nucleic acid binding / structural constituent of virion / zinc ion binding Similarity search - Function | ||||||
Biological species | EQUINE INFECTIOUS ANEMIA VIRUS | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING-ENERGY MINIMIZATION | ||||||
Authors | Amodeo, P. / Castiglione-Morelli, M.A. / Ostuni, A. / Bavoso, A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bl6.cif.gz | 332 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bl6.ent.gz | 274.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bl6_validation.pdf.gz | 365.8 KB | Display | wwPDB validaton report |
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Full document | 2bl6_full_validation.pdf.gz | 452.1 KB | Display | |
Data in XML | 2bl6_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2bl6_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2bl6 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2bl6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: NONE |
-Sample preparation
Details | Contents: 10% WATER/90% D2O |
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Sample conditions | Ionic strength: 210 mM / pH: 5.8 / Pressure: 1.0 atm / Temperature: 293.0 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING-ENERGY MINIMIZATION / Software ordinal: 1 Details: SIMULATED ANNEALING FOLLOWED BY ENERGY MINIMIZATION, BOTH PERFORMED WITH A GBSA IMPLICIT SOLVENT APPROACH | |||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, FAVORABLE ENERGY, THE LEAST RESTRAINT VIOLATIONS Conformers calculated total number: 150 / Conformers submitted total number: 30 |