+Open data
-Basic information
Entry | Database: PDB / ID: 1qa4 | ||||||
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Title | HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES | ||||||
Components | Protein Nef | ||||||
Keywords | VIRAL PROTEIN / HIV / AIDS / REGULATORY FACTOR / NEGATIVE FACTOR / NEF / MYRISTOYLATION / MYRISTYLATION | ||||||
Function / homology | Function and homology information perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / host cell Golgi membrane / MHC class I protein binding ...perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / host cell Golgi membrane / MHC class I protein binding / regulation of calcium-mediated signaling / viral life cycle / virion component / SH3 domain binding / ATPase binding / signaling receptor binding / GTP binding / protein kinase binding / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | ||||||
Authors | Geyer, M. / Kalbitzer, H.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein. Authors: Geyer, M. / Munte, C.E. / Schorr, J. / Kellner, R. / Kalbitzer, H.R. #1: Journal: Protein Sci. / Year: 1997 Title: Refined solution structure and backbone dynamics of HIV-1 Nef. Authors: Grzesiek, S. / Bax, A. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Tjandra, N. / Wingfield, P.T. #2: Journal: Biochemistry / Year: 1997 Title: Solution structure of a polypeptide from the N terminus of the HIV protein Nef. Authors: Barnham, K.J. / Monks, S.A. / Hinds, M.G. / Azad, A.A. / Norton, R.S. #3: Journal: Structure / Year: 1997 Title: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Authors: Arold, S. / Franken, P. / Strub, M.P. / Hoh, F. / Benichou, S. / Benarous, R. / Dumas, C. #4: Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Authors: Lee, C.H. / Saksela, K. / Mirza, U.A. / Chait, B.T. / Kuriyan, J. #5: Journal: Nat.Struct.Biol. / Year: 1996 Title: The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Authors: Grzesiek, S. / Bax, A. / Clore, G.M. / Gronenborn, A.M. / Hu, J.S. / Kaufman, J. / Palmer, I. / Stahl, S.J. / Wingfield, P.T. #6: Journal: Eur.J.Biochem. / Year: 1994 Title: A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease. Authors: Freund, J. / Kellner, R. / Konvalinka, J. / Wolber, V. / Krausslich, H.G. / Kalbitzer, H.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qa4.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qa4.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qa4 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qa4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5817.458 Da / Num. of mol.: 1 / Fragment: ANCHOR DOMAIN, residues 2-57 / Source method: obtained synthetically Source: (synth.) Human immunodeficiency virus type 1 (isolate NL4-3) References: UniProt: P04324 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 1H |
-Sample preparation
Sample conditions | pH: 7.1 / Temperature: 285.0 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). | ||||||||||||||||
NMR ensemble | Conformer selection criteria: TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN Conformers calculated total number: 400 / Conformers submitted total number: 2 |