+Open data
-Basic information
Entry | Database: PDB / ID: 1avv | ||||||
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Title | HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN | ||||||
Components | NEGATIVE FACTOR | ||||||
Keywords | MYRISTYLATION / GTP-BINDING / PHOSPHORYLATION / HIV-1 / NEF / VIRUS / PXXP MOTIF | ||||||
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 / peptidase activator activity / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / regulation of T cell activation ...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 / peptidase activator activity / suppression by virus of host autophagy / thioesterase binding / CD4 receptor binding / regulation of T cell activation / host cell Golgi membrane / MHC class I protein binding / regulation of calcium-mediated signaling / viral life cycle / virion component / SH3 domain binding / ATPase binding / calmodulin binding / signaling receptor binding / GTP binding / protein kinase binding / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIRAS / Resolution: 3 Å | ||||||
Authors | Arold, S. / Franken, P. / Dumas, C. | ||||||
Citation | 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. #1: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avv.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avv.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1avv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avv ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avv | HTTPS FTP |
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-Related structure data
Related structure data | 1avzC 1efnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17568.723 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN Mutation: DEL(2-57), N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: HIV-1 NEF / Variant: ISOLATE LAI / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Gene (production host): HIV-1 NEF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03406 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 61 % |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown / Details: unpublished data |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0373 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 4, 1996 / Details: TWO BENT MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0373 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 3812 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9 |
Reflection | *PLUS Num. measured all: 18555 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, MIRAS Starting model: PDB ENTRY 1EFN Resolution: 3→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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