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- PDB-1avv: HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1avv
TitleHIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN
ComponentsNEGATIVE FACTOR
KeywordsMYRISTYLATION / GTP-BINDING / PHOSPHORYLATION / HIV-1 / NEF / VIRUS / PXXP MOTIF
Function / homology
Function and homology information


negative regulation of glycoprotein biosynthetic process / 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 / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / thioesterase binding / CD4 receptor binding / regulation of T cell activation / peptidase activator activity / MHC class I protein binding ...negative regulation of glycoprotein biosynthetic process / 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 / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / thioesterase binding / CD4 receptor binding / regulation of T cell activation / peptidase activator activity / MHC class I protein binding / host cell Golgi membrane / viral life cycle / regulation of calcium-mediated signaling / SH3 domain binding / virion component / ATPase binding / calmodulin binding / symbiont-mediated suppression of host innate immune response / signaling receptor binding / protein kinase binding / GTP binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIRAS / Resolution: 3 Å
AuthorsArold, 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
DepositionSep 21, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 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: NEGATIVE FACTOR


Theoretical massNumber of molelcules
Total (without water)17,5691
Polymers17,5691
Non-polymers00
Water00
1
A: NEGATIVE FACTOR

A: NEGATIVE FACTOR


Theoretical massNumber of molelcules
Total (without water)35,1372
Polymers35,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Unit cell
Length a, b, c (Å)85.160, 85.160, 85.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein NEGATIVE FACTOR / NEF / F-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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 61 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: unpublished data

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0373
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 4, 1996 / Details: TWO BENT MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0373 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIRAS
Starting model: PDB ENTRY 1EFN

1efn


Resolution: 3→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -7.4 %RANDOM
Rwork0.22 ---
obs0.22 3139 78.8 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 0 895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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