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- PDB-3tb8: Crystal structure of full-length myristoylated HIV-1 Nef -

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Basic information

Entry
Database: PDB / ID: 3tb8
TitleCrystal structure of full-length myristoylated HIV-1 Nef
ComponentsProtein Nef
KeywordsAPOPTOSIS / F-protein (PF00469)
Function / homology
Function and homology information


perturbation by virus of host immune response / negative regulation of CD4 production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / CD4 receptor binding / thioesterase 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 antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / CD4 receptor binding / thioesterase 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
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsDennis, C.A. / Harris, M. / Jaeger, J.
CitationJournal: To be Published
Title: Crystal structure of full-length myristoylated HIV-1 Nef
Authors: Dennis, C.A. / Harris, M. / Jaeger, J.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Nef


Theoretical massNumber of molelcules
Total (without water)23,4651
Polymers23,4651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.330, 89.330, 27.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein Nef / 3'ORF / Negative factor / F-protein / C-terminal core protein


Mass: 23464.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: myristoylated / Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: P03404

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% polyethyleneglycol 3350, lithium sulfate, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2004
RadiationMonochromator: Yale / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.71→28.25 Å / Num. all: 2629 / Num. obs: 2622 / % possible obs: 99.73 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX- Phasermodel building
PHENIX1.6.2_432 - Refinerefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX- Phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.71→28.25 Å / σ(F): 0.06 / Phase error: 41.66 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3366 86 3.28 %random
Rwork0.2308 ---
obs0.2334 2622 99.73 %-
all-2629 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.185 Å2 / ksol: 0 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.3662 Å20 Å2-0 Å2
2--11.2248 Å20 Å2
3----3.8587 Å2
Refinement stepCycle: LAST / Resolution: 3.71→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms203 0 0 0 203
LS refinement shellHighest resolution: 3.71 Å
RfactorNum. reflection% reflection
Rfree0.3366 86 -
Rwork0.2308 2436 -
obs--96 %

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