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- PDB-8f2p: Nef SF2 dimerization mutant bound to Hck SH3 -

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Basic information

Entry
Database: PDB / ID: 8f2p
TitleNef SF2 dimerization mutant bound to Hck SH3
Components
  • C-terminal core protein
  • Tyrosine-protein kinase HCK
KeywordsVIRAL PROTEIN / protein complex / Nef / Hck / SH3
Function / homology
Function and homology information


leukocyte degranulation / innate immune response-activating signaling pathway / respiratory burst after phagocytosis / leukocyte migration involved in 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 / regulation of podosome assembly / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases / regulation of phagocytosis ...leukocyte degranulation / innate immune response-activating signaling pathway / respiratory burst after phagocytosis / leukocyte migration involved in 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 / regulation of podosome assembly / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases / regulation of phagocytosis / Nef and signal transduction / regulation of DNA-binding transcription factor activity / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / host cell Golgi membrane / FCGR activation / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / transport vesicle / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / lipopolysaccharide-mediated signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / integrin-mediated signaling pathway / cell projection / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / peptidyl-tyrosine phosphorylation / caveola / SH3 domain binding / virion component / cytoplasmic side of plasma membrane / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein autophosphorylation / regulation of inflammatory response / protein tyrosine kinase activity / cell differentiation / cytoskeleton / lysosome / cell adhesion / intracellular signal transduction / protein phosphorylation / inflammatory response / endocytosis involved in viral entry into host cell / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / GTP binding / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / : / SH3 domain / SH2 domain ...Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein Nef / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsThomas, C.E. / Alvarado, J.J. / Smithgall, T.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057083 United States
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Neutron Reflectometry and Molecular Simulations Demonstrate HIV-1 Nef Homodimer Formation on Model Lipid Bilayers.
Authors: Heinrich, F. / Thomas, C.E. / Alvarado, J.J. / Eells, R. / Thomas, A. / Doucet, M. / Whitlatch, K.N. / Aryal, M. / Losche, M. / Smithgall, T.E.
History
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-terminal core protein
B: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)26,1502
Polymers26,1502
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Also determined by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.051, 84.051, 83.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein C-terminal core protein / Nef


Mass: 17594.859 Da / Num. of mol.: 1 / Fragment: Nef SF2 core domain (UNP residues 62-209) / Mutation: L116D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: isolate ARV2/SF2 / Gene: nef / Plasmid: pET21A+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)PLYSS / References: UniProt: P03407
#2: Protein Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 8555.456 Da / Num. of mol.: 1 / Fragment: Hck SH3 domain (UNP residues 77-140)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 STAR(DE3)
References: UniProt: P08631, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium chloride, 0.1 M sodium acetate, pH 4.6, 12% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 9299 / % possible obs: 100 % / Redundancy: 16.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.115 / Net I/σ(I): 16.47
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.63-2.791.79614580.8611.8521
2.79-2.980.99413830.9531.0261
2.98-3.220.49512850.9880.511
3.22-3.530.25911900.9950.2671
3.53-3.940.12910890.9980.1331
3.94-4.550.0889740.9990.0911
4.55-5.550.0798390.9980.0821
5.55-7.80.0726660.9980.0741
7.8-500.0544150.9990.0561

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSJan 10, 2022data scaling
XDSJan 10, 2022data reduction
PHASER1.19.1-4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4U5W

4u5w


Resolution: 2.63→48.37 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 820 4.86 %Random Selection
Rwork0.2123 ---
obs0.2142 9299 99.84 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 0 4 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031399
X-RAY DIFFRACTIONf_angle_d0.5171909
X-RAY DIFFRACTIONf_dihedral_angle_d14.535493
X-RAY DIFFRACTIONf_chiral_restr0.042195
X-RAY DIFFRACTIONf_plane_restr0.005243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.80.36131430.3322654X-RAY DIFFRACTION100
2.8-3.010.31711350.26262676X-RAY DIFFRACTION100
3.01-3.320.33581390.28672667X-RAY DIFFRACTION100
3.32-3.80.26441400.2262671X-RAY DIFFRACTION100
3.8-4.780.2161200.18222698X-RAY DIFFRACTION100
4.78-48.370.22791430.19152677X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.6191-0.41361.3355.3092.86892.68560.1357-0.11880.4612-0.3004-0.39180.2606-1.1768-0.17640.21140.75610.0958-0.05380.71440.00090.6574-6.154-34.507712.2096
26.62652.75943.84418.15155.03195.1458-0.0108-0.6370.03540.53830.08420.0146-0.15910.0524-0.10470.8276-0.00080.03760.69140.01670.6451-4.8019-28.565920.8145
37.061.44460.18037.9358-3.5098.1539-0.0124-0.00360.50870.0660.2128-0.4986-0.69480.2262-0.210.583-0.0428-0.00360.7382-0.02350.75168.0272-35.288122.5421
46.6054.3883.34533.83684.49047.3040.7033-0.5567-0.60551.3791-0.49160.26471.1302-0.9722-0.38810.9121-0.2007-0.10421.1763-0.00050.98585.2467-48.786329.6625
54.092-1.10555.17246.9058-4.0319.9052-0.1637-0.48230.0268-0.00620.2076-0.2786-1.0641-0.06410.07010.7690.13320.02220.6959-0.0630.5822-17.4047-32.46773.4735
63.10012.55423.25522.41031.92895.30090.4709-0.0314-0.5766-0.4536-0.58450.2425-0.0481-0.00210.04040.87650.1689-0.02090.7934-0.01230.6945-17.7213-33.87210.0834
78.26992.25673.37966.6104-5.77698.98640.1708-0.3369-0.7045-0.3939-0.1686-0.46940.33980.83930.050.66390.20650.00770.7428-0.07160.6423-18.9687-37.33851.6442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 202 )
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 209 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 97 )
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 112 )
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 139 )

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