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- PDB-5nuh: Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3... -

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Basic information

Entry
Database: PDB / ID: 5nuh
TitleCrystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain
Components
  • Protein Nef
  • Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK
KeywordsTRANSFERASE / SIV / Virus / Nef / SH3
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / receptor-mediated endocytosis of virus by host cell / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / lipid binding / positive regulation of cell population proliferation / GTP binding / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. ...Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase HCK / Protein Nef
Similarity search - Component
Biological speciesSimian immunodeficiency virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsHorenkamp, F.A. / Anand, K. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGE 976/6-1 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3.
Authors: Manrique, S. / Sauter, D. / Horenkamp, F.A. / Lulf, S. / Yu, H. / Hotter, D. / Anand, K. / Kirchhoff, F. / Geyer, M.
History
DepositionApr 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Nef
B: Protein Nef
C: Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK
D: Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)54,4334
Polymers54,4334
Non-polymers00
Water99155
1
A: Protein Nef
D: Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)27,2162
Polymers27,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area10240 Å2
MethodPISA
2
B: Protein Nef
C: Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)27,2162
Polymers27,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.000, 104.000, 53.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Protein Nef


Mass: 20221.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QGG3
#2: Protein Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 6994.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Production host: Escherichia coli (E. coli)
References: UniProt: P08631, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 3350, 0.15 M tri-lithium-citrat, 1% 1.6 hexandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→45.7 Å / Num. obs: 16118 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.7
Reflection shellResolution: 2.78→2.8 Å / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDS(1.10_2155: ???)data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IK5

3ik5


Resolution: 2.78→45.68 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.229 806 5 %
Rwork0.192 --
obs0.194 16114 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.78→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 0 55 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093114
X-RAY DIFFRACTIONf_angle_d1.0274249
X-RAY DIFFRACTIONf_dihedral_angle_d15.5471775
X-RAY DIFFRACTIONf_chiral_restr0.059425
X-RAY DIFFRACTIONf_plane_restr0.007535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7802-2.95430.3241330.25162527X-RAY DIFFRACTION100
2.9543-3.18240.29321350.22982558X-RAY DIFFRACTION100
3.1824-3.50250.2741340.20552551X-RAY DIFFRACTION100
3.5025-4.00910.21941360.18312590X-RAY DIFFRACTION100
4.0091-5.050.18941330.1642516X-RAY DIFFRACTION100
5.05-45.68430.21141350.18992566X-RAY DIFFRACTION100

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