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- PDB-3rea: HIV-1 Nef protein in complex with engineered Hck-SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3rea
TitleHIV-1 Nef protein in complex with engineered Hck-SH3 domain
Components
  • Protein Nef
  • Tyrosine-protein kinase HCK
KeywordsPROTEIN BINDING / HIV-1 Nef / SH3 domain binding / signaling / Hck SH3 domain
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / 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 / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / 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 / suppression by virus of host autophagy / regulation of phagocytosis / FLT3 signaling through SRC family kinases / 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 / host cell Golgi membrane / 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 / virion component / 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 / endocytosis involved in viral entry into host cell / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / SH3 domain binding / 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 / 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 / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / membrane / nucleus / 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 Domains / 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 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
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 Å
AuthorsSchulte, A. / Blankenfeldt, W. / Geyer, M.
CitationJournal: PLoS ONE / Year: 2011
Title: Molecular design, functional characterization and structural basis of a protein inhibitor against the HIV-1 pathogenicity factor Nef.
Authors: Breuer, S. / Schievink, S.I. / Schulte, A. / Blankenfeldt, W. / Fackler, O.T. / Geyer, M.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,3834
Polymers52,3834
Non-polymers00
Water5,963331
1
A: Protein Nef
B: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)26,1912
Polymers26,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7 kcal/mol
Surface area10900 Å2
MethodPISA
2
C: Protein Nef
D: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)26,1912
Polymers26,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-7 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.692, 65.692, 279.068
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 Protein Nef / 3'ORF / Negative factor / F-protein / C-terminal core protein


Mass: 19140.473 Da / Num. of mol.: 2 / Mutation: I47M, T48A, C59S, C210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: HIV-1 Nef, nef / Plasmid: pGEX-4T1 TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03407
#2: Protein Tyrosine-protein kinase HCK / Hemopoietic cell kinase / p59-HCK/p60-HCK


Mass: 7050.844 Da / Num. of mol.: 2 / Mutation: E90V, A91S, I92W, H93S, H94P, E95D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08631, non-specific protein-tyrosine kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2009
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→69.77 Å / Num. all: 40486 / Num. obs: 40486 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.05 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0102phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EFN

1efn


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.889 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20544 2148 5 %RANDOM
Rwork0.168 ---
obs0.16989 40486 99.97 %-
all-40486 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.995 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 0 331 3377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223188
X-RAY DIFFRACTIONr_bond_other_d0.0030.022193
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.944345
X-RAY DIFFRACTIONr_angle_other_deg1.02135288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17223.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1515503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9871523
X-RAY DIFFRACTIONr_chiral_restr0.1390.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02708
X-RAY DIFFRACTIONr_mcbond_it1.4661.51873
X-RAY DIFFRACTIONr_mcbond_other0.4321.5742
X-RAY DIFFRACTIONr_mcangle_it2.47223015
X-RAY DIFFRACTIONr_scbond_it3.3231315
X-RAY DIFFRACTIONr_scangle_it5.1274.51325
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 161 -
Rwork0.2 2934 -
obs--99.94 %
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)
11.8825-0.27810.56111.59210.0782.4022-0.06170.00690.15440.2249-0.0286-0.05250.0245-0.09020.09030.075-0.0669-0.05810.09450.07370.0842-14.97618.721-4.0375
23.8331-0.1603-0.47753.8339-1.33776.32460.09580.1291-0.1362-0.2691-0.2544-0.41350.1890.44860.15860.02630.01040.01490.19080.13490.142-0.46896.2628-26.4239
32.20221.1514-0.90962.247-1.86651.8992-0.12380.099-0.5134-0.1619-0.0084-0.25880.25790.03080.13230.0843-0.0501-0.02490.1280.04090.188-32.3749-8.2622-13.9319
43.2174-0.8350.92234.1512-2.28314.3204-0.0652-0.12710.17040.18760.16070.2086-0.23-0.5372-0.09550.0216-0.0033-0.01250.18130.07920.0807-40.603416.1208-23.6222
51.0221-0.12210.07330.644-0.32430.66250.02530.0437-0.02650.0538-0.0203-0.05560.0082-0.053-0.0050.0745-0.0485-0.02410.1240.04810.0874-23.22615.9786-14.0988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 205
2X-RAY DIFFRACTION2B79 - 138
3X-RAY DIFFRACTION3C59 - 210
4X-RAY DIFFRACTION4D78 - 137
5X-RAY DIFFRACTION5A301 - 429
6X-RAY DIFFRACTION5B301 - 352
7X-RAY DIFFRACTION5C301 - 389
8X-RAY DIFFRACTION5D301 - 361

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