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

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Basic information

Entry
Database: PDB / ID: 3reb
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: 3.45 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)58,8424
Polymers58,8424
Non-polymers00
Water00
1
A: Protein Nef
B: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)29,4212
Polymers29,4212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area9570 Å2
MethodPISA
2
C: Protein Nef
D: Tyrosine-protein kinase HCK


Theoretical massNumber of molelcules
Total (without water)29,4212
Polymers29,4212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.460, 112.460, 130.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 78:154 OR RESSEQ 183:205 )
211CHAIN C AND (RESSEQ 78:155 OR RESSEQ 181:205 )
112CHAIN B AND (RESSEQ 82:136 )
212CHAIN D AND (RESSEQ 82:136 )

NCS ensembles :
ID
1
2

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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: 10280.574 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

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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: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 0.05 M sodium citrate, 15% isopropanol, 30% glycerol, 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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→20 Å / Num. all: 12282 / Num. obs: 12282 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Net I/σ(I): 16.6
Reflection shellResolution: 3.45→3.55 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 3REA

3rea


Resolution: 3.45→19.86 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 634 5.16 %RANDOM
Rwork0.2157 ---
obs0.2171 12282 99.98 %-
all-12282 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.689 Å2 / ksol: 0.261 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0032 Å20 Å20 Å2
2---1.0032 Å20 Å2
3---2.0064 Å2
Refinement stepCycle: LAST / Resolution: 3.45→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 0 0 2761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162854
X-RAY DIFFRACTIONf_angle_d1.5843887
X-RAY DIFFRACTIONf_dihedral_angle_d22.829995
X-RAY DIFFRACTIONf_chiral_restr0.082396
X-RAY DIFFRACTIONf_plane_restr0.011492
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A817X-RAY DIFFRACTIONPOSITIONAL
12C817X-RAY DIFFRACTIONPOSITIONAL0.181
21B443X-RAY DIFFRACTIONPOSITIONAL
22D443X-RAY DIFFRACTIONPOSITIONAL0.09
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.71480.35491210.27992321X-RAY DIFFRACTION100
3.7148-4.08570.27341370.21932305X-RAY DIFFRACTION100
4.0857-4.67020.21321250.18712344X-RAY DIFFRACTION100
4.6702-5.85880.22751260.18732320X-RAY DIFFRACTION100
5.8588-19.86030.22261250.22312358X-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)
17.03322.2722-2.47958.61950.83556.7958-1.0622.31240.2351-2.21160.7510.4008-1.1049-1.0202-01.2837-0.4276-0.13481.7166-0.02650.6259-46.289142.42477.3628
28.56782.6816-2.79143.18342.3243.1892-0.7654-0.0574-1.39780.24510.6277-1.1232-0.3946-0.446501.025-0.19340.17070.98530.06111.4387-22.319740.92119.8466
310.5309-3.0725-1.07554.24121.03144.5166-0.5285-0.61390.36690.45920.2075-0.8615-0.14580.628300.86980.15-0.14650.91050.04770.8783-47.154821.908-7.9378
46.9919-1.1814-5.33976.341-1.76214.666-0.068-0.24220.06650.0349-0.20041.1192-0.0595-0.371800.8160.0179-0.16630.9816-0.28781.2186-73.908124.3088-11.1676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 207
2X-RAY DIFFRACTION2B80 - 138
3X-RAY DIFFRACTION3C69 - 207
4X-RAY DIFFRACTION4D79 - 138

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