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- PDB-4d8d: Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant -

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Basic information

Entry
Database: PDB / ID: 4d8d
TitleCrystal structure of HIV-1 NEF Fyn-SH3 R96W variant
Components
  • Protein Nef
  • Tyrosine-protein kinase Fyn
KeywordsTRANSFERASE/PROTEIN BINDING / signaling molecules / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


perturbation by virus of host immune response / negative regulation of CD4 production / response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / 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 / perinuclear endoplasmic reticulum / peptidase activator activity ...perturbation by virus of host immune response / negative regulation of CD4 production / response to singlet oxygen / Reelin signalling pathway / negative regulation of hydrogen peroxide biosynthetic process / 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 / perinuclear endoplasmic reticulum / peptidase activator activity / NTRK2 activates RAC1 / growth factor receptor binding / Activated NTRK2 signals through FYN / heart process / cellular response to L-glutamate / suppression by virus of host autophagy / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / G protein-coupled glutamate receptor signaling pathway / Platelet Adhesion to exposed collagen / CD28 co-stimulation / positive regulation of protein localization to membrane / activated T cell proliferation / CRMPs in Sema3A signaling / positive regulation of cysteine-type endopeptidase activity / FLT3 signaling through SRC family kinases / CD4 receptor binding / thioesterase binding / negative regulation of dendritic spine maintenance / feeding behavior / Nef and signal transduction / type 5 metabotropic glutamate receptor binding / Nephrin family interactions / DCC mediated attractive signaling / dendrite morphogenesis / EPH-Ephrin signaling / CD28 dependent Vav1 pathway / regulation of T cell activation / Ephrin signaling / dendritic spine maintenance / Regulation of KIT signaling / tau-protein kinase activity / CTLA4 inhibitory signaling / leukocyte migration / phospholipase activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / Dectin-2 family / host cell Golgi membrane / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / response to amyloid-beta / glial cell projection / Sema3A PAK dependent Axon repulsion / cellular response to glycine / FCGR activation / alpha-tubulin binding / EPH-ephrin mediated repulsion of cells / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / vascular endothelial growth factor receptor signaling pathway / detection of mechanical stimulus involved in sensory perception of pain / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of peptidyl-tyrosine phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of calcium-mediated signaling / forebrain development / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / negative regulation of protein ubiquitination / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / cell surface receptor protein tyrosine kinase signaling pathway / viral life cycle / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / FCGR3A-mediated IL10 synthesis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / learning / virion component / actin filament / Regulation of signaling by CBL / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / axon guidance / non-specific protein-tyrosine kinase / neuron migration / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / : / Fyn/Yrk, SH3 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 ...Nef Regulatory Factor / Nef Regulatory Factor / : / Fyn/Yrk, SH3 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 Fyn
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5201 Å
AuthorsArold, S.T. / Hoh, F. / Dumas, C.
Citation
#1: Journal: Structure / Year: 1997
Title: The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling.
Authors: Arold, S. / Franken, P. / Strub, M.P. / Hoh, F. / Benichou, S. / Benarous, R. / Dumas, C.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain.
Authors: Lee, C.H. / Saksela, K. / Mirza, U.A. / Chait, B.T. / Kuriyan, J.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 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: Tyrosine-protein kinase Fyn
B: Protein Nef
C: Tyrosine-protein kinase Fyn
D: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5345
Polymers48,4424
Non-polymers921
Water79344
1
A: Tyrosine-protein kinase Fyn
B: Protein Nef


Theoretical massNumber of molelcules
Total (without water)24,2212
Polymers24,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area9320 Å2
MethodPISA
2
C: Tyrosine-protein kinase Fyn
D: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3133
Polymers24,2212
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-8 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.010, 108.010, 224.961
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

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Components

#1: Protein Tyrosine-protein kinase Fyn / Proto-oncogene Syn / Proto-oncogene c-Fyn / Src-like kinase / SLK / p59-Fyn


Mass: 6652.212 Da / Num. of mol.: 2 / Fragment: SRC-HOMOLOGY 3 DOMAIN (UNP Residues 84-141) / Mutation: R96W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN, FYN TYROSINE KINASE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P06241, non-specific protein-tyrosine kinase
#2: Protein Protein Nef / 3'ORF / Negative factor / F-protein / C-terminal core protein


Mass: 17568.723 Da / Num. of mol.: 2 / Fragment: CONSERVED CORE DOMAIN (UNP Residues 58-204)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: LAI-BRU ISOLATE / Gene: nef / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P03406
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.95 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.3 M sodium potassium tartrate, 0.5 M bicine buffer , 1cmc D-octylglucopyranoside, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98064 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98064 Å / Relative weight: 1
ReflectionResolution: 2.52→58.51 Å / Num. all: 27024 / Num. obs: 26791 / % possible obs: 99.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 73.99 Å2 / Rsym value: 0.067

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVZ

1avz


Resolution: 2.5201→52.513 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8259 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.4 / σ(I): 0 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1350 5.04 %RANDOM
Rwork0.2121 ---
obs0.2135 26778 99.1 %-
all-27024 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.421 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 176.65 Å2 / Biso mean: 83.287 Å2 / Biso min: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1--6.1391 Å2-0 Å2-0 Å2
2---6.1391 Å20 Å2
3---12.2782 Å2
Refinement stepCycle: LAST / Resolution: 2.5201→52.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 6 44 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072830
X-RAY DIFFRACTIONf_angle_d0.9773860
X-RAY DIFFRACTIONf_chiral_restr0.07391
X-RAY DIFFRACTIONf_plane_restr0.005490
X-RAY DIFFRACTIONf_dihedral_angle_d13.9471000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5201-2.61020.34141100.33772407251796
2.6102-2.71470.34211320.28252510264299
2.7147-2.83820.28931330.25932483261699
2.8382-2.98780.28721570.22422449260699
2.9878-3.1750.26581250.21772505263099
3.175-3.42010.26361250.215425362661100
3.4201-3.76420.24341200.199225772697100
3.7642-4.30870.22651560.185925582714100
4.3087-5.42760.19231410.175326302771100
5.4276-52.52440.22681510.23152773292499
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)
13.7194-0.53582.86421.3958-0.13622.5747-0.4312-1.9038-0.77570.83780.29930.2364-0.1309-0.51110.13920.87150.37910.2920.96180.3670.826213.634528.600857.3543
22.61233.24911.04767.42661.20147.1606-0.9136-1.17680.91260.68650.39091.1122-0.5725-1.28150.47920.67140.24890.22510.98950.23530.88212.600934.454653.289
35.3597-4.4464-1.62844.38623.89969.80770.41240.5338-0.0826-0.4127-1.01750.6959-0.7889-1.10860.44880.7280.12990.28431.01340.22361.06968.970231.678949.3837
45.0665-1.1682-0.62552.68962.43912.2525-0.0819-0.9063-0.1468-0.0302-0.65610.58310.78590.40470.66810.69070.1720.21750.96350.30830.75112.716327.712152.6363
56.2853-1.07370.95142.422-1.21965.1575-0.4995-0.89150.09380.80320.1491-1.115-0.3855-0.54050.22660.5920.1575-0.10010.43690.14630.567127.937739.282444.9893
62.04112.6774-1.11616.0546-0.22353.2334-0.5584-0.62320.56210.51640.2399-0.7852-0.35940.21220.51520.57420.1311-0.06660.47830.0720.664834.42533.202946.1702
70.736-0.89620.14123.8811-0.94731.6701-0.07460.28690.3517-0.3084-0.5541-1.64640.02910.68170.37360.54140.21070.2520.45610.57941.065934.36240.04435.0611
87.626-1.49162.09270.3251-0.14082.6699-0.33370.53531.37110.1527-0.5953-1.7021-0.59591.01610.86120.571-0.0497-0.08920.60680.34081.433137.540448.214637.4739
91.75480.23080.59524.5284-1.87512.3551-0.17280.1124-0.4653-0.3694-0.09130.01011.23370.84490.32540.87880.5730.32350.53430.43850.708431.873141.055324.215
108.6185-4.7084-4.88637.82450.43933.7189-0.1803-0.36990.37020.18640.16010.1884-0.4126-1.60280.1170.57510.27440.28350.64410.11990.401736.721714.333166.1844
118.28030.69923.97024.86540.01627.50960.13520.41280.0735-0.7279-0.22450.20350.8034-0.14140.05070.75840.05350.19470.3510.04820.435141.185110.955361.8764
124.6161-2.62892.89673.6066-4.82546.78510.18520.34450.5894-0.6303-0.7699-1.2348-0.2187-0.35930.50880.77660.03490.2180.50280.02890.473645.747914.275564.4086
135.9285-4.10123.95677.1295-0.73324.38550.78770.45020.1769-0.1763-0.5766-0.5644-0.7442-1.037-0.23060.67030.0620.21990.42480.03760.516140.029716.933264.3806
148.739-2.4551-1.63996.48294.41566.7005-0.1614-0.581-1.08360.18310.38090.974-0.2845-0.5521-0.05950.68590.23370.22450.41450.22390.568941.838813.796147.7
156.2433-1.28322.63784.1664-0.81561.80910.41690.5158-1.09010.12940.08320.89430.2852-0.2608-0.41890.57020.15940.01590.34850.02620.725634.607317.451638.6828
164.4078-0.56150.26911.1877-0.22510.04560.33741.11480.2063-0.7647-0.43640.3172-0.69930.0439-0.0280.97920.30540.10110.47930.11910.349545.197318.583934.5336
177.7657-2.62110.92836.3992-2.13132.12770.96451.7477-0.342-0.8706-0.75440.9550.0459-0.5542-0.11660.71510.38320.00630.7049-0.23670.458543.414311.360629.1744
188.42260.42791.7146.2249-5.59215.54980.3761.71541.6301-1.2478-0.484-0.9344-0.76230.5270.14820.89380.21430.22840.76480.32040.765156.125121.459632.8642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 85:94)A85 - 94
2X-RAY DIFFRACTION2chain 'A' and (resseq 95:113)A95 - 113
3X-RAY DIFFRACTION3chain 'A' and (resseq 114:129)A114 - 129
4X-RAY DIFFRACTION4chain 'A' and (resseq 130:141)A130 - 141
5X-RAY DIFFRACTION5chain 'B' and (resseq 69:103)B69 - 103
6X-RAY DIFFRACTION6chain 'B' and (resseq 104:118)B104 - 118
7X-RAY DIFFRACTION7chain 'B' and (resseq 119:147)B119 - 147
8X-RAY DIFFRACTION8chain 'B' and (resseq 148:190)B148 - 190
9X-RAY DIFFRACTION9chain 'B' and (resseq 191:204)B191 - 204
10X-RAY DIFFRACTION10chain 'C' and (resseq 84:94)C84 - 94
11X-RAY DIFFRACTION11chain 'C' and (resseq 95:113)C95 - 113
12X-RAY DIFFRACTION12chain 'C' and (resseq 114:129)C114 - 129
13X-RAY DIFFRACTION13chain 'C' and (resseq 130:141)C130 - 141
14X-RAY DIFFRACTION14chain 'D' and (resseq 70:94)D70 - 94
15X-RAY DIFFRACTION15chain 'D' and (resseq 95:118)D95 - 118
16X-RAY DIFFRACTION16chain 'D' and (resseq 119:147)D119 - 147
17X-RAY DIFFRACTION17chain 'D' and (resseq 148:190)D148 - 190
18X-RAY DIFFRACTION18chain 'D' and (resseq 191:204)D191 - 204

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