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- PDB-7d7s: HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant -

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Basic information

Entry
Database: PDB / ID: 7d7s
TitleHIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant
Components
  • Protein Nef
  • Tyrosine-protein kinase Fyn
KeywordsVIRAL PROTEIN / Complex / mutant / kinase / SH3
Function / homology
Function and homology information


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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / virion component / endocytosis involved in viral entry into host cell / SH3 domain binding / virus-mediated perturbation of host defense response / GTP binding ...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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / virion component / endocytosis involved in viral entry into host cell / SH3 domain binding / virus-mediated perturbation of host defense response / GTP binding / host cell plasma membrane / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
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 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...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 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn / Protein Nef
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å
AuthorsAldehaiman, A. / Shahul Hamed, U.F. / Arold, S.T.
CitationJournal: Biochem.J. / Year: 2021
Title: Synergy and allostery in ligand binding by HIV-1 Nef.
Authors: Aldehaiman, A. / Momin, A.A. / Restouin, A. / Wang, L. / Shi, X. / Aljedani, S. / Opi, S. / Lugari, A. / Shahul Hameed, U.F. / Ponchon, L. / Morelli, X. / Huang, M. / Dumas, C. / Collette, Y. / Arold, S.T.
History
DepositionOct 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,6824
Polymers67,6824
Non-polymers00
Water0
1
A: Protein Nef
D: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)33,8412
Polymers33,8412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-4 kcal/mol
Surface area9050 Å2
MethodPISA
2
B: Protein Nef
C: Tyrosine-protein kinase Fyn


Theoretical massNumber of molelcules
Total (without water)33,8412
Polymers33,8412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.110, 122.110, 145.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 25585.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)
Strain: isolate ARV2/SF2 / Gene: nef / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / References: UniProt: P03407
#2: Protein Tyrosine-protein kinase Fyn


Mass: 8254.987 Da / Num. of mol.: 2 / Mutation: R96I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYN / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / References: UniProt: E5RFS5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3246.97
22.3246.97
32.3246.97hexagonal crystal
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop4.50.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
2932vapor diffusion, sitting drop4.50.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
2933vapor diffusion, sitting drop4.50.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 11, 2020
Details: focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration
RadiationMonochromator: cryogenically cooled channel-cut Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.32→48.68 Å / Num. obs: 9209 / % possible obs: 94.6 % / Redundancy: 155.4 % / CC1/2: 1 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.018 / Rrim(I) all: 0.219 / Net I/σ(I): 33.6
Reflection shellResolution: 3.324→3.46 Å / Redundancy: 165.4 % / Rmerge(I) obs: 9.136 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 461 / CC1/2: 0.486 / Rpim(I) all: 0.71 / Rrim(I) all: 9.163 / % possible all: 42.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d8d

4d8d


Resolution: 3.32→48.68 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.9 / SU B: 109.02 / SU ML: 0.715 / Cross valid method: THROUGHOUT / ESU R: 6.24 / ESU R Free: 0.609 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29953 923 10 %RANDOM
Rwork0.28616 ---
obs0.28763 8283 92.24 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 150.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å2-0 Å2
3----3.19 Å2
Refinement stepCycle: LAST / Resolution: 3.32→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 0 0 2737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192833
X-RAY DIFFRACTIONr_bond_other_d0.0010.022521
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.8613859
X-RAY DIFFRACTIONr_angle_other_deg1.0032.945835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73823.05141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36415437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4451516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.324→3.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 22 -
Rwork0.389 178 -
obs--27.59 %
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)
17.82320.2224-1.791315.2771.62676.07780.1503-1.5755-0.4362-2.3940.921-0.2921-0.14360.5788-1.07130.4233-0.10090.04710.58350.23390.513731.30539.556-18.348
23.52810.8003-0.719815.3188.38578.60050.56651.1142-0.2982-2.2255-1.50882.0057-2.1431-2.13910.94231.2850.4483-1.10141.73450.59831.69810.5527.634-35.119
38.24540.6725-5.074710.15773.097510.872-0.46980.8374-0.766-0.6912-0.44220.82520.6454-1.26490.9120.6323-0.092-0.47240.64430.29360.923124.4774.703-37.388
49.35330.8553-0.681719.03890.083611.49220.4479-1.36140.31152.4723-0.48081.81290.1866-0.55550.0330.3462-0.01330.28041.490.37211.138511.3746.202-0.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 207
2X-RAY DIFFRACTION2B74 - 207
3X-RAY DIFFRACTION3C84 - 142
4X-RAY DIFFRACTION4D84 - 144

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