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- PDB-3rbb: HIV-1 NEF protein in complex with engineered HCK SH3 domain -

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Basic information

Entry
Database: PDB / ID: 3rbb
TitleHIV-1 NEF protein in complex with engineered HCK SH3 domain
Components
  • Protein Nef
  • Tyrosine-protein kinase HCK
KeywordsVIRAL PROTEIN / PROTEIN BINDING / HIV-1 Nef / dileucine motif / SH3 domain / receptor internalization / PXXP motif
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 / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / virion component / cell projection / caveola / 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 / SH3 domain binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / 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 / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / innate immune 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 / SH2 domain / SH3 type barrels. / 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: 2.35 Å
AuthorsHorenkamp, F.A. / Schulte, A. / Weyand, M. / Geyer, M.
CitationJournal: Traffic / Year: 2011
Title: Conformation of the Dileucine-Based Sorting Motif in HIV-1 Nef Revealed by Intermolecular Domain Assembly.
Authors: Horenkamp, F.A. / Breuer, S. / Schulte, A. / Lulf, S. / Weyand, M. / Saksela, K. / Geyer, M.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6996
Polymers52,5754
Non-polymers1242
Water3,747208
1
A: Protein Nef
B: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3503
Polymers26,2872
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-2 kcal/mol
Surface area12530 Å2
MethodPISA
2
C: Protein Nef
D: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3503
Polymers26,2872
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.190, 90.880, 169.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 7146.974 Da / Num. of mol.: 2 / Mutation: E90Y, A91S, I92P, H93F, H94S, E95W
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.977032 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: 0.977032 Å / Relative weight: 1
ReflectionResolution: 2.35→48 Å / Num. all: 28573 / Num. obs: 28573 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Net I/σ(I): 22.18
Reflection shellResolution: 2.35→2.4 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EFN

1efn


Resolution: 2.35→47.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.523 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24513 1429 5 %RANDOM
Rwork0.20379 ---
obs0.20589 27143 100 %-
all-27143 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--2.58 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 8 208 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223268
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9434450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61623.043161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.431520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212554
X-RAY DIFFRACTIONr_mcbond_it0.7391.51901
X-RAY DIFFRACTIONr_mcangle_it1.36423068
X-RAY DIFFRACTIONr_scbond_it1.96631367
X-RAY DIFFRACTIONr_scangle_it3.1944.51378
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 104 -
Rwork0.304 1984 -
obs--100 %
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)
11.4880.10110.49792.26130.07622.63340.05560.0006-0.0988-0.001-0.05010.13410.2641-0.1123-0.00540.0309-0.01450.0230.1352-0.01440.155335.39859.26433.0359
23.4501-1.8964-1.72043.77581.55519.60260.1405-0.37130.18380.624-0.1109-0.3956-0.44640.6004-0.02960.3147-0.1401-0.02520.28080.01170.070243.175870.786133.301
31.9350.87340.93884.11621.65434.05610.0520.08080.20020.1786-0.16420.18690.41120.04120.11210.0902-0.02410.01120.0296-0.00470.06732.447830.6924-4.7379
42.97650.27551.88165.01673.287410.34640.01330.2912-0.2655-0.31760.1489-0.18050.9010.7994-0.16210.42140.03970.00030.2886-0.00460.033433.616418.7551-31.6847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 208
2X-RAY DIFFRACTION2B79 - 138
3X-RAY DIFFRACTION3C69 - 208
4X-RAY DIFFRACTION4D80 - 137

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