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- PDB-4u5w: Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with th... -

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Basic information

Entry
Database: PDB / ID: 4u5w
TitleCrystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains
Components
  • Protein Nef
  • Tyrosine-protein kinase HCK
KeywordsViral protein/Transferase / Hck / SH3-SH2 regulatory domains / SH3 / SH2 / Src Family Kinase / SFK / HIV-1 / Nef / virus / protein-protein complex / Nef-Hck complex / viral protein-transferase complex
Function / homology
Function and homology information


leukocyte degranulation / activation of transmembrane receptor protein tyrosine kinase activity / leukocyte migration involved in immune response / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / 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 / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases ...leukocyte degranulation / activation of transmembrane receptor protein tyrosine kinase activity / leukocyte migration involved in immune response / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / 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 / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases / regulation of phagocytosis / : / Nef and signal transduction / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / host cell Golgi membrane / FCGR activation / type II interferon-mediated signaling pathway / transport vesicle / Signaling by CSF3 (G-CSF) / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / lipopolysaccharide-mediated signaling pathway / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / cell projection / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / Inactivation of CSF3 (G-CSF) signaling / caveola / virion component / SH3 domain binding / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein autophosphorylation / regulation of inflammatory response / protein tyrosine kinase activity / cell differentiation / cytoskeleton / lysosome / protein phosphorylation / cell adhesion / defense response to Gram-positive bacterium / intracellular signal transduction / endocytosis involved in viral entry into host cell / inflammatory response / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / GTP binding / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / nucleus / membrane / 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 / SH2 domain / SHC Adaptor Protein / SH3 Domains ...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 / SH2 domain / SHC Adaptor Protein / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
IODIDE ION / Protein Nef / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAlvarado, J.J. / Yeh, J.I. / Smithgall, T.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057083 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI102724 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082251 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment.
Authors: Alvarado, J.J. / Tarafdar, S. / Yeh, J.I. / Smithgall, T.E.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Sep 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
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: Tyrosine-protein kinase HCK
C: Protein Nef
D: Tyrosine-protein kinase HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,78613
Polymers76,6704
Non-polymers1,1169
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-69 kcal/mol
Surface area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.489, 57.265, 72.111
Angle α, β, γ (deg.)112.28, 96.09, 106.00
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17592.930 Da / Num. of mol.: 2 / Fragment: UNP residues 62-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: isolate ARV2/SF2 / Gene: nef / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P03407
#2: Protein Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 20742.232 Da / Num. of mol.: 2 / Fragment: SH3-SH2 domain, UNP residues 72-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: P08631, non-specific protein-tyrosine kinase
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09 M ADA, pH 6.5, 10.8% (v/v) 2-methyl-2,4-pentanediol, 100 mM NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 64501 / % possible obs: 97.8 % / Redundancy: 4 % / Net I/σ(I): 13.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.59 / % possible all: 96.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NHN, 3RBB

3nhn

3rbb


Resolution: 1.86→26.377 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 3249 5.04 %
Rwork0.1686 --
obs0.1699 64424 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→26.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 30 525 5013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044702
X-RAY DIFFRACTIONf_angle_d0.8036388
X-RAY DIFFRACTIONf_dihedral_angle_d13.591738
X-RAY DIFFRACTIONf_chiral_restr0.033655
X-RAY DIFFRACTIONf_plane_restr0.004818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.8830.3161320.27222485X-RAY DIFFRACTION91
1.883-1.91250.31791450.282611X-RAY DIFFRACTION96
1.9125-1.94380.30791390.27652614X-RAY DIFFRACTION96
1.9438-1.97730.25371360.21832643X-RAY DIFFRACTION97
1.9773-2.01330.21821470.19182665X-RAY DIFFRACTION97
2.0133-2.0520.24321410.19562602X-RAY DIFFRACTION97
2.052-2.09380.28231310.21042663X-RAY DIFFRACTION96
2.0938-2.13930.20511410.1862659X-RAY DIFFRACTION97
2.1393-2.18910.19851470.17552646X-RAY DIFFRACTION97
2.1891-2.24380.20091280.18752650X-RAY DIFFRACTION97
2.2438-2.30440.21121550.18992652X-RAY DIFFRACTION97
2.3044-2.37220.19621310.16642682X-RAY DIFFRACTION98
2.3722-2.44870.19031470.17512686X-RAY DIFFRACTION98
2.4487-2.53620.19651430.17262652X-RAY DIFFRACTION98
2.5362-2.63760.20781450.16682681X-RAY DIFFRACTION98
2.6376-2.75750.17751400.17032688X-RAY DIFFRACTION98
2.7575-2.90280.19331350.17222679X-RAY DIFFRACTION98
2.9028-3.08440.18781480.17222678X-RAY DIFFRACTION99
3.0844-3.32210.18331440.16452734X-RAY DIFFRACTION99
3.3221-3.65560.18591410.14632689X-RAY DIFFRACTION99
3.6556-4.18280.15111450.13612691X-RAY DIFFRACTION99
4.1828-5.2630.16111480.12952725X-RAY DIFFRACTION99
5.263-26.380.19111400.16512700X-RAY DIFFRACTION99
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)
15.685-2.1067-0.38465.95880.98396.6032-0.01660.1226-0.4268-0.16520.09040.19250.5367-0.088-0.08910.1077-0.0097-0.00860.16140.01180.1169-1.40320.64822.3827
20.8459-0.6442-0.35131.6520.35322.8809-0.137-0.08210.00350.38960.16890.071-0.17310.1017-0.02030.21760.03880.01340.1164-0.00670.1444-1.0478.210319.5628
31.4711.1368-3.0045.33820.15638.59580.3319-1.556-0.03280.6012-0.32440.3446-0.02190.1568-0.13430.62420.0911-0.00390.68930.00330.4505-6.00672.073643.101
43.5093-2.08741.8365.98990.46773.0026-0.2928-0.10510.34950.32490.2252-0.0928-0.29990.15880.06140.28990.05070.04240.1467-0.02250.1676-2.20218.955325.0348
52.2337-0.11561.20221.87620.10411.270.00730.38760.13420.03540.12760.34450.0401-0.56130.00780.12-0.0326-0.02320.31130.03990.2109-12.17964.2815-3.202
66.5816-4.5034-1.37174.0236-0.67314.1809-0.26971.0865-0.753-0.99150.02410.4454-0.0531-0.44850.20790.4806-0.0481-0.0620.7387-0.11010.4429-7.3468-3.9736-15.4885
75.4845-0.235-1.34957.0381-0.4234.92190.3104-0.6499-0.1752-0.0365-0.4016-0.0284-0.27630.13030.16380.5089-0.0410.03780.5902-0.03910.42132.9911-19.181-15.6195
82.9113-2.7428-0.79754.9472-2.83775.67150.08160.12020.2586-0.0244-0.094-0.2317-0.08220.1404-0.02030.0232-0.0259-0.00370.1834-0.00640.120511.0346-3.50475.4373
91.6287-0.1144-1.10422.4822-1.1542.5454-0.120.0031-0.05830.11530.11220.11440.0802-0.04730.00640.17060.0116-0.00020.0959-0.01910.15432.2436-13.999818.7488
102.89332.78821.21622.72881.55634.19840.0202-1.3918-0.45640.90610.1160.76670.4631-1.68670.07940.4430.1010.19250.60470.15280.4882-12.0944-14.196631.4846
112.5334-1.447-1.45755.19020.35941.2931-0.18150.1024-0.43220.05420.05570.34070.3563-0.11340.09450.27610.01620.0310.1275-0.00980.25320.6911-25.574322.3758
122.59580.2134-1.45151.7162-0.28150.8424-0.0935-0.0727-0.16510.2313-0.3431-0.620.22590.88590.04710.15490.04050.00410.4060.09820.317722.5304-6.89615.3309
134.59121.4675.91932.21512.10859.739-0.05440.6077-0.2848-0.3085-1.0092-0.45390.23661.07680.74850.36780.04570.0880.68130.1480.479723.92643.4792-9.345
141.34890.2118-0.33552.6828-1.32075.10290.1001-0.0162-0.0062-0.1307-0.1022-0.1458-0.44790.22310.00410.2015-0.0325-0.00260.1746-0.01370.177511.061716.8543-14.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 72:82)
2X-RAY DIFFRACTION2chain 'A' and (resseq 83:151)
3X-RAY DIFFRACTION3chain 'A' and (resseq 152:184)
4X-RAY DIFFRACTION4chain 'A' and (resseq 185:208)
5X-RAY DIFFRACTION5chain 'B' and (resseq 83:138)
6X-RAY DIFFRACTION6chain 'B' and (resseq 139:147)
7X-RAY DIFFRACTION7chain 'B' and (resseq 148:246)
8X-RAY DIFFRACTION8chain 'C' and (resseq 71:82)
9X-RAY DIFFRACTION9chain 'C' and (resseq 83:151)
10X-RAY DIFFRACTION10chain 'C' and (resseq 152:184)
11X-RAY DIFFRACTION11chain 'C' and (resseq 185:208)
12X-RAY DIFFRACTION12chain 'D' and (resseq 83:138)
13X-RAY DIFFRACTION13chain 'D' and (resseq 139:147)
14X-RAY DIFFRACTION14chain 'D' and (resseq 148:248)

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