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- PDB-8cz9: Crystal Structure of the E372K LNK SH2 Domain mutant in Complex w... -

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Basic information

Entry
Database: PDB / ID: 8cz9
TitleCrystal Structure of the E372K LNK SH2 Domain mutant in Complex with a JAK2 pY813 Phosphopeptide
Components
  • JAK2 pY813 phosphopeptide
  • SH2B adapter protein 3
KeywordsSIGNALING PROTEIN / LNK / SH2B3 / JAK/STAT / MPNs
Function / homology
Function and homology information


negative regulation of Kit signaling pathway / monocyte homeostasis / thrombopoietin-mediated signaling pathway / stem cell factor receptor binding / negative regulation of sprouting angiogenesis / negative regulation of chemokine-mediated signaling pathway / negative regulation of response to cytokine stimulus / regulation of regulatory T cell differentiation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of receptor signaling pathway via JAK-STAT ...negative regulation of Kit signaling pathway / monocyte homeostasis / thrombopoietin-mediated signaling pathway / stem cell factor receptor binding / negative regulation of sprouting angiogenesis / negative regulation of chemokine-mediated signaling pathway / negative regulation of response to cytokine stimulus / regulation of regulatory T cell differentiation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of receptor signaling pathway via JAK-STAT / neutrophil homeostasis / negative regulation of platelet aggregation / cellular response to chemokine / cellular response to interleukin-3 / embryonic hemopoiesis / megakaryocyte development / erythrocyte development / phosphate ion binding / hemopoiesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hematopoietic stem cell differentiation / protein tyrosine kinase binding / negative regulation of MAP kinase activity / signaling receptor complex adaptor activity / cell differentiation / intracellular signal transduction / negative regulation of cell population proliferation / protein-containing complex binding
Similarity search - Function
SH2B3, SH2 domain / SH2B adapter protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
SH2B adapter protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMorris, R. / Kershaw, N.J. / Babon, J.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Exp.Med. / Year: 2024
Title: Rare SH2B3 coding variants in lupus patients impair B cell tolerance and predispose to autoimmunity.
Authors: Zhang, Y. / Morris, R. / Brown, G.J. / Lorenzo, A.M.D. / Meng, X. / Kershaw, N.J. / Kiridena, P. / Burgio, G. / Gross, S. / Cappello, J.Y. / Shen, Q. / Wang, H. / Turnbull, C. / Lea-Henry, T. ...Authors: Zhang, Y. / Morris, R. / Brown, G.J. / Lorenzo, A.M.D. / Meng, X. / Kershaw, N.J. / Kiridena, P. / Burgio, G. / Gross, S. / Cappello, J.Y. / Shen, Q. / Wang, H. / Turnbull, C. / Lea-Henry, T. / Stanley, M. / Yu, Z. / Ballard, F.D. / Chuah, A. / Lee, J.C. / Hatch, A.M. / Enders, A. / Masters, S.L. / Headley, A.P. / Trnka, P. / Mallon, D. / Fletcher, J.T. / Walters, G.D. / Sestan, M. / Jelusic, M. / Cook, M.C. / Athanasopoulos, V. / Fulcher, D.A. / Babon, J.J. / Vinuesa, C.G. / Ellyard, J.I.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Mar 13, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH2B adapter protein 3
C: JAK2 pY813 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6763
Polymers13,6412
Non-polymers351
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-16 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.829, 37.618, 50.497
Angle α, β, γ (deg.)90.000, 108.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-651-

HOH

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Components

#1: Protein SH2B adapter protein 3 / Lymphocyte adapter protein / Lymphocyte-specific adapter protein Lnk / Signal transduction protein Lnk


Mass: 12581.616 Da / Num. of mol.: 1 / Mutation: E372K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh2b3, Lnk / Production host: Escherichia coli (E. coli) / References: UniProt: P50745
#2: Protein/peptide JAK2 pY813 phosphopeptide


Mass: 1059.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 8000, 0.05 M MgAc , 0.1 M Tris ph 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.64→35.9 Å / Num. obs: 111266 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 20.45
Reflection shellResolution: 1.65→1.7 Å / Mean I/σ(I) obs: 2.49 / Num. unique obs: 11000 / CC1/2: 0.818 / Rrim(I) all: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R8W

7r8w


Resolution: 1.65→35.9 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1633 10 %
Rwork0.1846 14702 -
obs0.1877 16335 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.04 Å2 / Biso mean: 32.7311 Å2 / Biso min: 17.26 Å2
Refinement stepCycle: final / Resolution: 1.65→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 1 76 975
Biso mean--67.36 42.96 -
Num. residues----116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.70.27271350.23361207134297
1.7-1.750.26851330.23641198133199
1.75-1.810.32861310.25231191132298
1.81-1.890.27561360.22751222135899
1.89-1.970.29811360.19341214135099
1.97-2.080.21461360.18461226136299
2.08-2.210.21351360.19941229136599
2.21-2.380.22481350.18771213134899
2.38-2.610.22531370.207612341371100
2.62-2.990.22521380.19731242138099
2.99-3.770.19391390.177512491388100
3.77-35.90.19311410.15821277141899

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