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- PDB-7r8w: Crystal Structure of the LNK SH2 Domain in Complex with a JAK2 pY... -

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Basic information

Entry
Database: PDB / ID: 7r8w
TitleCrystal Structure of the LNK SH2 Domain 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 / stem cell factor receptor binding / Regulation of KIT signaling / Negative regulation of FLT3 / negative regulation of chemokine-mediated signaling pathway / Factors involved in megakaryocyte development and platelet production / thrombopoietin-mediated signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of platelet aggregation ...negative regulation of Kit signaling pathway / monocyte homeostasis / stem cell factor receptor binding / Regulation of KIT signaling / Negative regulation of FLT3 / negative regulation of chemokine-mediated signaling pathway / Factors involved in megakaryocyte development and platelet production / thrombopoietin-mediated signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of platelet aggregation / neutrophil homeostasis / cellular response to chemokine / cellular response to interleukin-3 / negative regulation of receptor signaling pathway via STAT / embryonic hemopoiesis / megakaryocyte development / erythrocyte development / hemopoiesis / hematopoietic stem cell differentiation / negative regulation of MAPK cascade / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine kinase binding / signaling receptor complex adaptor activity / intracellular signal transduction / negative regulation of cell population proliferation
Similarity search - Function
SH2B3, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like 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: 1.9 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: Nat Commun / Year: 2021
Title: Structural and functional analysis of target recognition by the lymphocyte adaptor protein LNK.
Authors: Morris, R. / Zhang, Y. / Ellyard, J.I. / Vinuesa, C.G. / Murphy, J.M. / Laktyushin, A. / Kershaw, N.J. / Babon, J.J.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH2B adapter protein 3
B: JAK2 pY813 phosphopeptide


Theoretical massNumber of molelcules
Total (without water)13,6722
Polymers13,6722
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-9 kcal/mol
Surface area6070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.060, 37.875, 38.883
Angle α, β, γ (deg.)90.000, 97.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12953.989 Da / Num. of mol.: 1 / Fragment: UNP residues 325-437
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: O09039
#2: Protein/peptide JAK2 pY813 phosphopeptide


Mass: 717.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.37 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20% PEG3350

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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: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.9→39.59 Å / Num. obs: 8093 / % possible obs: 99.62 % / Redundancy: 3.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03577 / Rpim(I) all: 0.02259 / Rrim(I) all: 0.04243 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 798 / CC1/2: 0.863 / Rpim(I) all: 0.2479 / Rrim(I) all: 0.4651 / % possible all: 98.88

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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: PDB entry 2HDX

2hdx


Resolution: 1.9→38.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 811 10.02 %
Rwork0.195 7280 -
obs0.2004 8091 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.51 Å2 / Biso mean: 38.6619 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: final / Resolution: 1.9→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 25 923
Biso mean---39.93 -
Num. residues----118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.020.28961330.22771191132499
2.02-2.180.30341340.209812101344100
2.18-2.390.25441340.203112051339100
2.39-2.740.33971350.240412121347100
2.74-3.450.25061370.2061223136099
3.45-38.590.21151380.169612391377100

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