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- PDB-7r8x: Crystal Structure of the LNK SH2 Domain in Complex with an EPOR p... -

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Basic information

Entry
Database: PDB / ID: 7r8x
TitleCrystal Structure of the LNK SH2 Domain in Complex with an EPOR pY454 Phosphopeptide
Components
  • EPOR pY454 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 platelet aggregation / neutrophil homeostasis ...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 platelet aggregation / neutrophil homeostasis / negative regulation of receptor signaling pathway via JAK-STAT / 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: 2.3 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 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: SH2B adapter protein 3
C: EPOR pY454 phosphopeptide


Theoretical massNumber of molelcules
Total (without water)13,7482
Polymers13,7482
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.157, 86.157, 38.052
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 12682.654 Da / Num. of mol.: 1 / Fragment: UNP residues 328-438
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 EPOR pY454 phosphopeptide


Mass: 1065.177 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.: 13 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 20% PEG8000, 0.05 M magnesium acetate, 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: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.3→33.9 Å / Num. obs: 7318 / % possible obs: 99.78 % / Redundancy: 9.6 % / Biso Wilson estimate: 53.5 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04408 / Rpim(I) all: 0.01481 / Rrim(I) all: 0.04655 / Net I/σ(I): 31
Reflection shellResolution: 2.301→2.383 Å / Rmerge(I) obs: 0.4924 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 724 / CC1/2: 0.904 / CC star: 0.974 / Rrim(I) all: 0.539 / % possible all: 99.45

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HDV

2hdv


Resolution: 2.3→33.9 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 710 9.71 %
Rwork0.1965 6604 -
obs0.1998 7314 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 53.8189 Å2 / Biso min: 30.34 Å2
Refinement stepCycle: final / Resolution: 2.3→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 0 13 930
Biso mean---52.83 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.480.32411450.28551289143499
2.48-2.730.30991330.249913051438100
2.73-3.120.29561400.262413221462100
3.12-3.930.2651450.201913301475100
3.93-33.90.1731470.155813581505100

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