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- PDB-2hdx: Crystal structure of the Src homology-2 domain of SH2-B in comple... -

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Basic information

Entry
Database: PDB / ID: 2hdx
TitleCrystal structure of the Src homology-2 domain of SH2-B in complex with Jak2 pTyr813 phosphopeptide
Components
  • Jak2 proteinJanus kinase 2
  • SH2-B PH domain containing signaling mediator 1 gamma isoform
KeywordsSIGNALING PROTEIN / SH2 / Jak2 / phosphotyrosine / adapter protein
Function / homology
Function and homology information


: / response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / : / positive regulation of cell activation / Regulation of IFNG signaling / positive regulation of tumor necrosis factor production => GO:0032760 / : / Signaling by Erythropoietin / Growth hormone receptor signaling ...: / response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / : / positive regulation of cell activation / Regulation of IFNG signaling / positive regulation of tumor necrosis factor production => GO:0032760 / : / Signaling by Erythropoietin / Growth hormone receptor signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-12 signaling / Prolactin receptor signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-23 signaling / Interleukin-20 family signaling / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / Interleukin-6 signaling / regulation of DNA biosynthetic process / Interleukin-35 Signalling / : / Inactivation of CSF3 (G-CSF) signaling / : / Signaling by SCF-KIT / RAF activation / Cyclin D associated events in G1 / RAF/MAP kinase cascade / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / : / Interleukin receptor SHC signaling / negative regulation of heart contraction / Factors involved in megakaryocyte development and platelet production / intracellular mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / Interleukin-3, Interleukin-5 and GM-CSF signaling / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-12 receptor binding / post-embryonic hemopoiesis / collagen-activated signaling pathway / interleukin-5-mediated signaling pathway / response to interleukin-12 / myeloid cell differentiation / positive regulation of leukocyte proliferation / activation of Janus kinase activity / interleukin-12 receptor complex / interleukin-23 receptor complex / positive regulation of platelet aggregation / tyrosine phosphorylation of STAT protein / positive regulation of platelet activation / postsynapse to nucleus signaling pathway / positive regulation of MHC class II biosynthetic process / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / acetylcholine receptor binding / interleukin-12-mediated signaling pathway / interleukin-3-mediated signaling pathway / regulation of nitric oxide biosynthetic process / cellular response to interleukin-3 / positive regulation of signaling receptor activity / positive regulation of cell-substrate adhesion / response to hydroperoxide / growth hormone receptor binding / negative regulation of cardiac muscle cell apoptotic process / positive regulation of epithelial cell apoptotic process / lamellipodium assembly / axon regeneration / peptide hormone receptor binding / growth hormone receptor signaling pathway / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic component of plasma membrane / enzyme-linked receptor protein signaling pathway / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / negative regulation of DNA binding / response to amine / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of natural killer cell proliferation / positive regulation of SMAD protein signal transduction / cell surface receptor signaling pathway via JAK-STAT / positive regulation of phosphoprotein phosphatase activity / platelet-derived growth factor receptor signaling pathway / insulin receptor substrate binding / endomembrane system / positive regulation of DNA binding / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor
Similarity search - Function
SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe ...SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / SH2 domain / SHC Adaptor Protein / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase JAK2 / Tyrosine-protein kinase JAK2 / SH2B adapter protein 1 / SH2B adapter protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHu, J. / Hubbard, S.R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Phosphotyrosine Recognition by the Src Homology-2 Domains of the Adapter Proteins SH2-B and APS.
Authors: Hu, J. / Hubbard, S.R.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH2-B PH domain containing signaling mediator 1 gamma isoform
B: SH2-B PH domain containing signaling mediator 1 gamma isoform
C: SH2-B PH domain containing signaling mediator 1 gamma isoform
D: SH2-B PH domain containing signaling mediator 1 gamma isoform
E: SH2-B PH domain containing signaling mediator 1 gamma isoform
F: SH2-B PH domain containing signaling mediator 1 gamma isoform
G: Jak2 protein
H: Jak2 protein
I: Jak2 protein
J: Jak2 protein
K: Jak2 protein
L: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)81,99212
Polymers81,99212
Non-polymers00
Water5,765320
1
A: SH2-B PH domain containing signaling mediator 1 gamma isoform
G: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area6470 Å2
MethodPISA
2
B: SH2-B PH domain containing signaling mediator 1 gamma isoform
H: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area6330 Å2
MethodPISA
3
C: SH2-B PH domain containing signaling mediator 1 gamma isoform
I: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area6280 Å2
MethodPISA
4
D: SH2-B PH domain containing signaling mediator 1 gamma isoform
J: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area6290 Å2
MethodPISA
5
E: SH2-B PH domain containing signaling mediator 1 gamma isoform
K: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area6360 Å2
MethodPISA
6
F: SH2-B PH domain containing signaling mediator 1 gamma isoform
L: Jak2 protein


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.21, 74.19, 239.22
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsSix biological units pack in 12 5 screw axis

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Components

#1: Protein
SH2-B PH domain containing signaling mediator 1 gamma isoform


Mass: 12275.992 Da / Num. of mol.: 6 / Fragment: SH2 (Residues: 499-607) / Mutation: E583A, E584A, W593H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh2bpsm1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WVM5, UniProt: Q91ZM2*PLUS
#2: Protein/peptide
Jak2 protein / Janus kinase 2


Mass: 1389.312 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Sequence occurs naturally in Mus musculus (mouse). / References: UniProt: Q7TQD0, UniProt: Q62120*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growpH: 5.6
Details: 25% PEG 4000, 0.1 M sodium citrate, 0.3 M ammonium acetate., pH 5.6

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 33327 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 10.2 / Rsym value: 0.103 / % possible all: 97.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HDV

2hdv


Resolution: 2.35→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 1604 Random
Rwork0.21 --
all0.24 33858 -
obs0.24 32298 -
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5373 0 0 320 5693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d0.7

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