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- PDB-8atk: The SH2 domain of mouse SH2B1 -

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Basic information

Entry
Database: PDB / ID: 8atk
TitleThe SH2 domain of mouse SH2B1
ComponentsSH2B adapter protein 1
KeywordsSIGNALING PROTEIN / SH2 domain / phosphotyrosine binding / JAK2 binding
Function / homology
Function and homology information


Growth hormone receptor signaling / Prolactin receptor signaling / regulation of DNA biosynthetic process / Factors involved in megakaryocyte development and platelet production / transmembrane receptor protein tyrosine kinase adaptor activity / lamellipodium assembly / positive regulation of SMAD protein signal transduction / ruffle / positive regulation of mitotic nuclear division / cell motility ...Growth hormone receptor signaling / Prolactin receptor signaling / regulation of DNA biosynthetic process / Factors involved in megakaryocyte development and platelet production / transmembrane receptor protein tyrosine kinase adaptor activity / lamellipodium assembly / positive regulation of SMAD protein signal transduction / ruffle / positive regulation of mitotic nuclear division / cell motility / intracellular signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. ...SH2B1, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / 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 / PH-like domain superfamily
Similarity search - Domain/homology
SH2B adapter protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsFowler, N.J. / Williamson, M.P. / Albalwi, M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P020038/1 United Kingdom
CitationJournal: Structure / Year: 2023
Title: Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: The SH2 domain of SH2B1.
Authors: Fowler, N.J. / Albalwi, M.F. / Lee, S. / Hounslow, A.M. / Williamson, M.P.
History
DepositionAug 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 16, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH2B adapter protein 1


Theoretical massNumber of molelcules
Total (without water)13,5551
Polymers13,5551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR relaxation is also indicative of monomer
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1best ansurr score

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Components

#1: Protein SH2B adapter protein 1 / Pro-rich / PH and SH2 domain-containing signaling mediator / PSM / SH2 domain-containing protein 1B ...Pro-rich / PH and SH2 domain-containing signaling mediator / PSM / SH2 domain-containing protein 1B / SH2-B PH domain-containing signaling mediator 1


Mass: 13555.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sh2b1, Sh2bpsm1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91ZM2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic12D 1H-13C HSQC
1121isotropic13D HBHA(CO)NH
191isotropic13D H(CCO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic12D 1H-13C HSQC aromatic
1131isotropic12D (HB)CB(CGCD)HD
1141isotropic13D 1H-15N NOESY
1151isotropic13D 1H-13C NOESY
1161isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 50 mM potassium phosphate, 1 mM trimethylsilyl propionate, 0.8 mM [U-100% 13C; U-100% 15N] SH2, 90% H2O/10% D2O
Label: double labeled sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphatenatural abundance1
1 mMtrimethylsilyl propionatenatural abundance1
0.8 mMSH2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz / Details: with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 2
Details: NOE restraints were consensus restraints, appearing in at least 60% of the calculations from the previous calculation
NMR representativeSelection criteria: best ansurr score
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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