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- PDB-2eo6: Solution structure of the SH2 domain from mouse B-cell linker pro... -

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Basic information

Entry
Database: PDB / ID: 2eo6
TitleSolution structure of the SH2 domain from mouse B-cell linker protein BLNK
ComponentsB-cell linker protein
KeywordsSIGNALING PROTEIN / sh2 / Cytoplasmic adapter protein / B-cell adapter containing SH2 domain protein / B-cell adapter containing Src homology 2 domain protein / Src homology 2 domain-containing leukocyte protein of 65 kDa / Slp-65 / Lymphocyte antigen 57 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell activation / phospholipase binding / cell surface receptor protein tyrosine kinase signaling pathway / signaling adaptor activity / protein tyrosine kinase binding / SH2 domain binding / molecular condensate scaffold activity / B cell receptor signaling pathway / intracellular signal transduction ...Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / B cell activation / phospholipase binding / cell surface receptor protein tyrosine kinase signaling pathway / signaling adaptor activity / protein tyrosine kinase binding / SH2 domain binding / molecular condensate scaffold activity / B cell receptor signaling pathway / intracellular signal transduction / intracellular membrane-bounded organelle / lipid binding / positive regulation of gene expression / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell linker protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSano, R. / Hayashi, F. / Kurosaki, C. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SH2 domain from mouse B-cell linker protein BLNK
Authors: Sano, R. / Hayashi, F. / Kurosaki, C. / Yoshida, M. / Yokoyama, S.
History
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: B-cell linker protein


Theoretical massNumber of molelcules
Total (without water)15,4971
Polymers15,4971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein B-cell linker protein / Cytoplasmic adapter protein / B-cell adapter containing SH2 domain protein / B-cell adapter ...Cytoplasmic adapter protein / B-cell adapter containing SH2 domain protein / B-cell adapter containing Src homology 2 domain protein / Src homology 2 domain-containing leukocyte protein of 65 kDa / Slp-65 / Lymphocyte antigen 57


Mass: 15497.202 Da / Num. of mol.: 1 / Fragment: SH2 domain, UNP residues 330-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell free protein synthesis / Gene: Blnk / Plasmid: P050815-08 / References: UniProt: Q9QUN3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.23 mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9742Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.data analysis
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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