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- PDB-1i3z: MURINE EAT2 SH2 DOMAIN IN COMPLEX WITH SLAM PHOSPHOPEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1i3z
TitleMURINE EAT2 SH2 DOMAIN IN COMPLEX WITH SLAM PHOSPHOPEPTIDE
Components
  • EWS/FLI1 ACTIVATED TRANSCRIPT 2
  • SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE
KeywordsSIGNALING PROTEIN / SH2 domain Phosphotyrosine signal transduction lymphocyte
Function / homology
Function and homology information


natural killer cell inhibitory signaling pathway / natural killer cell proliferation / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / regulation of vesicle fusion / positive regulation of natural killer cell mediated immunity / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of signal transduction ...natural killer cell inhibitory signaling pathway / natural killer cell proliferation / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / regulation of vesicle fusion / positive regulation of natural killer cell mediated immunity / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of signal transduction / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / leukocyte activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-12 production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of innate immune response / natural killer cell mediated cytotoxicity / positive regulation of macrophage chemotaxis / positive regulation of activated T cell proliferation / negative regulation of type II interferon production / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / phagocytosis / antigen binding / phagocytic vesicle / phosphotyrosine residue binding / signaling adaptor activity / SH2 domain binding / positive regulation of JNK cascade / positive regulation of type II interferon production / transmembrane signaling receptor activity / signaling receptor activity / virus receptor activity / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / immune response / innate immune response / external side of plasma membrane / positive regulation of cell population proliferation / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
EAT-2, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...EAT-2, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / SH2 domain-containing protein 1B / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLu, J. / Poy, F. / Morra, M. / Terhorst, C. / Eck, M.J.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells.
Authors: Morra, M. / Lu, J. / Poy, F. / Martin, M. / Sayos, J. / Calpe, S. / Gullo, C. / Howie, D. / Rietdijk, S. / Thompson, A. / Coyle, A.J. / Denny, C. / Yaffe, M.B. / Engel, P. / Eck, M.J. / Terhorst, C.
#1: Journal: Mol.Cell / Year: 1999
Title: Crystal Structures of the XLP Protein SAP Reveal a Class of SH2 Domains with Extended, Phosphotyrosine-independent Sequence Recognition
Authors: Poy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Morra, M. / Sumegi, J. / Cantley, L.C. / Terhorst, C. / Eck, M.J.
History
DepositionFeb 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EWS/FLI1 ACTIVATED TRANSCRIPT 2
B: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


Theoretical massNumber of molelcules
Total (without water)13,5002
Polymers13,5002
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.994, 59.500, 34.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein EWS/FLI1 ACTIVATED TRANSCRIPT 2


Mass: 11781.718 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN (RESIDUES 1-103)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O35324
#2: Protein/peptide SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


Mass: 1717.915 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide is naturally found in Homo sapiens (humans).
References: GenBank: 9588411, UniProt: Q13291*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate, 30% PEG 8000, 10mM DTT, 25 mM ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
230 %PEG80001reservoir
3100 mMsodium citrate1reservoirpH5.6
425 mMammonium sulfate1reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 7460 / Num. obs: 7460 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 75
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 24668
Reflection shell
*PLUS
Rmerge(I) obs: 0.33

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAP SH2

Resolution: 2.15→5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 286 5 %random
Rwork0.216 ---
all0.25 7025 --
obs0.219 5888 95.3 %-
Displacement parametersBiso mean: 34.396 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.15→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 86 992
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.151

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