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- PDB-1m27: Crystal structure of SAP/FynSH3/SLAM ternary complex -

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Basic information

Entry
Database: PDB / ID: 1m27
TitleCrystal structure of SAP/FynSH3/SLAM ternary complex
Components
  • Proto-oncogene tyrosine-protein kinase FYN
  • SH2 domain protein 1A
  • Signaling lymphocytic activation molecule
KeywordsSIGNALING PROTEIN / TRANSFERASE / SH2-SH3 interaction
Function / homology
Function and homology information


natural killer cell proliferation / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / negative regulation of T cell cytokine production / regulation of vesicle fusion / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of dendritic cell chemotaxis / negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen ...natural killer cell proliferation / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / negative regulation of T cell cytokine production / regulation of vesicle fusion / leukocyte chemotaxis involved in inflammatory response / cell adhesion mediator activity / positive regulation of dendritic cell chemotaxis / negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / perinuclear endoplasmic reticulum / NTRK2 activates RAC1 / growth factor receptor binding / heart process / regulation of glutamate receptor signaling pathway / Activated NTRK2 signals through FYN / positive regulation of natural killer cell mediated cytotoxicity / reelin-mediated signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of calcium ion import across plasma membrane / negative regulation of interleukin-12 production / Co-stimulation by CD28 / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / activated T cell proliferation / FLT3 signaling through SRC family kinases / type 5 metabotropic glutamate receptor binding / Nef and signal transduction / negative regulation of dendritic spine maintenance / feeding behavior / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Ephrin signaling / dendritic spine maintenance / CD28 dependent Vav1 pathway / dendrite morphogenesis / Regulation of KIT signaling / leukocyte migration / natural killer cell mediated cytotoxicity / phospholipase activator activity / tau-protein kinase activity / Co-inhibition by CTLA4 / negative regulation of T cell receptor signaling pathway / EPHA-mediated growth cone collapse / positive regulation of macrophage chemotaxis / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / positive regulation of activated T cell proliferation / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / response to amyloid-beta / PECAM1 interactions / negative regulation of interleukin-6 production / CD28 dependent PI3K/Akt signaling / negative regulation of type II interferon production / humoral immune response / glial cell projection / FCGR activation / cellular response to glycine / negative regulation of tumor necrosis factor production / ephrin receptor signaling pathway / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / EPH-ephrin mediated repulsion of cells / alpha-tubulin binding / Role of LAT2/NTAL/LAB on calcium mobilization / regulation of immune response / vascular endothelial growth factor receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / cellular defense response / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / forebrain development / antigen binding / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / phagocytic vesicle / cellular response to platelet-derived growth factor stimulus / T cell costimulation / Signaling by ERBB2 / ephrin receptor binding / EPHB-mediated forward signaling / negative regulation of protein ubiquitination / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SH2 domain binding / FCGR3A-mediated IL10 synthesis / negative regulation of angiogenesis / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants
Similarity search - Function
SH2 protein 1A / SH2D1A, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / : / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains ...SH2 protein 1A / SH2D1A, SH2 domain / Signaling lymphocytic activation molecule, N-terminal / Signaling lymphocytic activation molecule (SLAM) protein / : / : / Fyn/Yrk, SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / SH2 domain-containing protein 1A / Tyrosine-protein kinase Fyn / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChan, B. / Griesbach, J. / Song, H.K. / Poy, F. / Terhorst, C. / Eck, M.J.
CitationJournal: NAT.CELL BIOL. / Year: 2003
Title: SAP couples Fyn to SLAM immune receptors.
Authors: Chan, B. / Lanyi, A. / Song, H.K. / Griesbach, J. / Simarro-Grande, M. / Poy, F. / Howie, D. / Sumegi, J. / Terhorst, C. / Eck, M.J.
History
DepositionJun 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH2 domain protein 1A
B: Signaling lymphocytic activation molecule
C: Proto-oncogene tyrosine-protein kinase FYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1114
Polymers19,9213
Non-polymers1891
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.909, 52.909, 183.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SH2 domain protein 1A / XLP gene product / SAP / SLAM-associated protein / T cell signal transduction molecule SAP / ...XLP gene product / SAP / SLAM-associated protein / T cell signal transduction molecule SAP / Duncan's disease SH2-protein


Mass: 11702.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60880
#2: Protein/peptide Signaling lymphocytic activation molecule / SLAM / IPO-3 / CD150 antigen / CDw150


Mass: 1280.512 Da / Num. of mol.: 1 / Fragment: SLAM peptide (residues 276-286) / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. This sequence was chemically synthesized.
References: UniProt: Q13291
#3: Protein Proto-oncogene tyrosine-protein kinase FYN / Fyn / P59-FYN / SYN / SLK


Mass: 6938.519 Da / Num. of mol.: 1 / Fragment: SH3 domain (residues 82-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06241, EC: 2.7.1.112
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
350 mM1dropNaCl
45 mMdithiothreitol1drop
51.2 Msodium tartrate1reservoir
6100 mMTris-HCl1reservoirpH8.0
75 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 2001 / Details: Osmic Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 62846 / Num. obs: 62846 / % possible obs: 97.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 9233 / % possible obs: 95.5 % / Redundancy: 3.2 % / Num. measured all: 29117 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.246

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 967 RANDOM
Rwork0.213 --
all0.213 9258 -
obs0.213 8291 -
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 13 86 1506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.258
LS refinement shellResolution: 2.5→20 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.266 967 -
Rwork0.213 --
obs-9258 96 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.25
LS refinement shell
*PLUS
Lowest resolution: 2.6 Å

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