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- PDB-1d4w: CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHO... -

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Basic information

Entry
Database: PDB / ID: 1d4w
TitleCRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHOSPHOPEPTIDE
Components
  • SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE
  • T CELL SIGNAL TRANSDUCTION MOLECULE SAP
KeywordsSIGNALING PROTEIN / SH2 DOMAIN / PHOSPHOTYROSINE RECOGNIITON / PEPTIDE RECOGNITION / SIGNAL TRANSDUCTION / LYMPHOPROLIFERATIVE DISEASE
Function / homology
Function and homology information


natural killer cell proliferation / regulation of vesicle fusion / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / leukocyte chemotaxis involved in inflammatory response / negative regulation of T cell cytokine production / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / negative regulation of interleukin-12 production ...natural killer cell proliferation / regulation of vesicle fusion / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / leukocyte chemotaxis involved in inflammatory response / negative regulation of T cell cytokine production / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / negative regulation of interleukin-12 production / natural killer cell mediated cytotoxicity / negative regulation of T cell receptor signaling pathway / positive regulation of macrophage chemotaxis / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of activated T cell proliferation / negative regulation of interleukin-6 production / humoral immune response / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / regulation of immune response / cellular defense response / phagocytic vesicle / phagocytosis / antigen binding / SH2 domain binding / positive regulation of JNK cascade / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / positive regulation of type II interferon production / virus receptor activity / cell-cell signaling / signaling receptor activity / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
SH2 protein 1A / SH2D1A, 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 protein 1A / SH2D1A, 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 1A / Signaling lymphocytic activation molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPoy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Eck, M.J.
Citation
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.
#1: Journal: Nature / Year: 1998
Title: The X-linked lymphoproliferative disease gene product SAP regulates signals induced through the co-receptor SLAM
Authors: Sayos, J. / Wu, C. / Morra, M. / Wang, N. / Terhorst, C.
History
DepositionOct 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T CELL SIGNAL TRANSDUCTION MOLECULE SAP
B: T CELL SIGNAL TRANSDUCTION MOLECULE SAP
C: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE
D: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


Theoretical massNumber of molelcules
Total (without water)26,1264
Polymers26,1264
Non-polymers00
Water7,440413
1
A: T CELL SIGNAL TRANSDUCTION MOLECULE SAP
C: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


Theoretical massNumber of molelcules
Total (without water)13,0632
Polymers13,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area6270 Å2
MethodPISA
2
B: T CELL SIGNAL TRANSDUCTION MOLECULE SAP
D: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE


Theoretical massNumber of molelcules
Total (without water)13,0632
Polymers13,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area5930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.2, 49.0, 55.6
Angle α, β, γ (deg.)90., 94.2, 90.
Int Tables number5
Space group name H-MC121

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Components

#1: Protein T CELL SIGNAL TRANSDUCTION MOLECULE SAP / SAP


Mass: 11702.393 Da / Num. of mol.: 2 / Fragment: SH2 DOMAIN / Mutation: RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: T CELL / Plasmid: T7-PRSET / Production host: Escherichia coli (E. coli) / References: UniProt: O60880
#2: Protein/peptide SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE / / SLAM


Mass: 1360.491 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC TAIL SYNTHETIC PHOSPOPEPTIDE / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. / References: UniProt: Q13291
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 8000, 20% GLYCEROL, 100 MM SODIUM CITRATE, 10MM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1dropNaCl
410 mMdithiothreitol1drop
530 %PEG80001reservoir
620 %glycerol1reservoir
7100 mMsodium citrate1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 23946 / % possible obs: 94.8 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. obs: 23946 / Num. measured all: 113987

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→10 Å / σ(F): 4 / Stereochemistry target values: ENGH& HUBER
RfactorNum. reflectionSelection details
Rfree0.24 -THIN SHELLS, 5%
Rwork0.153 --
all0.172 --
obs-22677 -
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 413 2203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 4 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025

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