[English] 日本語
Yorodumi
- PDB-1d4w: CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH SLAM PHO... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / regulation of vesicle fusion / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / positive regulation of natural killer cell mediated cytotoxicity ...natural killer cell proliferation / negative regulation of CD40 signaling pathway / myeloid dendritic cell activation involved in immune response / regulation of vesicle fusion / negative regulation of T cell cytokine production / leukocyte chemotaxis involved in inflammatory response / positive regulation of dendritic cell chemotaxis / positive regulation of T-helper 1 cell cytokine production / natural killer cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-12 production / natural killer cell activation / negative regulation of T cell receptor signaling pathway / natural killer cell mediated cytotoxicity / positive regulation of macrophage chemotaxis / positive regulation of activated T cell proliferation / negative regulation of interleukin-6 production / negative regulation of type II interferon production / humoral immune response / negative regulation of tumor necrosis factor production / phagocytosis / regulation of immune response / cellular defense response / antigen binding / phagocytic vesicle / SH2 domain binding / positive regulation of JNK cascade / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / cell-cell signaling / signaling receptor activity / virus receptor activity / protein-macromolecule adaptor 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 / cytoplasm / cytosol
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 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
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more