[English] 日本語
Yorodumi
- PDB-2l1c: Shc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l1c
TitleShc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1)
Components
  • Integrin beta-3
  • SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d
KeywordsCELL ADHESION / Shc-PTB / integrin beta3 / cytoplasmic tail
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / XBP1(S) activates chaperone genes / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / neurotrophin TRKA receptor binding / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / transmembrane receptor protein tyrosine kinase adaptor activity / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / cell-substrate junction assembly / Interleukin-15 signaling / regulation of release of sequestered calcium ion into cytosol / positive regulation of bone resorption / mesodermal cell differentiation / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / Interleukin-2 signaling / filopodium membrane / glycinergic synapse / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of cell adhesion mediated by integrin / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / smooth muscle cell migration / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / Signaling by LTK / wound healing, spreading of epidermal cells / positive regulation of smooth muscle cell migration / Shc-EGFR complex / integrin complex / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / epidermal growth factor binding / epidermal growth factor receptor binding / negative chemotaxis / positive regulation of osteoblast proliferation / Signaling by ALK / platelet-derived growth factor receptor signaling pathway / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / cellular response to insulin-like growth factor stimulus / regulation of postsynaptic neurotransmitter receptor internalization / cell-substrate adhesion / protein disulfide isomerase activity / microvillus membrane / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / RET signaling / negative regulation of macrophage derived foam cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of lipid storage / blood coagulation, fibrin clot formation / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Interleukin receptor SHC signaling / Signal attenuation / ECM proteoglycans / Integrin cell surface interactions / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of T cell migration / Signalling to RAS / cellular response to platelet-derived growth factor stimulus / SHC-related events triggered by IGF1R / embryo implantation / ephrin receptor binding / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / coreceptor activity / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / substrate adhesion-dependent cell spreading
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SHC-transforming protein 1 / Integrin beta-3 / SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsDeshmukh, L. / Gorbatyuk, V. / Vinogradova, O.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Integrin {beta}3 phosphorylation dictates its complex with the Shc phosphotyrosine-binding (PTB) domain.
Authors: Deshmukh, L. / Gorbatyuk, V. / Vinogradova, O.
History
DepositionJul 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Oct 9, 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 / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d
B: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)26,4522
Polymers26,4522
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)15 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d


Mass: 23167.484 Da / Num. of mol.: 1 / Fragment: PTB domain (UNP residues 17-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHC1, hCG_1997126 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DV78, UniProt: P29353*PLUS
#2: Protein/peptide Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 3284.377 Da / Num. of mol.: 1 / Fragment: UNP residues 762-788 / Source method: obtained synthetically
Details: The peptide was chemically synthesized based on the sequence of the human integrin beta3 cytoplasmic tail (representing residues 736R-762G)
References: UniProt: P05106
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N edited NOESY
1813D 1H-13C edited NOESY
1913D HN(CA)CO
11013D 1H-13C aromatic NOESY
11112D 13C,15N FilteredTOCSY
11212D 13C,15N Filtered NOESY
11313D F1 13C,15N Filtered, F2 13C edited NOESY-HSQC

-
Sample preparation

DetailsContents: 0.4 mM [U-99% 13C; U-99% 15N] Shc, 0.8 mM integrin beta3, 5 mM DTT, 50 mM sodium chloride, 50 mM sodium phosphate, 1 mM DSS, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity_1-1[U-99% 13C; U-99% 15N]1
0.8 mMentity_2-21
5 mMDTT-31
50 mMsodium chloride-41
50 mMsodium phosphate-51
1 mMDSS-61
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
CCPN-Analysis2.1.3(CCPN-Analysis)-Vranken,Boucher, Stevens, Fogh, Pajon,Llinas,Ulrich,Markley,Ionides,Lauedata analysis
CCPN-Analysis2.1.3(CCPN-Analysis)-Vranken,Boucher, Stevens, Fogh, Pajon,Llinas,Ulrich,Markley,Ionides,Lauepeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: refinement in explicit water
NMR constraintsNOE constraints total: 4196 / NOE intraresidue total count: 1793 / NOE medium range total count: 1704 / NOE sequential total count: 699 / Hydrogen bond constraints total count: 166
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 15

+
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