[English] 日本語
Yorodumi
- PDB-1mil: TRANSFORMING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mil
TitleTRANSFORMING PROTEIN
ComponentsSHC ADAPTOR PROTEIN
KeywordsTRANSFORMING PROTEIN / SH2 DOMAIN / PHOSPHORYLATION / COLLAGEN / GROWTH REGULATION / ALTERNATIVE INITIATION
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor binding ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor binding / Signaling by ALK / Signaling by ALK fusions and activated point mutants / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / Tie2 Signaling / insulin-like growth factor receptor binding / SHC1 events in EGFR signaling / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Integrin signaling / negative regulation of angiogenesis / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / insulin-like growth factor receptor signaling pathway / phospholipid binding / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / insulin receptor binding / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / cell-cell adhesion / receptor tyrosine kinase binding / cellular response to growth factor stimulus / GPER1 signaling / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / mitochondrial matrix / intracellular signal transduction / defense response to bacterium / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / plasma membrane / cytosol
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 / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. ...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 / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsMikol, V.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of the SH2 domain from the adaptor protein SHC: a model for peptide binding based on X-ray and NMR data.
Authors: Mikol, V. / Baumann, G. / Zurini, M.G. / Hommel, U.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization of the Complex between Cyclophilin a and Cyclosporin Derivatives: The Use of Cross-Seeding
Authors: Mikol, V. / Duc, D.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: X-Ray Structure of a Monomeric Cyclophilin A-Cyclosporin a Crystal Complex at 2.1 A Resolution
Authors: Mikol, V. / Kallen, J. / Pflugl, G. / Walkinshaw, M.D.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: A Novel Transforming Protein (Shc) with an Sh2 Domain is Implicated in Mitogenic Signal Transduction
Authors: Pelicci, G. / Lanfrancone, L. / Grignani, F. / Mcglade, J. / Cavallo, F. / Forni, G. / Nicoletti, I. / Grignani, F. / Pawson, T. / Pelicci, P.G.
History
DepositionSep 20, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SHC ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,7131
Polymers11,7131
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.370, 41.550, 97.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SHC ADAPTOR PROTEIN


Mass: 11713.277 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE RECOGNITION DOMAIN SH2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: T7 / Plasmid: T7 / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P29353
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE ARG 16 OF SHC ADOPTS ALTERNATE CONFORMATIONS.
Sequence detailsRESIDUES 1 AND 2 CORRESPOND TO RESIDUES OF THE T7 GENE LEADER SEQUENCE REQUIRED FOR EXPRESSION AND ...RESIDUES 1 AND 2 CORRESPOND TO RESIDUES OF THE T7 GENE LEADER SEQUENCE REQUIRED FOR EXPRESSION AND RESIDUES 3 - 104 CORRESPOND TO RESIDUES 372 - 473 IN THE FULL LENGTH PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal
*PLUS
Density % sol: 46.2 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropNa2HPO4/citrate
29 %(w/v)PEG80001drop
31 mMdithiothreitol1drop
40.02 %(w/v)1dropNaN3
51 mMShc1drop
6100 mM1reservoirNa2HPO4/citrate
718 %(w/v)PEG80001reservoir
80.04 %(w/v)1reservoirNaN3

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 3028 / % possible obs: 94 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 7344 / Rmerge(I) obs: 0.051

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.173 -
obs0.173 2943
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 0 85 881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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