[English] 日本語
Yorodumi
- PDB-1dk8: CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dk8
TitleCRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN
ComponentsAXIN
KeywordsSIGNALING PROTEIN / ALPHA-HELIX / PI-HELIX
Function / homology
Function and homology information


beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / axial mesoderm formation / dorsal/ventral axis specification / activation of protein kinase activity / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding ...beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / axial mesoderm formation / dorsal/ventral axis specification / activation of protein kinase activity / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / negative regulation of protein metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / lateral plasma membrane / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / signaling adaptor activity / protein serine/threonine kinase binding / cytoplasmic microtubule organization / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT / positive regulation of JNK cascade / sensory perception of sound / Degradation of AXIN / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Degradation of beta-catenin by the destruction complex / protein polyubiquitination / positive regulation of protein catabolic process / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein phosphorylation / microtubule cytoskeleton / cell cortex / protein-containing complex assembly / cytoplasmic vesicle / molecular adaptor activity / Estrogen-dependent gene expression / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / nucleolus / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Axin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.57 Å
AuthorsSpink, K.E. / Polakis, P. / Weis, W.I.
CitationJournal: EMBO J. / Year: 2000
Title: Structural basis of the Axin-adenomatous polyposis coli interaction.
Authors: Spink, K.E. / Polakis, P. / Weis, W.I.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,98513
Polymers16,7941
Non-polymers1,19112
Water3,207178
1
A: AXIN
hetero molecules

A: AXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,97026
Polymers33,5882
Non-polymers2,38224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)32.570, 117.880, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-603-

GOL

21A-605-

GOL

31A-605-

GOL

Detailsfull-length Axin exists as a dimer in vivo

-
Components

#1: Protein AXIN


Mass: 16794.104 Da / Num. of mol.: 1 / Fragment: RGS-HOMOLOGOUS DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O15169
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: sodium acetate, ammonium sulfate, glycerol, dithiothreitol, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlAxin-RGS1drop
21.6 Mammonium sulfate1reservoir
375 mM1reservoirNaOAc
45 %glycerol1reservoir
54 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.57→29.3 Å / Num. all: 22567 / Num. obs: 22359 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.5
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.186 / Num. unique all: 688 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.57→29.3 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1491306.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2211 9.9 %RANDOM
Rwork0.172 ---
obs0.172 22338 98.9 %-
all-22567 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.91 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.33 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.57→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 68 178 1425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.443
X-RAY DIFFRACTIONc_scangle_it3.423.5
LS refinement shellResolution: 1.57→1.67 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 321 8.9 %
Rwork0.185 3296 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

+
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