[English] 日本語
Yorodumi
- PDB-5y3b: Crystal structure of mouse Ccd1 DIX domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y3b
TitleCrystal structure of mouse Ccd1 DIX domain
ComponentsDixin
KeywordsSIGNALING PROTEIN / Wnt signal
Function / homology
Function and homology information


forebrain ventricular zone progenitor cell division / cerebral cortex radially oriented cell migration / cell proliferation in forebrain / cerebellar cortex development / mitogen-activated protein kinase kinase kinase binding / gamma-tubulin binding / positive regulation of axonogenesis / cerebral cortex cell migration / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation ...forebrain ventricular zone progenitor cell division / cerebral cortex radially oriented cell migration / cell proliferation in forebrain / cerebellar cortex development / mitogen-activated protein kinase kinase kinase binding / gamma-tubulin binding / positive regulation of axonogenesis / cerebral cortex cell migration / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation / canonical Wnt signaling pathway / axon terminus / regulation of microtubule cytoskeleton organization / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / actin binding / cytoskeleton / protein domain specific binding / focal adhesion / neuronal cell body / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Dixin / Ribosomal Protein L25; Chain P - #130 / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Ribosomal Protein L25; Chain P / Calponin homology domain ...Dixin / Ribosomal Protein L25; Chain P - #130 / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Ribosomal Protein L25; Chain P / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ubiquitin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsTerawaki, S. / Shibata, N. / Higuchi, Y.
Funding support Japan, 17items
OrganizationGrant numberCountry
MEXT22121519 Japan
MEXT23121527 Japan
MEXT25121705 Japan
MEXT23121526 Japan
MEXT25121731 Japan
JSPS22370061 Japan
JSPS22770112 Japan
JSPS25840017 Japan
Hyogo Science and Technology Association Japan
Sasakawa Scienti c Research Grant from the Japan Science Society Japan
Sumitomo Foundation Japan
Leave a Nest Grants Caliper Life Science Award Japan
Uehara Memorial Foundation Japan
Takeda Medical Science Japan
Inamori Foundation Japan
JAXA Japan
Grant-in-Aid from the Global COE program Japan
Citation
Journal: Sci Rep / Year: 2017
Title: Structural basis for Ccd1 auto-inhibition in the Wnt pathway through homomerization of the DIX domain.
Authors: Terawaki, S.I. / Fujita, S. / Katsutani, T. / Shiomi, K. / Keino-Masu, K. / Masu, M. / Wakamatsu, K. / Shibata, N. / Higuchi, Y.
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2007
Title: The DIX domain of Dishevelled confers Wnt signaling by dynamic polymerization.
Authors: Schwarz-Romond, T. / Fiedler, M. / Shibata, N. / Butler, P.J. / Kikuchi, A. / Higuchi, Y. / Bienz, M.
History
DepositionJul 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dixin
B: Dixin
C: Dixin
D: Dixin
E: Dixin
F: Dixin
G: Dixin


Theoretical massNumber of molelcules
Total (without water)68,4887
Polymers68,4887
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-30 kcal/mol
Surface area29580 Å2
Unit cell
Length a, b, c (Å)72.854, 75.660, 125.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 392:398 or resseq 412:416 or resseq...
211chain B and (resseq 392:398 or resseq 412:416 or resseq...
311chain C and (resseq 392:398 or resseq 412:416 or resseq...
411chain D and (resseq 392:398 or resseq 412:416 or resseq...
511chain E and (resseq 392:398 or resseq 412:416 or resseq...
611chain F and (resseq 392:398 or resseq 412:416 or resseq...
711chain G and (resseq 392:398 or resseq 412:416 or resseq...

-
Components

#1: Protein
Dixin / Coiled-coil protein DIX1 / Coiled-coil-DIX1 / DIX domain-containing protein 1


Mass: 9783.971 Da / Num. of mol.: 7 / Fragment: UNP RESIDUES 625-707
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dixdc1, Ccd1, Kiaa1735 / Plasmid: pET49b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-CodonPlus-RILP / References: UniProt: Q80Y83

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M Na HEPES pH 7.8, 15%(v/v) ethylene glycol, 3%(v/v) glycerol, 4%(v/v) 1,3-propanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14312 / % possible obs: 99 % / Redundancy: 6.2 % / Net I/σ(I): 16.3

-
Processing

Software
NameVersionClassification
PHENIX1.6.1_357refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→29.088 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.51
RfactorNum. reflection% reflection
Rfree0.2894 713 4.97 %
Rwork0.2475 --
obs0.2496 14312 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 27.027 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0409 Å20 Å2-0 Å2
2--0.6151 Å20 Å2
3----2.656 Å2
Refinement stepCycle: LAST / Resolution: 3→29.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 0 0 4665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034791
X-RAY DIFFRACTIONf_angle_d0.7986488
X-RAY DIFFRACTIONf_dihedral_angle_d15.7891736
X-RAY DIFFRACTIONf_chiral_restr0.058691
X-RAY DIFFRACTIONf_plane_restr0.003838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A377X-RAY DIFFRACTIONPOSITIONAL
12B377X-RAY DIFFRACTIONPOSITIONAL0.01
13C377X-RAY DIFFRACTIONPOSITIONAL0.012
14D377X-RAY DIFFRACTIONPOSITIONAL0.012
15E377X-RAY DIFFRACTIONPOSITIONAL0.016
16F377X-RAY DIFFRACTIONPOSITIONAL0.009
17G377X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23140.37821270.31022636X-RAY DIFFRACTION98
3.2314-3.55610.31021420.27962697X-RAY DIFFRACTION100
3.5561-4.06950.31351530.25332701X-RAY DIFFRACTION100
4.0695-5.12250.26851510.21562740X-RAY DIFFRACTION100
5.1225-29.08920.23231400.21842869X-RAY DIFFRACTION100

+
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