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- PDB-5y3b: Crystal structure of mouse Ccd1 DIX domain -

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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 / cell proliferation in forebrain / cerebral cortex radially oriented cell migration / cerebellar cortex development / modification of postsynaptic actin cytoskeleton / gamma-tubulin binding / positive regulation of axonogenesis / mitogen-activated protein kinase kinase kinase binding / negative regulation of neuron differentiation / cerebral cortex cell migration ...forebrain ventricular zone progenitor cell division / cell proliferation in forebrain / cerebral cortex radially oriented cell migration / cerebellar cortex development / modification of postsynaptic actin cytoskeleton / gamma-tubulin binding / positive regulation of axonogenesis / mitogen-activated protein kinase kinase kinase binding / negative regulation of neuron differentiation / cerebral cortex cell migration / positive regulation of Wnt signaling pathway / canonical Wnt signaling pathway / stress fiber / axon terminus / regulation of microtubule cytoskeleton organization / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / actin binding / postsynapse / protein domain specific binding / focal adhesion / neuronal cell body / glutamatergic synapse / protein-containing complex / cytosol
Similarity search - Function
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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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...

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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

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Experimental details

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Experiment

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

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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

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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

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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

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