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- PDB-9sni: CTLH-CRA domain of murine Twa1 -

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Basic information

Entry
Database: PDB / ID: 9sni
TitleCTLH-CRA domain of murine Twa1
ComponentsGlucose-induced degradation protein 8 homolog
KeywordsLIGASE / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


Regulation of pyruvate metabolism / ubiquitin ligase complex / Wnt signaling pathway / cell junction / positive regulation of canonical Wnt signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of cell population proliferation / protein homodimerization activity / nucleoplasm / nucleus ...Regulation of pyruvate metabolism / ubiquitin ligase complex / Wnt signaling pathway / cell junction / positive regulation of canonical Wnt signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of cell population proliferation / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif ...: / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif
Similarity search - Domain/homology
Glucose-induced degradation protein 8 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
Authorsvan gen Hassend, P.M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2243 Germany
CitationJournal: To Be Published
Title: Engineering CTLH-CRA domains with swapped binding specificity
Authors: van gen Hassend, P.M. / Schindelin, H.
History
DepositionSep 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glucose-induced degradation protein 8 homolog
A: Glucose-induced degradation protein 8 homolog


Theoretical massNumber of molelcules
Total (without water)31,5352
Polymers31,5352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-46 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.843, 118.843, 56.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
DetailsTwa1 showed mass for a stable monomer in our SEC-MALS measurements. / Twa1 also shows helix swapping in crystallization, and the dimer would be relevant to interpret this.

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Components

#1: Protein Glucose-induced degradation protein 8 homolog / Two hybrid-associated protein 1 with RanBPM / Twa1


Mass: 15767.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gid8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q9D7M1
Has protein modificationN

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris 8.0, 1.6 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.113→46.882 Å / Num. obs: 18249 / % possible obs: 93.9 % / Redundancy: 25 % / Biso Wilson estimate: 63.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.019 / Rrim(I) all: 0.096 / Net I/σ(I): 18.3
Reflection shellResolution: 2.113→2.282 Å / Rmerge(I) obs: 3.06 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 913 / CC1/2: 0.44 / Rpim(I) all: 0.631 / Rrim(I) all: 3.125

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.113→46.88 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 950 5.21 %
Rwork0.2379 17299 -
obs0.2392 18249 76.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.62 Å2
Refinement stepCycle: LAST / Resolution: 2.113→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 0 0 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172132
X-RAY DIFFRACTIONf_angle_d0.38962877
X-RAY DIFFRACTIONf_chiral_restr0.0299322
X-RAY DIFFRACTIONf_plane_restr0.0045382
X-RAY DIFFRACTIONf_dihedral_angle_d13.5475827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.113-2.220.3693120.3662365X-RAY DIFFRACTION11.39
2.22-2.360.3775760.35441445X-RAY DIFFRACTION45.51
2.36-2.550.34141380.33252456X-RAY DIFFRACTION77.97
2.55-2.80.33791870.3383177X-RAY DIFFRACTION99.94
2.8-3.210.3281860.31033196X-RAY DIFFRACTION100
3.21-4.040.2581720.24953249X-RAY DIFFRACTION99.97
4.04-46.880.22581790.1883411X-RAY DIFFRACTION99.97

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