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- PDB-9soi: CTLH-CRA domains of Maea-Twa1 mutant (A125G, Q126R, T127del, Q128... -

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Basic information

Entry
Database: PDB / ID: 9soi
TitleCTLH-CRA domains of Maea-Twa1 mutant (A125G, Q126R, T127del, Q128E, A130Q, M143L, E144Q, L147F, A148S, F152Y and F160V) complex
Components
  • E3 ubiquitin-protein transferase MAEA
  • Glucose-induced degradation protein 8 homolog
KeywordsLIGASE / RanBPM / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


GID complex / Regulation of pyruvate metabolism / actomyosin contractile ring / enucleate erythrocyte development / negative regulation of myeloid cell apoptotic process / erythrocyte maturation / ubiquitin ligase complex / erythrocyte development / cytoskeleton organization / RING-type E3 ubiquitin transferase ...GID complex / Regulation of pyruvate metabolism / actomyosin contractile ring / enucleate erythrocyte development / negative regulation of myeloid cell apoptotic process / erythrocyte maturation / ubiquitin ligase complex / erythrocyte development / cytoskeleton organization / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / Wnt signaling pathway / ubiquitin protein ligase activity / cell junction / positive regulation of canonical Wnt signaling pathway / actin cytoskeleton / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / cell adhesion / cell division / positive regulation of cell population proliferation / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / : / 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. ...Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / : / 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
E3 ubiquitin-protein transferase MAEA / Glucose-induced degradation protein 8 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 12, 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

Downloads & links

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Assembly

Deposited unit
A: Glucose-induced degradation protein 8 homolog
B: E3 ubiquitin-protein transferase MAEA
C: Glucose-induced degradation protein 8 homolog
D: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)61,5964
Polymers61,5964
Non-polymers00
Water00
1
A: Glucose-induced degradation protein 8 homolog
B: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)30,7982
Polymers30,7982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucose-induced degradation protein 8 homolog
D: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)30,7982
Polymers30,7982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.346, 142.346, 213.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "C" and resid 7 through 133)
d_1ens_2chain "B"
d_2ens_2(chain "D" and resid 1 through 124)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1THRTHRPROPROAA7 - 1337 - 133
d_2ens_1THRTHRPROPROCC7 - 1337 - 133
d_1ens_2ASNASNGLNGLNBB1 - 1243 - 126
d_2ens_2ASNASNGLNGLNDD1 - 1243 - 126

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.0442478315788, -0.397497390771, -0.916535844215), (-0.424296479686, -0.838056656657, 0.342977459257), (-0.904441610457, 0.373706923354, -0.205738933386)-8.24399584544, 64.1663585318, -38.1504928504
2given(-0.0199112081272, -0.396287371347, -0.917910596465), (-0.445802523859, -0.81825401149, 0.362933165198), (-0.894909857758, 0.41643329837, -0.160373484396)-13.292593439, 61.1393953803, -40.314617091

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Components

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


Mass: 15681.562 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
#2: Protein E3 ubiquitin-protein transferase MAEA / Erythroblast macrophage protein / Macrophage erythroblast attacher


Mass: 15116.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Maea, Emp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q4VC33, RING-type E3 ubiquitin transferase
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M hepes 7.0, 1 M sodium malonate, 0.5% Jeffamine ED2001

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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: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.307→48.93 Å / Num. obs: 17940 / % possible obs: 93.4 % / Redundancy: 19.7 % / Biso Wilson estimate: 145.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.026 / Rrim(I) all: 0.118 / Net I/σ(I): 11.1
Reflection shellResolution: 3.307→3.659 Å / Rmerge(I) obs: 1.987 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 901 / CC1/2: 0.012 / Rpim(I) all: 0.455 / Rrim(I) all: 2.04

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→48.93 Å / SU ML: 0.4771 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.6646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.263 1579 4.74 %
Rwork0.2292 31750 -
obs0.2308 17917 46.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 156.98 Å2
Refinement stepCycle: LAST / Resolution: 3.31→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 0 0 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294328
X-RAY DIFFRACTIONf_angle_d0.66875825
X-RAY DIFFRACTIONf_chiral_restr0.0414628
X-RAY DIFFRACTIONf_plane_restr0.0058768
X-RAY DIFFRACTIONf_dihedral_angle_d14.75871697
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.23882762274
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS2.04072932503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.410.4601200.4647305X-RAY DIFFRACTION4.98
3.41-3.530.3825400.465601X-RAY DIFFRACTION9.81
3.54-3.680.47240.418732X-RAY DIFFRACTION11.63
3.68-3.840.5197380.4097869X-RAY DIFFRACTION13.76
3.84-4.050.3293540.39391198X-RAY DIFFRACTION19.26
4.05-4.30.34951010.35611924X-RAY DIFFRACTION31.16
4.3-4.630.36811550.33042766X-RAY DIFFRACTION44.47
4.63-5.10.37052160.33794612X-RAY DIFFRACTION73.6
5.1-5.830.34752760.3276273X-RAY DIFFRACTION99.92
5.83-7.340.29793430.2646213X-RAY DIFFRACTION99.91
7.35-48.930.17233120.13676257X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: -62.4852371903 Å / Origin y: 55.6055764627 Å / Origin z: 32.0482423373 Å
111213212223313233
T0.440674171996 Å2-0.0265354323917 Å20.083747610003 Å2-0.217266831572 Å20.107110629029 Å2--0.402810993643 Å2
L3.98997892183 °2-0.542013426078 °23.32334395431 °2--0.064875308889 °2-0.011446688857 °2--3.96276997194 °2
S0.146845983395 Å °0.270273933706 Å °-0.207763442561 Å °0.124065478776 Å °0.00858805010442 Å °0.0914308308908 Å °0.0427467949162 Å °0.213524369014 Å °0.00896675326762 Å °
Refinement TLS groupSelection details: all

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