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- PDB-9snh: CTLH-CRA domain of murine Maea -

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Basic information

Entry
Database: PDB / ID: 9snh
TitleCTLH-CRA domain of murine Maea
ComponentsE3 ubiquitin-protein transferase MAEA
KeywordsLIGASE / 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 / ubiquitin protein ligase activity / actin cytoskeleton / actin binding / cytoskeleton / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / cell division / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm
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 / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. ...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 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein transferase MAEA
B: E3 ubiquitin-protein transferase MAEA
C: E3 ubiquitin-protein transferase MAEA
D: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)60,4664
Polymers60,4664
Non-polymers00
Water6,954386
1
A: E3 ubiquitin-protein transferase MAEA
D: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)30,2332
Polymers30,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: E3 ubiquitin-protein transferase MAEA
C: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)30,2332
Polymers30,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.075, 76.181, 108.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
E3 ubiquitin-protein transferase MAEA / Erythroblast macrophage protein / Macrophage erythroblast attacher


Mass: 15116.379 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M sodium acetate, 23% PEG 4k

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.43→48.122 Å / Num. obs: 67576 / % possible obs: 94.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Net I/σ(I): 12.9
Reflection shellResolution: 1.431→1.583 Å / Rmerge(I) obs: 2.855 / Mean I/σ(I) obs: 1 / Num. unique obs: 3379 / CC1/2: 0.429 / Rpim(I) all: 0.822 / Rrim(I) all: 2.974

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→32.59 Å / SU ML: 0.1478 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 3387 5.02 %
Rwork0.1989 64099 -
obs0.2003 67486 71.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.43→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 0 386 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734379
X-RAY DIFFRACTIONf_angle_d0.81575897
X-RAY DIFFRACTIONf_chiral_restr0.055611
X-RAY DIFFRACTIONf_plane_restr0.0291778
X-RAY DIFFRACTIONf_dihedral_angle_d14.02611732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.323430.394965X-RAY DIFFRACTION1.75
1.45-1.470.764330.4041122X-RAY DIFFRACTION3.21
1.47-1.50.3579150.3658251X-RAY DIFFRACTION6.88
1.5-1.520.4494330.3706496X-RAY DIFFRACTION13.43
1.52-1.550.3667480.3603775X-RAY DIFFRACTION21.17
1.55-1.580.3346470.33231115X-RAY DIFFRACTION29.8
1.58-1.610.2878970.31431561X-RAY DIFFRACTION42.33
1.61-1.640.3981120.32372078X-RAY DIFFRACTION55.18
1.64-1.670.34921040.30512382X-RAY DIFFRACTION63.87
1.67-1.710.30931400.29632855X-RAY DIFFRACTION76.21
1.71-1.760.34331630.29113396X-RAY DIFFRACTION90.61
1.76-1.80.29141920.27473670X-RAY DIFFRACTION98.52
1.8-1.860.311970.26713764X-RAY DIFFRACTION100
1.86-1.920.26851980.25993739X-RAY DIFFRACTION99.95
1.92-1.980.26731850.23433734X-RAY DIFFRACTION99.92
1.98-2.060.24591980.2183767X-RAY DIFFRACTION99.92
2.06-2.160.23162240.20113713X-RAY DIFFRACTION99.47
2.16-2.270.23321890.19943732X-RAY DIFFRACTION99.32
2.27-2.410.23322090.18813733X-RAY DIFFRACTION98.97
2.41-2.60.22551990.18713738X-RAY DIFFRACTION98.52
2.6-2.860.21742110.19823779X-RAY DIFFRACTION99.82
2.86-3.280.2091990.19423832X-RAY DIFFRACTION99.95
3.28-4.130.1942180.16013833X-RAY DIFFRACTION99.7
4.13-32.590.18982030.17253969X-RAY DIFFRACTION98.49

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