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- PDB-9snf: CTLH-CRA domain of murine RanBP10 -

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Basic information

Entry
Database: PDB / ID: 9snf
TitleCTLH-CRA domain of murine RanBP10
ComponentsRan-binding protein 10
KeywordsLIGASE / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


MET activates RAS signaling / ubiquitin ligase complex / beta-tubulin binding / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / microtubule cytoskeleton organization / microtubule cytoskeleton / nucleus / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / : / 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. ...Ran binding protein 9/10, SPRY domain / : / 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. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ran-binding protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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
A: Ran-binding protein 10
B: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)33,0592
Polymers33,0592
Non-polymers00
Water1,13563
1
A: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)16,5301
Polymers16,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)16,5301
Polymers16,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.331, 75.500, 76.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Ran-binding protein 10 / RanBP10


Mass: 16529.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ranbp10, Kiaa1464 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q6VN19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M tris pH 7.8, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.069→44.81 Å / Num. obs: 14606 / % possible obs: 91.3 % / Redundancy: 11.3 % / Biso Wilson estimate: 38.33 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.051 / Rrim(I) all: 0.174 / Net I/σ(I): 11.5
Reflection shellResolution: 2.069→2.294 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.797 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 859 / CC1/2: 0.602 / Rpim(I) all: 0.552 / Rrim(I) all: 1.882 / % possible all: 57.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→38.53 Å / SU ML: 0.2464 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.8541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 699 4.79 %
Rwork0.2018 13884 -
obs0.204 14583 72.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.76 Å2
Refinement stepCycle: LAST / Resolution: 2.07→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 0 63 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182207
X-RAY DIFFRACTIONf_angle_d0.36862978
X-RAY DIFFRACTIONf_chiral_restr0.0313330
X-RAY DIFFRACTIONf_plane_restr0.0035397
X-RAY DIFFRACTIONf_dihedral_angle_d12.5429844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.230.2751170.3177414X-RAY DIFFRACTION10.88
2.23-2.450.34791010.27651920X-RAY DIFFRACTION51.05
2.45-2.810.29561730.24653758X-RAY DIFFRACTION98.3
2.81-3.540.26822120.21083793X-RAY DIFFRACTION99.5
3.54-38.530.21061960.17473999X-RAY DIFFRACTION99.48

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