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- PDB-9sne: CTLH-CRA domain of murine RanBP9 -

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Basic information

Entry
Database: PDB / ID: 9sne
TitleCTLH-CRA domain of murine RanBP9
ComponentsRan-binding protein 9
KeywordsLIGASE / RanBPM / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


L1CAM interactions / MET activates RAS signaling / Regulation of pyruvate metabolism / positive regulation of amyloid precursor protein catabolic process / RAF/MAP kinase cascade / ubiquitin ligase complex / cytoskeleton organization / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / nuclear body ...L1CAM interactions / MET activates RAS signaling / Regulation of pyruvate metabolism / positive regulation of amyloid precursor protein catabolic process / RAF/MAP kinase cascade / ubiquitin ligase complex / cytoskeleton organization / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / nuclear body / enzyme binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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. / Lissencephaly type-1-like homology motif / 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 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 1.0Mar 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: Ran-binding protein 9
B: Ran-binding protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3395
Polymers38,2322
Non-polymers1063
Water75742
1
A: Ran-binding protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1522
Polymers19,1161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ran-binding protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1873
Polymers19,1161
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.277, 80.320, 45.017
Angle α, β, γ (deg.)90.000, 101.608, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ran-binding protein 9 / RanBP9 / B-cell antigen receptor Ig beta-associated protein 1 / IBAP-1 / Ran-binding protein M / RanBPM


Mass: 19116.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ranbp9, Ranbpm / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P69566
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M natrium citrate, 0.01 M strontium chloride, 20% PEG 3350

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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: 0.9779 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.81→44.096 Å / Num. obs: 13616 / % possible obs: 89.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Net I/σ(I): 9
Reflection shellResolution: 1.81→2.006 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.253 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 681 / CC1/2: 0.445 / Rpim(I) all: 0.528 / Rrim(I) all: 1.363 / % possible all: 61.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→44.096 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 682 5.02 %
Rwork0.2005 12910 -
obs0.2024 13592 51.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.15 Å2
Refinement stepCycle: LAST / Resolution: 1.81→44.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 3 42 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382270
X-RAY DIFFRACTIONf_angle_d0.41293053
X-RAY DIFFRACTIONf_chiral_restr0.0333343
X-RAY DIFFRACTIONf_plane_restr0.004404
X-RAY DIFFRACTIONf_dihedral_angle_d11.3485891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.950.3942240.2985363X-RAY DIFFRACTION7.45
1.95-2.150.3439740.25631289X-RAY DIFFRACTION26.09
2.15-2.460.30091270.23552368X-RAY DIFFRACTION47.63
2.46-3.090.2532030.23043864X-RAY DIFFRACTION77.56
3.09-44.0960.21712540.17985026X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: 25.9992468569 Å / Origin y: -5.31708413088 Å / Origin z: 30.6378130382 Å
111213212223313233
T0.0961503724681 Å20.0376784452861 Å20.064257954612 Å2-0.149010459203 Å20.00163717458863 Å2--0.140383846617 Å2
L1.71822848957 °20.687475728015 °21.98744313926 °2-0.904114551677 °20.790730154893 °2--2.70145480933 °2
S-0.0328601497176 Å °-0.186702955974 Å °0.0363802425838 Å °-0.0279748545015 Å °-0.0142442107948 Å °0.111665718116 Å °-0.0550701525694 Å °-0.256044519969 Å °0.0106698474772 Å °
Refinement TLS groupSelection details: all

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