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- PDB-9snv: CTLH-CRA domains of the RanBP9-muskelin complex -

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Basic information

Entry
Database: PDB / ID: 9snv
TitleCTLH-CRA domains of the RanBP9-muskelin complex
Components
  • Muskelin
  • Ran-binding protein 9
KeywordsLIGASE / RanBPM / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


L1CAM interactions / postsynaptic specialization membrane of symmetric synapse / postsynaptic endosome membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / MET activates RAS signaling / Regulation of pyruvate metabolism / Regulation of pyruvate metabolism / regulation of receptor internalization / positive regulation of amyloid precursor protein catabolic process / RAF/MAP kinase cascade ...L1CAM interactions / postsynaptic specialization membrane of symmetric synapse / postsynaptic endosome membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / MET activates RAS signaling / Regulation of pyruvate metabolism / Regulation of pyruvate metabolism / regulation of receptor internalization / positive regulation of amyloid precursor protein catabolic process / RAF/MAP kinase cascade / vesicle-mediated transport in synapse / ubiquitin ligase complex / ruffle / cytoskeleton organization / cell-matrix adhesion / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / GABA-ergic synapse / regulation of cell shape / actin cytoskeleton organization / cell cortex / nuclear body / enzyme binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Attractin/LZTR1 beta-propeller / Muskelin, N-terminal / : / Muskelin N-terminus / Ran binding protein 9/10, SPRY domain / : / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain ...: / Attractin/LZTR1 beta-propeller / Muskelin, N-terminal / : / Muskelin N-terminus / 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. / Galactose oxidase/kelch, beta-propeller / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / 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 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Ran-binding protein 9 / Muskelin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 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 11, 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: Muskelin
B: Ran-binding protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3247
Polymers35,1002
Non-polymers2245
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-51 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.086, 84.086, 228.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

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Components

#1: Protein Muskelin


Mass: 15983.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mkln1, Msk / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q99PV3
#2: 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.: 1
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
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris 8.5, 0.01 M nickel chloride, 30% PEG 400

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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: Sep 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.965→44.919 Å / Num. obs: 24304 / % possible obs: 94.9 % / Redundancy: 39 % / Biso Wilson estimate: 48.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.03 / Rrim(I) all: 0.191 / Net I/σ(I): 16.9
Reflection shellResolution: 1.965→2.15 Å / Rmerge(I) obs: 6.557 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1215 / CC1/2: 0.363 / Rpim(I) all: 1.074 / Rrim(I) all: 6.645

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.965→44.919 Å / SU ML: 0.2789 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.5253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 1218 5.02 %
Rwork0.228 23066 -
obs0.2294 24284 69.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.16 Å2
Refinement stepCycle: LAST / Resolution: 1.965→44.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 5 23 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312237
X-RAY DIFFRACTIONf_angle_d0.54793011
X-RAY DIFFRACTIONf_chiral_restr0.034330
X-RAY DIFFRACTIONf_plane_restr0.0037396
X-RAY DIFFRACTIONf_dihedral_angle_d13.8209862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.965-2.040.4439100.4522175X-RAY DIFFRACTION4.91
2.04-2.140.4017410.36788X-RAY DIFFRACTION21.91
2.14-2.250.4332660.34171546X-RAY DIFFRACTION42.33
2.25-2.390.33531220.32142368X-RAY DIFFRACTION65.08
2.39-2.570.31211390.31353101X-RAY DIFFRACTION84.46
2.57-2.830.32132050.29543647X-RAY DIFFRACTION99.56
2.83-3.240.3112010.27683703X-RAY DIFFRACTION100
3.24-4.090.23422110.21023739X-RAY DIFFRACTION100
4.09-44.9190.21562230.1843999X-RAY DIFFRACTION99.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.869043983160.285424314183-0.7148516484544.52220487614-0.3353649535053.72481595836-0.001200030715510.1769707711110.0377956114696-0.14063128235-0.166388355590.673838928705-0.110858660296-0.2356835024630.1699017205520.43144847398-0.0420191014133-0.1109936389360.123770062284-0.018515744780.37005405932438.6727793417-7.86947635014-9.54932180995
23.046316891252.91498659016-1.242921906274.17240437281-2.980241695391.813349871650.364172431485-0.4328694189810.4992400459750.466027826103-0.09146235392420.109138968603-0.252055851599-0.00777715296535-0.05583268529980.754361058304-0.2421980792720.3145952531090.0107168957563-0.06721616020790.45972498112125.5891489829-38.39645029464.32384687494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 137)AA1 - 1371 - 128
22(chain 'B' and resid 0 through 147)BC0 - 1471 - 144

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