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- PDB-9sng: CTLH-CRA domain of murine RanBP10 mutant Q519G, F543L, Y548F and V556F -

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Basic information

Entry
Database: PDB / ID: 9sng
TitleCTLH-CRA domain of murine RanBP10 mutant Q519G, F543L, Y548F and V556F
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: 1.74 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: Ran-binding protein 10
B: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)32,9132
Polymers32,9132
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.079, 68.629, 76.453
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: 16456.619 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.: 164 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris 6.5, 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: 1.737→43.042 Å / Num. obs: 23475 / % possible obs: 91.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.043 / Rrim(I) all: 0.159 / Net I/σ(I): 13.1
Reflection shellResolution: 1.737→1.87 Å / Rmerge(I) obs: 1.979 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1201 / CC1/2: 0.619 / Rpim(I) all: 0.545 / Rrim(I) all: 2.054 / % possible all: 50.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→43.04 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 1128 4.87 %
Rwork0.2102 22012 -
obs0.212 23140 79.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.4 Å2
Refinement stepCycle: LAST / Resolution: 1.74→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 0 164 2332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552212
X-RAY DIFFRACTIONf_angle_d0.72512984
X-RAY DIFFRACTIONf_chiral_restr0.037332
X-RAY DIFFRACTIONf_plane_restr0.0056397
X-RAY DIFFRACTIONf_dihedral_angle_d13.9497843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.820.504480.3415245X-RAY DIFFRACTION7.17
1.82-1.910.3432960.30491847X-RAY DIFFRACTION54.29
1.91-2.030.32621480.28773057X-RAY DIFFRACTION90.46
2.03-2.190.25171670.22573425X-RAY DIFFRACTION99.86
2.19-2.410.27031410.2332947X-RAY DIFFRACTION86.16
2.41-2.760.24121610.19643452X-RAY DIFFRACTION99.81
2.76-3.470.24732170.19953437X-RAY DIFFRACTION99.89
3.47-43.040.21431900.18353602X-RAY DIFFRACTION99.42
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)
12.39614847924-0.441101677784-0.5790636922860.897367018136-0.5138696899051.0871759572-0.0951791229544-0.207128385595-0.009337654570670.1181829208920.1032655839670.0476331017316-0.0264255833074-0.1312311303810.01049151276080.09599909145260.0005306419926720.005837091779260.157708113703-0.008236904583690.096087008009811.98299398956.4989707166412.3819589113
22.932170524160.2611265730110.490573885451.5365349822-0.3132830310640.812281619312-0.05709335575470.1274729928650.297751521477-0.0436122182069-0.00923395695057-0.0202751699335-0.1536897090660.03562092296560.03108179080760.1084801124220.00774970904563-0.0008974337829650.138723973134-0.009937685620950.12601540150640.661263681517.94033749813.0828448096
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 8 through 151)AA8 - 1511 - 140
22(chain 'B' and resid 9 through 152)BB9 - 1521 - 135

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