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- PDB-9soc: Murine RanBP10-Twa1 complex -

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Basic information

Entry
Database: PDB / ID: 9soc
TitleMurine RanBP10-Twa1 complex
Components
  • Glucose-induced degradation protein 8 homolog
  • Ran-binding protein 10
KeywordsLIGASE / RanBPM / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


MET activates RAS signaling / Regulation of pyruvate metabolism / ubiquitin ligase complex / beta-tubulin binding / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / microtubule cytoskeleton organization / Wnt signaling pathway / cell junction ...MET activates RAS signaling / Regulation of pyruvate metabolism / ubiquitin ligase complex / beta-tubulin binding / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / microtubule cytoskeleton organization / Wnt signaling pathway / cell junction / positive regulation of canonical Wnt signaling pathway / microtubule cytoskeleton / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of cell population proliferation / protein homodimerization activity / nucleoplasm / nucleus / 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 10 / Glucose-induced degradation protein 8 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 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 12, 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: Glucose-induced degradation protein 8 homolog
C: Ran-binding protein 10
D: Glucose-induced degradation protein 8 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,1016
Polymers183,9504
Non-polymers1512
Water00
1
A: Ran-binding protein 10
B: Glucose-induced degradation protein 8 homolog


Theoretical massNumber of molelcules
Total (without water)91,9752
Polymers91,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ran-binding protein 10
D: Glucose-induced degradation protein 8 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1264
Polymers91,9752
Non-polymers1512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.920, 124.920, 479.645
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
11C-701-

GOL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 27 through 624)
d_2ens_1(chain "C" and resid 27 through 624)
d_1ens_2(chain "B" and resid 7 through 227)
d_2ens_2(chain "D" and resid 7 through 227)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LEULEULEULEUAA27 - 6242 - 594
d_2ens_1LEULEULEULEUCC27 - 6242 - 594
d_1ens_2PROPROPROPROBB7 - 2277 - 227
d_2ens_2PROPROPROPRODD7 - 2277 - 227

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999989395564, -0.00340164595698, -0.00310444267969), (-0.00334042945564, 0.999803971947, -0.0195156145329), (0.00317021933311, -0.0195050374091, -0.999804732548)126.649740987, 0.103305741433, -0.967965557532
2given(-0.999991620691, 0.00379814190425, 0.00152730704804), (0.00376994846868, 0.999829849447, -0.0180571216688), (-0.00159563068639, -0.0180512124937, -0.999835790363)126.818061908, -0.199463657524, -0.552316549427

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Components

#1: Protein Ran-binding protein 10 / RanBP10


Mass: 65162.199 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: Protein Glucose-induced degradation protein 8 homolog / Two hybrid-associated protein 1 with RanBPM / Twa1


Mass: 26812.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gid8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q9D7M1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M BisTris 6.0, 0.02 M hexaamminecobalt chloride, 0.18 magnesium chloride, 9% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 3.175→49.307 Å / Num. obs: 11177 / % possible obs: 88.7 % / Redundancy: 28.1 % / Biso Wilson estimate: 97.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.367 / Rpim(I) all: 0.069 / Rrim(I) all: 0.373 / Net I/σ(I): 9.3
Reflection shellResolution: 3.175→3.788 Å / Redundancy: 33.8 % / Rmerge(I) obs: 3.891 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 559 / CC1/2: 0.726 / Rpim(I) all: 0.67 / Rrim(I) all: 3.95 / % possible all: 49.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→20 Å / SU ML: 0.3824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.0495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.312 501 4.58 %
Rwork0.2993 10442 -
obs0.2998 10943 28.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.73 Å2
Refinement stepCycle: LAST / Resolution: 3.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10574 0 7 0 10581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005110807
X-RAY DIFFRACTIONf_angle_d0.896414615
X-RAY DIFFRACTIONf_chiral_restr0.04691572
X-RAY DIFFRACTIONf_plane_restr0.00711928
X-RAY DIFFRACTIONf_dihedral_angle_d23.31054088
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.854759803197
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.821391753494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.490.790630.520784X-RAY DIFFRACTION0.93
3.49-3.990.4519360.4483893X-RAY DIFFRACTION9.85
4-5.020.3751140.35542329X-RAY DIFFRACTION25.51
5.02-200.2923480.27787136X-RAY DIFFRACTION74.65
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)
10.824331862659-0.5022359224250.02373986833892.31841802044-0.03774763512673.388597927280.242830484197-0.1495144395790.0985542348361-0.09923684099580.02744854893290.462218653411-0.525764226721-0.1682542549411.86367833521E-101.21384014934-0.04582637800720.1006886553050.6127060662120.01471891296780.93325865162149.0461509416-22.6904690278-8.887870056
23.541890312940.8041360756170.1288920972210.460445608156-0.1852805899912.94015226707-0.1261385597360.499682662079-0.228840834043-0.06706187133050.385931553772-0.3636644610670.2274340472980.4169174323790.005424733386731.257933893880.1671166823890.2470001857540.358256451249-0.08209372915710.93709590094278.2142089927-37.6399236546-20.2667231061
30.87194085319-0.2377008098730.9660746283622.516679281160.4934708312754.964414649480.03588747887270.07881513166830.40420040277-0.1430695265060.205635813533-0.507131442435-0.4952986714560.3670610124427.46664275865E-50.878438107888-0.02564762080270.2573623167550.704340816846-0.07146258545541.0426618621977.6748558862-22.52315248588.67518001018
42.39545101482-0.353317981816-1.12774707450.6603734191160.3696599054772.576240340350.1795902255060.131526690236-0.09166893398520.154594846047-0.003145415021530.252687956063-0.0394588885688-0.08280575827260.001337110620721.03727502047-0.2535322751560.1671128974710.3013431600360.1049894156611.104098382848.5010742211-37.195939734120.1830581238
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 6 through 228)BB6 - 2281 - 223
22(chain 'C' and resid 26 through 625)CC26 - 6251 - 442
33(chain 'D' and resid 6 through 228)DE6 - 2281 - 223
44(chain 'A' and resid 26 through 625)AA26 - 6251 - 442

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