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- PDB-9soh: CTLH-CRA domains of the Maea-RanBP10 mutant (Q519G, F543L, Y548F ... -

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Basic information

Entry
Database: PDB / ID: 9soh
TitleCTLH-CRA domains of the Maea-RanBP10 mutant (Q519G, F543L, Y548F and V556F) complex
Components
  • E3 ubiquitin-protein transferase MAEA
  • Ran-binding protein 10
KeywordsLIGASE / RanBPM / CTLH complex / Gid complex / E3 ligase
Function / homology
Function and homology information


MET activates RAS signaling / GID complex / Regulation of pyruvate metabolism / actomyosin contractile ring / enucleate erythrocyte development / negative regulation of myeloid cell apoptotic process / erythrocyte maturation / ubiquitin ligase complex / beta-tubulin binding / erythrocyte development ...MET activates RAS signaling / GID complex / Regulation of pyruvate metabolism / actomyosin contractile ring / enucleate erythrocyte development / negative regulation of myeloid cell apoptotic process / erythrocyte maturation / ubiquitin ligase complex / beta-tubulin binding / erythrocyte development / cytoskeleton organization / guanyl-nucleotide exchange factor activity / RING-type E3 ubiquitin transferase / small GTPase binding / microtubule cytoskeleton organization / spindle / nuclear matrix / ubiquitin protein ligase activity / actin cytoskeleton / microtubule cytoskeleton / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / cell adhesion / cell division / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / : / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH ...Ran binding protein 9/10, SPRY domain / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / : / 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
E3 ubiquitin-protein transferase MAEA / Ran-binding protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.545 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: E3 ubiquitin-protein transferase MAEA
C: Ran-binding protein 10
D: E3 ubiquitin-protein transferase MAEA
E: Ran-binding protein 10
G: Ran-binding protein 10
H: E3 ubiquitin-protein transferase MAEA
F: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)125,6758
Polymers125,6758
Non-polymers00
Water00
1
A: Ran-binding protein 10
B: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers31,4192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ran-binding protein 10
D: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers31,4192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ran-binding protein 10
F: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers31,4192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ran-binding protein 10
H: E3 ubiquitin-protein transferase MAEA


Theoretical massNumber of molelcules
Total (without water)31,4192
Polymers31,4192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)359.825, 359.825, 359.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 64 or resid 70 through 95 or resid 98 through 144))
d_2ens_1(chain "C" and (resid 4 through 64 or resid 70 through 95 or resid 98 through 144))
d_3ens_1(chain "E" and (resid 4 through 95 or resid 98 through 144))
d_4ens_1(chain "G" and (resid 4 through 66 or resid 70 through 144))
d_1ens_2(chain "B" and (resid 9 through 20 or resid 24 through 124))
d_2ens_2(chain "D" and (resid 9 through 20 or resid 24 through 124))
d_3ens_2(chain "F" and (resid 9 through 20 or resid 24 through 124))
d_4ens_2(chain "H" and resid 9 through 124)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALASERSERAA4 - 644 - 64
d_12ens_1ASNASNTYRTYRAA70 - 9570 - 95
d_13ens_1ASNASNGLUGLUAA98 - 14498 - 144
d_21ens_1ALAALASERSERCC4 - 644 - 64
d_22ens_1ASNASNTYRTYRCC70 - 9570 - 95
d_23ens_1ASNASNGLUGLUCC98 - 14498 - 144
d_31ens_1ALAALATYRTYREE4 - 954 - 95
d_32ens_1ASNASNGLUGLUEE98 - 14498 - 144
d_41ens_1ALAALASERSERGF4 - 664 - 66
d_42ens_1ASNASNGLUGLUGF70 - 14470 - 144
d_11ens_2THRTHRARGARGBB9 - 209 - 20
d_12ens_2THRTHRLEULEUBB24 - 12424 - 124
d_21ens_2THRTHRARGARGDD9 - 209 - 20
d_22ens_2THRTHRLEULEUDD24 - 12424 - 124
d_31ens_2THRTHRARGARGFH9 - 209 - 20
d_32ens_2THRTHRLEULEUFH24 - 12424 - 124
d_41ens_2THRTHRLEULEUHG9 - 1249 - 124

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999766405392, 0.0212747718539, -0.00381034542731), (-0.00406282080978, -0.0118367765812, 0.999921689037), (0.0212280035986, 0.999703593473, 0.0119204471598)-179.533058981, -0.460724051059, 1.66534402868
2given(-0.998328807089, 0.0573762376021, -0.0068963971792), (0.0574427584606, 0.998300020001, -0.00986912186459), (0.0063184203609, -0.0102487767355, -0.999927517443)-178.540212959, 5.24854063426, 1.90570618632
3given(0.997233500471, -0.0743036523517, -0.00207672471744), (-0.00308896743186, -0.0135107294933, -0.999903954622), (0.0742684577634, 0.997144135738, -0.0137028736287)-0.219009800224, 0.848962007355, 6.58579775637
4given(-0.999814508249, -0.0108275925011, 0.0159283500738), (0.0161909276132, -0.0246119167013, 0.999565959514), (-0.0104308656623, 0.999638443037, 0.0247826601602)-179.319763696, 1.25633420546, -0.663091442148
5given(-0.996320902452, 0.0792413438566, -0.0326415189742), (0.0793914864793, 0.996837960233, -0.00332759882091), (0.0322746217908, -0.00590681497256, -0.999461584217)-178.618789023, 6.81892916489, 3.42634835751
6given(0.998387351067, -0.0363106600002, 0.0436375205602), (0.0426948153303, -0.0263450605345, -0.998740752412), (0.0374145690099, 0.998993230085, -0.0247522982775)-2.05692366403, 4.40975748826, 4.27344680908

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Components

#1: Protein
Ran-binding protein 10 / RanBP10


Mass: 16302.450 Da / Num. of mol.: 4
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
E3 ubiquitin-protein transferase MAEA / Erythroblast macrophage protein / Macrophage erythroblast attacher


Mass: 15116.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Maea, Emp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q4VC33, RING-type E3 ubiquitin transferase
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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris 8.0, 0.2 M sodium chloride, 20% PEG 6k

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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: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.545→48.084 Å / Num. obs: 21897 / % possible obs: 95.4 % / Redundancy: 158.5 % / Biso Wilson estimate: 150.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.023 / Rrim(I) all: 0.283 / Net I/σ(I): 27.3
Reflection shellResolution: 3.545→3.774 Å / Rmerge(I) obs: 4.684 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1288 / CC1/2: 0.331 / Rpim(I) all: 0.368 / Rrim(I) all: 4.698 / % possible all: 53.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.545→46.85 Å / SU ML: 0.5713 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.2443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 1126 5.19 %
Rwork0.2824 20589 -
obs0.2831 21715 87.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 179.72 Å2
Refinement stepCycle: LAST / Resolution: 3.545→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8379 0 0 0 8379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418526
X-RAY DIFFRACTIONf_angle_d0.810211464
X-RAY DIFFRACTIONf_chiral_restr0.04551241
X-RAY DIFFRACTIONf_plane_restr0.00691506
X-RAY DIFFRACTIONf_dihedral_angle_d12.85913291
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.6152718442
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.32554114015
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.51297805155
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.60802039973
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS1.2311331928
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS2.05026110151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.545-3.710.4658350.4375397X-RAY DIFFRACTION14.3
3.71-3.90.3971290.38332621X-RAY DIFFRACTION91.09
3.9-4.140.35491640.34082861X-RAY DIFFRACTION100
4.15-4.460.3071640.30222895X-RAY DIFFRACTION100
4.47-4.910.31341640.31482909X-RAY DIFFRACTION100
4.92-5.620.31071660.29932915X-RAY DIFFRACTION99.97
5.63-7.080.29721540.32572985X-RAY DIFFRACTION99.97
7.08-46.850.24681500.22673006X-RAY DIFFRACTION94.55
Refinement TLS params.Method: refined / Origin x: -89.75595654 Å / Origin y: 14.9111419255 Å / Origin z: 14.6481627489 Å
111213212223313233
T1.36015102921 Å2-0.214154693544 Å2-0.26325046957 Å2-1.42460086219 Å20.00718066420218 Å2--0.815751815275 Å2
L0.0584221407826 °2-0.709189888489 °21.477274951 °2-2.28898614281 °2-0.0332538349022 °2--0.104787146553 °2
S-0.1309682252 Å °0.436346412266 Å °-0.729513651806 Å °1.12142986046 Å °-0.37830251845 Å °0.381821805088 Å °0.300195904295 Å °0.0534145389218 Å °-0.710662447945 Å °
Refinement TLS groupSelection details: all

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