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- PDB-4eoz: Crystal structure of the SPOP BTB domain complexed with the Cul3 ... -

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Basic information

Entry
Database: PDB / ID: 4eoz
TitleCrystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain
Components
  • Cullin-3
  • Speckle-type POZ protein
KeywordsPROTEIN BINDING / E3 Ubiquitin Ligase / Nucleus
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / RHOBTB3 ATPase cycle ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / RHOBTB3 ATPase cycle / positive regulation of mitotic metaphase/anaphase transition / cell projection organization / embryonic cleavage / Notch binding / fibroblast apoptotic process / RHOBTB1 GTPase cycle / negative regulation of type I interferon production / stem cell division / molecular function inhibitor activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / stress fiber assembly / positive regulation of cytokinesis / negative regulation of Rho protein signal transduction / regulation of proteolysis / sperm flagellum / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / RHOBTB2 GTPase cycle / protein K48-linked ubiquitination / protein autoubiquitination / gastrulation / positive regulation of protein ubiquitination / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / cyclin binding / Degradation of DVL / integrin-mediated signaling pathway / Hedgehog 'on' state / cellular response to amino acid stimulus / kidney development / G1/S transition of mitotic cell cycle / protein destabilization / Regulation of RAS by GAPs / Wnt signaling pathway / KEAP1-NFE2L2 pathway / protein polyubiquitination / spindle pole / mitotic spindle / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / cell migration / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / gene expression / postsynapse / protein ubiquitination / nuclear speck / inflammatory response / positive regulation of cell population proliferation / ubiquitin protein ligase binding / centrosome / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #240 / Cullin Repeats / 5 helical Cullin repeat like / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / MATH/TRAF domain / MATH/TRAF domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #240 / Cullin Repeats / 5 helical Cullin repeat like / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Helix non-globular / Special / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Cullin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsPrive, G.G. / Errington, W.J.
CitationJournal: Structure / Year: 2012
Title: Adaptor protein self-assembly drives the control of a cullin-RING ubiquitin ligase.
Authors: Errington, W.J. / Khan, M.Q. / Bueler, S.A. / Rubinstein, J.L. / Chakrabartty, A. / Prive, G.G.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
C: Speckle-type POZ protein
B: Cullin-3
D: Cullin-3


Theoretical massNumber of molelcules
Total (without water)119,2584
Polymers119,2584
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-40 kcal/mol
Surface area40740 Å2
MethodPISA
2
A: Speckle-type POZ protein
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)59,6292
Polymers59,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10 kcal/mol
Surface area21660 Å2
MethodPISA
3
C: Speckle-type POZ protein
D: Cullin-3


Theoretical massNumber of molelcules
Total (without water)59,6292
Polymers59,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.166, 76.944, 85.834
Angle α, β, γ (deg.)90.00, 108.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 16167.548 Da / Num. of mol.: 2 / Fragment: BTB domain from SPOP, unp residues 177-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O43791
#2: Protein Cullin-3 / CUL-3


Mass: 43461.695 Da / Num. of mol.: 2 / Fragment: N-terminal domain from Cul3, unp residue 20-381 / Mutation: I342R, L346D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13618
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2007 / Details: mirrors
RadiationMonochromator: Double-crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→19.61 Å / Num. all: 51676 / Num. obs: 49937 / % possible obs: 95.6 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.052 / Net I/σ(I): 20.4
Reflection shellResolution: 2.4→2.4856 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.495 / % possible all: 74

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.61 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 30.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 2513 5.09 %Random
Rwork0.211 ---
obs0.2137 49397 95.59 %-
all-51676 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.202 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.225 Å20 Å2-0.7866 Å2
2--0.356 Å2-0 Å2
3---0.8691 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6739 0 0 46 6785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136839
X-RAY DIFFRACTIONf_angle_d1.4499186
X-RAY DIFFRACTIONf_dihedral_angle_d17.7312636
X-RAY DIFFRACTIONf_chiral_restr0.11014
X-RAY DIFFRACTIONf_plane_restr0.0051193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44610.4281010.32571860X-RAY DIFFRACTION69
2.4461-2.49590.34331270.3092193X-RAY DIFFRACTION81
2.4959-2.55010.34641360.31462498X-RAY DIFFRACTION92
2.5501-2.60930.38311410.30082669X-RAY DIFFRACTION98
2.6093-2.67440.33061470.27742702X-RAY DIFFRACTION100
2.6744-2.74650.31241330.28392729X-RAY DIFFRACTION100
2.7465-2.82710.39771400.27472711X-RAY DIFFRACTION100
2.8271-2.9180.34831270.26252684X-RAY DIFFRACTION100
2.918-3.0220.32861180.2472759X-RAY DIFFRACTION100
3.022-3.14250.3081570.25282692X-RAY DIFFRACTION100
3.1425-3.28490.27641400.23172704X-RAY DIFFRACTION99
3.2849-3.45720.25641400.22072707X-RAY DIFFRACTION99
3.4572-3.67250.27591600.20882688X-RAY DIFFRACTION99
3.6725-3.95390.25271460.18742681X-RAY DIFFRACTION99
3.9539-4.34790.22671640.16832663X-RAY DIFFRACTION98
4.3479-4.96810.20171570.16572682X-RAY DIFFRACTION98
4.9681-6.22580.27151520.20042728X-RAY DIFFRACTION99
6.2258-19.61060.2471270.21662534X-RAY DIFFRACTION90
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)
17.8533-1.86412.93223.5855-1.9052.870.09331.4474-0.15451.9121-0.38541.5989-0.37710.4144-0.14871.3741-0.49180.29891.0608-0.08321.667355.960324.856817.2368
23.15730.9621-0.84016.0905-4.19833.77060.19820.679-0.689-0.12580.49061.82752.166-0.582-0.56220.7078-0.151-0.02330.57230.06230.670868.778226.48715.1072
35.3893-5.5762-5.9235.9416.41437.02280.57031.75820.2605-0.7463-1.04050.09910.0199-1.49330.34470.7782-0.11470.03350.8376-0.03980.505579.239529.3095-2.354
48.3993-0.815-4.6327.2986-4.50396.55560.08680.0349-0.13820.7134-0.1559-0.05080.4646-0.24930.06290.433-0.11560.01610.4251-0.02090.489784.649830.491810.0558
54.211-3.0214.08062.2749-2.94943.9390.5191-0.36270.5591-1.86750.3751-0.2924-1.033-0.3882-0.9320.8502-0.18820.1660.72350.10320.767492.944336.78632.9094
64.231-1.2123-2.08574.3455-2.42875.0545-1.38631.3965-0.2034-2.16151.0591-0.8175-0.54540.35130.01810.8625-0.34040.02570.6773-0.03180.630488.721624.3991-1.6699
79.0837-7.7948-4.84757.64565.54366.5260.27870.7287-1.329-1.32380.18750.68530.5276-0.6953-0.32350.9331-0.1806-0.03810.4529-0.03020.647377.976520.05074.222
86.6738-6.22520.48346.12150.77254.34310.5706-0.5074-1.6746-1.9428-0.02481.24650.3124-0.0837-0.72770.9108-0.2898-0.02630.5440.03141.066574.905911.46456.2145
92.61340.9189-1.80629.2962-0.34984.3181-0.0669-0.528-0.53460.2877-0.10480.27760.13680.34430.07560.7899-0.07460.10380.47020.10260.673383.746913.871911.9932
102.57421.2921-0.28872.1896-1.53221.2256-0.0586-0.2236-0.87171.5699-0.0021-0.92741.1704-0.74740.2250.9761-0.2306-0.07120.73990.16890.619475.322727.198519.5413
118.4088-7.2455-6.32536.67576.11515.6092-0.4124-0.39960.7731-0.75110.6446-0.5149-0.35650.4979-0.05890.5951-0.1097-0.05630.53670.06370.528173.858945.618313.7741
128.2684-3.1250.1493.768-3.84996.47350.05040.87520.6575-1.0721-0.6117-0.1874-0.2280.39540.1720.7374-0.1101-0.07680.57340.05890.444366.039142.78543.4039
138.2777-3.1771-6.30876.26171.25457.15741.7605-0.35841.7859-0.7930.20320.2806-1.94410.3082-1.51581.2345-0.2091-0.0850.68180.10731.038264.46450.81912.706
148.3746-1.3843-0.50146.1764-0.11856.1871-0.196-0.9043-0.16110.9302-0.00290.8860.1455-0.34040.24260.684-0.10520.08540.7049-0.00720.622158.894237.360720.8014
157.2295-1.287-0.06476.42481.19997.57540.00720.5722-0.4131-0.8011-0.0088-0.17930.50480.59980.06860.6633-0.0160.0970.53490.01740.4003104.026223.84236.1081
164.80683.42981.04979.07153.7465.2499-0.24060.18980.0327-0.2310.31820.14380.1440.3157-0.11070.40810.07090.01130.52650.03720.3553107.480834.118819.8665
175.1185-1.29660.58733.24644.37576.9152-0.38310.3508-0.0945-0.13170.09110.1974-0.05460.07230.20070.459-0.08480.00990.49540.00690.5261108.763348.593334.3185
185.85953.79663.36032.63231.7672.8028-0.432-0.26950.5523-0.66940.1644-0.4752-1.11030.3237-0.41420.7380.001-0.05290.58350.040.7278112.635255.969350.8182
193.6152-1.18211.34235.13872.98559.835-0.4031-0.08050.45290.2973-0.13130.4723-0.4808-0.39820.66860.43020.0404-0.01460.3898-0.02890.6081102.276754.966850.2254
206.3028-0.3734-0.66796.8161-0.10856.9818-0.3061-0.93131.14991.1572-0.04990.9049-0.9953-0.39880.24560.75110.1283-0.04540.6079-0.11980.7555101.852459.649667.7208
212.2464-0.1980.85191.4968-1.65484.65350.4631-1.29260.23891.0645-2.35442.4356-1.0568-1.13080.94851.3963-0.20390.61291.2585-0.08411.0812100.960355.372778.4239
225.8764-5.5009-5.7455.03215.30045.5550.2648-0.34571.1408-0.66280.47790.5257-0.7237-0.1865-0.61770.98430.012-0.13290.6958-0.14821.059447.356956.54191.8775
232.6951-0.1165-0.61953.09081.72727.4179-0.30090.25040.3284-0.32130.06770.1077-0.89330.05870.14930.6637-0.0375-0.19450.64070.00870.777949.587245.0803-8.7175
245.8724-1.4507-2.38415.96824.71546.1276-0.50180.6175-0.0385-0.8040.3044-0.4074-0.5330.6930.00660.879-0.244-0.0841.08220.0880.614652.702233.7424-31.6449
252.0285-0.9772-0.84377.77786.55745.2155-0.09690.2240.091-1.0836-0.23520.4682-1.151-0.16120.57160.6937-0.18350.04431.09-0.07550.592346.619523.7936-35.3756
262.1613-0.8703-3.65324.61021.14458.1505-0.26031.0527-0.0397-0.2050.1255-0.2444-0.5211.22020.41830.51440.03140.04731.477-0.110.815954.78816.6401-37.8097
273.1844-1.072-2.83475.34971.11773.2308-0.27721.04020.01610.19050.2071-0.41431.29090.3144-0.04990.73720.16360.0421.3378-0.05310.880853.56192.5967-48.4118
284.8494-0.5283-0.20117.88366.19674.8228-0.3211.42620.2145-0.9866-0.54780.8558-1.76460.26031.43691.12240.45440.0051.31150.12051.225349.6401-7.6435-48.9687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 179:185)
2X-RAY DIFFRACTION2chain 'A' and (resseq 186:196)
3X-RAY DIFFRACTION3chain 'A' and (resseq 197:214)
4X-RAY DIFFRACTION4chain 'A' and (resseq 215:230)
5X-RAY DIFFRACTION5chain 'A' and (resseq 231:238)
6X-RAY DIFFRACTION6chain 'A' and (resseq 239:247)
7X-RAY DIFFRACTION7chain 'A' and (resseq 248:260)
8X-RAY DIFFRACTION8chain 'A' and (resseq 261:269)
9X-RAY DIFFRACTION9chain 'A' and (resseq 270:292)
10X-RAY DIFFRACTION10chain 'C' and (resseq 180:196)
11X-RAY DIFFRACTION11chain 'C' and (resseq 197:214)
12X-RAY DIFFRACTION12chain 'C' and (resseq 215:238)
13X-RAY DIFFRACTION13chain 'C' and (resseq 239:247)
14X-RAY DIFFRACTION14chain 'C' and (resseq 248:295)
15X-RAY DIFFRACTION15chain 'B' and (resseq 24:69)
16X-RAY DIFFRACTION16chain 'B' and (resseq 70:154)
17X-RAY DIFFRACTION17chain 'B' and (resseq 155:205)
18X-RAY DIFFRACTION18chain 'B' and (resseq 206:227)
19X-RAY DIFFRACTION19chain 'B' and (resseq 228:268)
20X-RAY DIFFRACTION20chain 'B' and (resseq 269:308)
21X-RAY DIFFRACTION21chain 'B' and (resseq 309:325)
22X-RAY DIFFRACTION22chain 'D' and (resseq 24:45)
23X-RAY DIFFRACTION23chain 'D' and (resseq 46:154)
24X-RAY DIFFRACTION24chain 'D' and (resseq 155:194)
25X-RAY DIFFRACTION25chain 'D' and (resseq 195:226)
26X-RAY DIFFRACTION26chain 'D' and (resseq 227:268)
27X-RAY DIFFRACTION27chain 'D' and (resseq 269:308)
28X-RAY DIFFRACTION28chain 'D' and (resseq 309:324)

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