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- PDB-3hqm: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -

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Basic information

Entry
Database: PDB / ID: 3hqm
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2
Components
  • Protein cubitus interruptus
  • Speckle-type POZ protein
KeywordsPROTEIN BINDING / LIGASE / ubiquitin / E3 / SPOP / MATH / Ci / Nucleus / Ubl conjugation pathway / Developmental protein / DNA-binding / Metal-binding / Segmentation polarity protein / Zinc-finger
Function / homology
Function and homology information


N-HH ligand not bound to PTC receptor complex / Hedgehog signaling complex / Assembly of the CI containing complexes / Activation of CI / Activation of SMO / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Hedgehog 'off' state / cuticle pattern formation / Phosphorylation of CI ...N-HH ligand not bound to PTC receptor complex / Hedgehog signaling complex / Assembly of the CI containing complexes / Activation of CI / Activation of SMO / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Hedgehog 'off' state / cuticle pattern formation / Phosphorylation of CI / Phosphorylation of SMO / Nuclear CI is degraded / Assembly of the 'signalling complexes' / Ubiquitination and proteolysis of phosphorylated CI / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / heart formation / genital disc anterior/posterior pattern formation / compound eye morphogenesis / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / segment polarity determination / cAMP response element binding protein binding / positive regulation of epithelial cell differentiation / mucosal immune response / molecular function inhibitor activity / smoothened signaling pathway / Cul3-RING ubiquitin ligase complex / dendrite morphogenesis / regulation of proteolysis / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of hippo signaling / regulation of mitotic cell cycle / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hedgehog 'on' state / protein polyubiquitination / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / : / C2H2 zinc finger / MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain ...C2H2-type zinc-finger protein GLI-like / : / C2H2 zinc finger / MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Transcriptional activator cubitus interruptus
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhuang, M. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2009
Title: Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases.
Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Seyedin, S.N. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A.
History
DepositionJun 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
B: Speckle-type POZ protein
C: Protein cubitus interruptus
D: Protein cubitus interruptus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9678
Polymers35,5834
Non-polymers3844
Water6,918384
1
A: Speckle-type POZ protein
C: Protein cubitus interruptus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9834
Polymers17,7912
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-28 kcal/mol
Surface area7530 Å2
MethodPISA
2
B: Speckle-type POZ protein
D: Protein cubitus interruptus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9834
Polymers17,7912
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-28 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.281, 48.100, 49.860
Angle α, β, γ (deg.)63.00, 64.04, 62.89
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 16485.932 Da / Num. of mol.: 2 / Fragment: UNP residues 28-166 / Mutation: D140G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791
#2: Protein/peptide Protein cubitus interruptus


Mass: 1305.371 Da / Num. of mol.: 2 / Fragment: UNP residues 1356-1367 / Source method: obtained synthetically / References: UniProt: P19538
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.47 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorDate: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 31963 / Observed criterion σ(F): 0 / Redundancy: 2 % / Rsym value: 0.031 / Net I/σ(I): 30.3
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 2996 / Rsym value: 0.102

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HQH

3hqh


Resolution: 1.74→25.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.13 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21777 1582 5.1 %RANDOM
Rwork0.17717 ---
obs0.17928 29424 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0.14 Å20.12 Å2
2--0.12 Å20.29 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.74→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 20 384 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9713210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11923.786103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60115446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3891514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21082
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21619
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.51480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22322305
X-RAY DIFFRACTIONr_scbond_it1.92231038
X-RAY DIFFRACTIONr_scangle_it3.0844.5892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.8 Å / Num. reflection Rwork: 2067 / Total num. of bins used: 20
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)
10.4818-0.15410.15990.80880.18241.1570.02190.0193-0.03330.0829-0.00140.0120.06960.0104-0.0205-0.0319-0.0061-0.0042-0.01990.0054-0.0229-3.4632-6.11461.2369
20.53390.1667-0.26910.71560.20911.160.0202-0.02540.0339-0.0717-0.00640.0108-0.071-0.009-0.0138-0.02710.00570.0057-0.02450.0064-0.0239-3.9611.397722.9596
327.9033-4.5551-5.15785.84292.09556.06720.03370.5268-0.09580.31820.00740.06060.8271-0.2573-0.04120.0523-0.0754-0.0385-0.10990.0036-0.0903-7.1354-16.24272.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 165
2X-RAY DIFFRACTION2B29 - 164
3X-RAY DIFFRACTION3C1360 - 1366

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