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- PDB-7d3d: Crystal structure of SPOP bound with a peptide -

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Basic information

Entry
Database: PDB / ID: 7d3d
TitleCrystal structure of SPOP bound with a peptide
Components
  • GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR
  • Speckle-type POZ protein
KeywordsPROTEIN BINDING / ccRCC / E3 ligase adaptor SPOP / ubiquitination / SBC motif(F-pS-S/T-S/T / F is nonpolar / p is polar)
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SPOP, C-terminal BACK domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYang, C.-G. / Gan, J.H.
CitationJournal: Chin.J.Chem. / Year: 2021
Title: A peptide binder of E3 ligase adaptor SPOP disrupts oncogenic SPOP-protein interactions in kidney cancer cells.
Authors: Wang, Z. / Zhang, H. / Chen, B. / Ouyang, T. / Zheng, T. / Zhou, R. / Dong, Z. / Huang, Y. / Zhang, T. / Jiang, H. / Gan, J. / Luo, C. / Yang, C.-G.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
a: GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR
B: Speckle-type POZ protein
b: GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8165
Polymers34,7244
Non-polymers921
Water6,539363
1
A: Speckle-type POZ protein
a: GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4543
Polymers17,3622
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-5 kcal/mol
Surface area8030 Å2
MethodPISA
2
B: Speckle-type POZ protein
b: GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR


Theoretical massNumber of molelcules
Total (without water)17,3622
Polymers17,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.196, 58.555, 94.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16141.605 Da / Num. of mol.: 2 / Fragment: UNP residues 28-166
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 GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR


Mass: 1220.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium acetate trihydrate, pH 7.0, 20%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9735 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.44→49.73 Å / Num. obs: 50483 / % possible obs: 98.1 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Χ2: 1.011 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.56.90.47442770.8970.1890.5120.8984.4
1.5-1.568.50.36648920.9430.1290.3890.95996.3
1.56-1.6312.20.28850690.9780.0840.31.009100
1.63-1.7213.20.22550910.9870.0640.2341.054100
1.72-1.8312.60.17151120.9910.050.1791.106100
1.83-1.9713.30.12850980.9950.0360.1331.13100
1.97-2.1712.80.09851160.9960.0280.1021.151100
2.17-2.4813.20.08251670.9970.0230.0861.06100
2.48-3.12130.06652210.9980.0190.0690.917100
3.12-3012.60.05354400.9990.0160.0560.75100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVV

3ivv


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.153 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2576 5.1 %RANDOM
Rwork0.1625 ---
obs0.1639 47732 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.99 Å2 / Biso mean: 15.766 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 6 363 2754
Biso mean--29.65 28.75 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022473
X-RAY DIFFRACTIONr_bond_other_d0.0020.022305
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9653340
X-RAY DIFFRACTIONr_angle_other_deg0.86735356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05224.259108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1721513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
X-RAY DIFFRACTIONr_rigid_bond_restr1.31334778
X-RAY DIFFRACTIONr_sphericity_free25.559543
X-RAY DIFFRACTIONr_sphericity_bonded6.19755046
LS refinement shellResolution: 1.45→1.481 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.26 184 -
Rwork0.203 2660 -
obs--76.1 %
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)
10.3715-0.2180.0790.53080.28880.68320.0049-0.0154-0.01310.0176-0.0081-0.00580.0296-0.01940.00330.0134-0.00290.00590.0081-0.00180.00558.14960.7617.625
21.0099-0.2268-0.11640.6684-0.09380.47080.0935-0.0027-0.0093-0.0657-0.05390.05710.05560.0091-0.03960.03250.0114-0.00790.0109-0.00410.0071-11.08960.499-3.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 166
2X-RAY DIFFRACTION2B29 - 166

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