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- PDB-6i5p: Co-crystal structure of human SPOP MATH domain (E47K) and human B... -

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Basic information

Entry
Database: PDB / ID: 6i5p
TitleCo-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment
Components
  • Bromodomain-containing protein 3
  • Speckle-type POZ protein
KeywordsLIGASE / ligase nuclear cancer ubiquitination
Function / homology
Function and homology information


regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding ...regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / chromatin remodeling / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SPOP, C-terminal 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. ...SPOP, C-terminal 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. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / SKP1/BTB/POZ domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsOstertag, M.S. / Popowicz, G.M. / Sattler, M.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structural Insights into BET Client Recognition of Endometrial and Prostate Cancer-Associated SPOP Mutants.
Authors: Ostertag, M.S. / Hutwelker, W. / Plettenburg, O. / Sattler, M. / Popowicz, G.M.
History
DepositionNov 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 15, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 24, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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: Bromodomain-containing protein 3
C: Speckle-type POZ protein
D: Bromodomain-containing protein 3
E: Speckle-type POZ protein
F: Bromodomain-containing protein 3
G: Speckle-type POZ protein
H: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)70,2098
Polymers70,2098
Non-polymers00
Water8,755486
1
A: Speckle-type POZ protein
B: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5522
Polymers17,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-2 kcal/mol
Surface area7680 Å2
MethodPISA
2
C: Speckle-type POZ protein
D: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5522
Polymers17,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area7430 Å2
MethodPISA
3
E: Speckle-type POZ protein
F: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5522
Polymers17,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2 kcal/mol
Surface area7520 Å2
MethodPISA
4
G: Speckle-type POZ protein
H: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5522
Polymers17,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-1 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.962, 90.334, 88.863
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16616.203 Da / Num. of mol.: 4 / Mutation: E47K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43791
#2: Protein/peptide
Bromodomain-containing protein 3 / RING3-like protein


Mass: 935.995 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15059
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200mM Ammonium Acetate, 100mM Tris pH 8.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.71→45.17 Å / Num. obs: 71635 / % possible obs: 98.6 % / Redundancy: 3.23 % / Rrim(I) all: 0.058 / Net I/σ(I): 11.82
Reflection shellResolution: 1.71→1.754 Å / Num. unique obs: 11784

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVV

3ivv


Resolution: 1.81→19.931 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 3085 4.84 %RANDOM
Rwork0.1885 ---
obs0.1904 63697 98.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→19.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 0 486 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014569
X-RAY DIFFRACTIONf_angle_d1.0536168
X-RAY DIFFRACTIONf_dihedral_angle_d5.9792712
X-RAY DIFFRACTIONf_chiral_restr0.069694
X-RAY DIFFRACTIONf_plane_restr0.007774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.83830.39741230.32142745X-RAY DIFFRACTION99
1.8383-1.86840.34031370.31062786X-RAY DIFFRACTION99
1.8684-1.90060.32791560.28472687X-RAY DIFFRACTION97
1.9006-1.93510.30961470.26242631X-RAY DIFFRACTION95
1.9351-1.97230.25581010.2412760X-RAY DIFFRACTION98
1.9723-2.01250.2995950.22932819X-RAY DIFFRACTION99
2.0125-2.05630.23451410.22842788X-RAY DIFFRACTION99
2.0563-2.1040.27711420.23212680X-RAY DIFFRACTION98
2.104-2.15660.25611330.21622780X-RAY DIFFRACTION100
2.1566-2.21480.2521610.20352758X-RAY DIFFRACTION100
2.2148-2.27990.28171510.2112724X-RAY DIFFRACTION98
2.2799-2.35340.27191380.20332802X-RAY DIFFRACTION100
2.3534-2.43740.25751370.2092747X-RAY DIFFRACTION100
2.4374-2.53480.24611190.20362839X-RAY DIFFRACTION100
2.5348-2.64990.22931340.20072779X-RAY DIFFRACTION99
2.6499-2.78920.25881630.19922690X-RAY DIFFRACTION97
2.7892-2.96350.24471630.18732762X-RAY DIFFRACTION99
2.9635-3.19140.20921690.17462751X-RAY DIFFRACTION100
3.1914-3.5110.24231470.1742748X-RAY DIFFRACTION98
3.511-4.01540.22121220.16282771X-RAY DIFFRACTION98
4.0154-5.04540.15161670.14272754X-RAY DIFFRACTION98
5.0454-19.93260.2121390.18792811X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -1.3348 Å / Origin y: -9.7848 Å / Origin z: 23.0198 Å
111213212223313233
T0.1529 Å20.0148 Å20.0045 Å2-0.2175 Å2-0.0317 Å2--0.2401 Å2
L0.1173 °20.1986 °2-0.1829 °2-1.7161 °2-1.7129 °2--2.1621 °2
S-0.0121 Å °0.0055 Å °-0.019 Å °-0.1758 Å °0.0486 Å °0.0053 Å °0.1902 Å °-0.0263 Å °-0.0453 Å °
Refinement TLS groupSelection details: all

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