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- PDB-6i68: Co-crystal structure of human SPOP MATH domain (M117V) and human ... -

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Basic information

Entry
Database: PDB / ID: 6i68
TitleCo-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment
Components
  • Bromodomain-containing protein 3
  • Speckle-type POZ protein
KeywordsLIGASE / ligase nuclear cancer ubiquitination
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / lncRNA binding / endodermal cell differentiation / regulation of proteolysis / : ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / lncRNA binding / endodermal cell differentiation / regulation of proteolysis / : / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / protein polyubiquitination / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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 ...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. / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 1.85 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 15, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)70,0808
Polymers70,0808
Non-polymers00
Water8,503472
1
A: Speckle-type POZ protein
B: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5202
Polymers17,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area7560 Å2
MethodPISA
2
C: Speckle-type POZ protein
D: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5202
Polymers17,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-1 kcal/mol
Surface area7360 Å2
MethodPISA
3
E: Speckle-type POZ protein
F: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5202
Polymers17,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-1 kcal/mol
Surface area7470 Å2
MethodPISA
4
G: Speckle-type POZ protein
H: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)17,5202
Polymers17,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-2 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.775, 90.128, 88.563
Angle α, β, γ (deg.)90.00, 91.17, 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: 16584.072 Da / Num. of mol.: 4 / Mutation: M117V
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.: 472 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (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: 1.75→90.13 Å / Num. obs: 70332 / % possible obs: 99.2 % / Redundancy: 3.07 % / Rrim(I) all: 0.054 / Net I/σ(I): 10.9
Reflection shellResolution: 1.75→4.75 Å / Num. unique obs: 3410

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Processing

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

3ivv


Resolution: 1.85→19.868 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.34 / Phase error: 26.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 2795 4.69 %RANDOM
Rwork0.1964 ---
obs0.1983 59532 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 0 472 5005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064624
X-RAY DIFFRACTIONf_angle_d0.8236247
X-RAY DIFFRACTIONf_dihedral_angle_d7.5552745
X-RAY DIFFRACTIONf_chiral_restr0.053705
X-RAY DIFFRACTIONf_plane_restr0.004787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88190.38031200.32032843X-RAY DIFFRACTION99
1.8819-1.91610.31171600.27852788X-RAY DIFFRACTION99
1.9161-1.95290.29111580.25172856X-RAY DIFFRACTION100
1.9529-1.99270.26951140.24422782X-RAY DIFFRACTION99
1.9927-2.0360.25611700.23342812X-RAY DIFFRACTION99
2.036-2.08330.30221400.23442812X-RAY DIFFRACTION100
2.0833-2.13540.2936990.22322936X-RAY DIFFRACTION100
2.1354-2.19310.26111080.21942828X-RAY DIFFRACTION100
2.1931-2.25750.23961370.21612852X-RAY DIFFRACTION100
2.2575-2.33030.25321620.21772817X-RAY DIFFRACTION100
2.3303-2.41340.27181510.2232828X-RAY DIFFRACTION100
2.4134-2.50990.28241300.2232869X-RAY DIFFRACTION100
2.5099-2.62380.27731300.21472836X-RAY DIFFRACTION100
2.6238-2.76180.2751380.21532852X-RAY DIFFRACTION99
2.7618-2.93440.24911580.20632795X-RAY DIFFRACTION99
2.9344-3.16010.23691170.20442866X-RAY DIFFRACTION99
3.1601-3.47660.22471730.18462826X-RAY DIFFRACTION100
3.4766-3.97610.22971170.1722877X-RAY DIFFRACTION100
3.9761-4.99630.1771480.14582846X-RAY DIFFRACTION98
4.9963-19.86950.21431650.17922816X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 23.2426 Å / Origin y: -13.0866 Å / Origin z: 66.957 Å
111213212223313233
T0.17 Å2-0.0118 Å2-0.0029 Å2-0.1805 Å2-0.0403 Å2--0.2365 Å2
L0.1345 °2-0.0545 °2-0.0095 °2-0.468 °2-0.899 °2--2.5441 °2
S0.0051 Å °-0.008 Å °-0.0255 Å °-0.1035 Å °0.0066 Å °0.0482 Å °0.3179 Å °-0.0364 Å °-0.0151 Å °
Refinement TLS groupSelection details: all

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