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- PDB-6i7a: Co-crystal structure of human SPOP MATH domain (D140N) and human ... -

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Basic information

Entry
Database: PDB / ID: 6i7a
TitleCo-crystal structure of human SPOP MATH domain (D140N) 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 / protein localization to chromatin ...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: 2.2 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 16, 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
Revision 1.4Nov 13, 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)70,2058
Polymers70,2058
Non-polymers00
Water4,702261
1
A: Speckle-type POZ protein
B: Bromodomain-containing protein 3
E: Speckle-type POZ protein
F: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)35,1024
Polymers35,1024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-9 kcal/mol
Surface area13410 Å2
MethodPISA
2
C: Speckle-type POZ protein
D: Bromodomain-containing protein 3
G: Speckle-type POZ protein
H: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)35,1024
Polymers35,1024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-8 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.351, 90.351, 166.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-226-

HOH

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Components

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


Mass: 16615.152 Da / Num. of mol.: 4 / Mutation: D140N
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.: 261 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM Sodium chloride, 100 mM HEPES pH 7.0, 20% (w/v) PEG 6000

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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: 1.95→8.72 Å / Num. obs: 51096 / % possible obs: 99.9 % / Redundancy: 8.48 % / CC1/2: 0.999 / Net I/σ(I): 14.71
Reflection shellResolution: 1.95→1.999 Å / Num. unique obs: 3725 / CC1/2: 0.271

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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: 6I41

6i41


Resolution: 2.2→19.912 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1468 4.11 %RANDOM
Rwork0.1981 ---
obs0.1996 48938 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 0 261 4673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034506
X-RAY DIFFRACTIONf_angle_d0.5596103
X-RAY DIFFRACTIONf_dihedral_angle_d2.5642886
X-RAY DIFFRACTIONf_chiral_restr0.041695
X-RAY DIFFRACTIONf_plane_restr0.004771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.30571440.26973351X-RAY DIFFRACTION100
2.2786-2.36970.28461440.24973364X-RAY DIFFRACTION100
2.3697-2.47730.31641430.25143348X-RAY DIFFRACTION100
2.4773-2.60770.29931460.24153391X-RAY DIFFRACTION100
2.6077-2.77060.29311450.23973393X-RAY DIFFRACTION100
2.7706-2.98390.30431450.23033387X-RAY DIFFRACTION100
2.9839-3.2830.27031470.20763434X-RAY DIFFRACTION100
3.283-3.75530.22921480.18793448X-RAY DIFFRACTION100
3.7553-4.72080.18041490.16243484X-RAY DIFFRACTION100
4.7208-19.91270.21191570.1923656X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.9389 Å / Origin y: 13.1948 Å / Origin z: -0.6617 Å
111213212223313233
T0.3468 Å2-0.0028 Å2-0.0636 Å2-0.3137 Å2-0.0412 Å2--0.3891 Å2
L1.1062 °20.2915 °2-1.1277 °2-0.3229 °2-0.5291 °2--1.8509 °2
S0.0391 Å °-0.0375 Å °0.0443 Å °0.0021 Å °-0.0061 Å °0.0346 Å °-0.0386 Å °0.0573 Å °-0.0358 Å °
Refinement TLS groupSelection details: all

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