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- PDB-8bdy: Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 9 -

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Basic information

Entry
Database: PDB / ID: 8bdy
TitleCrystal structure of TRIM33 alpha PHD-Bromo domain in complex with 9
ComponentsE3 ubiquitin-protein ligase TRIM33
KeywordsTRANSCRIPTION / TRIM33 alpha / PHD-Bromo domain / complex
Function / homology
Function and homology information


co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription ...co-SMAD binding / regulation of transforming growth factor beta receptor signaling pathway / Germ layer formation at gastrulation / R-SMAD binding / negative regulation of BMP signaling pathway / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger ...B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
1,3-dimethylbenzimidazol-2-one / E3 ubiquitin-protein ligase TRIM33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsTassone, G. / Pozzi, C. / Palomba, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2022
Title: Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design.
Authors: Palomba, T. / Tassone, G. / Vacca, C. / Bartalucci, M. / Valeri, A. / Pozzi, C. / Cross, S. / Siragusa, L. / Desantis, J.
History
DepositionOct 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4035
Polymers24,0701
Non-polymers3334
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-6 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.965, 79.965, 135.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1218-

HOH

21A-1219-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM33 / Ectodermin homolog / RET-fused gene 7 protein / Protein Rfg7 / RING-type E3 ubiquitin transferase ...Ectodermin homolog / RET-fused gene 7 protein / Protein Rfg7 / RING-type E3 ubiquitin transferase TRIM33 / Transcription intermediary factor 1-gamma / TIF1-gamma / Tripartite motif-containing protein 33


Mass: 24069.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UPN9, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-QCU / 1,3-dimethylbenzimidazol-2-one


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium chloride and 20 % wt/vol PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→135.5 Å / Num. obs: 5355 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.051 / Rrim(I) all: 0.189 / Net I/σ(I): 10
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.079 / Num. unique obs: 761 / CC1/2: 0.827 / R split: 2.2 / Rpim(I) all: 0.29 / Rrim(I) all: 1.118 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U5M

3u5m


Resolution: 3.05→69.25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.98 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33422 256 4.8 %RANDOM
Rwork0.22865 ---
obs0.23379 5062 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.6698 Å
Refinement stepCycle: 1 / Resolution: 3.05→69.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 15 20 1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151306
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6582042
X-RAY DIFFRACTIONr_angle_other_deg1.2061.5832991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8455187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30423.38268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.32515210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.558155
X-RAY DIFFRACTIONr_chiral_restr0.0680.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021704
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1057.834757
X-RAY DIFFRACTIONr_mcbond_other6.1067.835756
X-RAY DIFFRACTIONr_mcangle_it9.3911.716941
X-RAY DIFFRACTIONr_mcangle_other9.38511.715942
X-RAY DIFFRACTIONr_scbond_it5.7997.897734
X-RAY DIFFRACTIONr_scbond_other5.7957.9735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.04511.8121102
X-RAY DIFFRACTIONr_long_range_B_refined13.90293.7781752
X-RAY DIFFRACTIONr_long_range_B_other13.89893.7651753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 23 -
Rwork0.345 363 -
obs--100 %

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