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- PDB-7zdd: Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex ... -

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Basic information

Entry
Database: PDB / ID: 7zdd
TitleCrystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K10ac histone peptide.
Components
  • E3 ubiquitin-protein ligase TRIM33
  • Histone H3.X
KeywordsTRANSCRIPTION / E3 ubiquitin-protein ligase / acetylation
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 / structural constituent of chromatin / nucleosome ...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 / structural constituent of chromatin / nucleosome / protein ubiquitination / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / 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, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...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, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.X / E3 ubiquitin-protein ligase TRIM33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.625 Å
AuthorsCaria, S. / Duclos, S. / Crespillo, S. / Errey, J. / Barker, J.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other governmentOUI17491 United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands for the TRIM33 alpha and TRIM33 beta Bromodomains.
Authors: Sekirnik, A.R. / Reynolds, J.K. / See, L. / Bluck, J.P. / Scorah, A.R. / Tallant, C. / Lee, B. / Leszczynska, K.B. / Grimley, R.L. / Storer, R.I. / Malattia, M. / Crespillo, S. / Caria, S. / ...Authors: Sekirnik, A.R. / Reynolds, J.K. / See, L. / Bluck, J.P. / Scorah, A.R. / Tallant, C. / Lee, B. / Leszczynska, K.B. / Grimley, R.L. / Storer, R.I. / Malattia, M. / Crespillo, S. / Caria, S. / Duclos, S. / Hammond, E.M. / Knapp, S. / Morris, G.M. / Duarte, F. / Biggin, P.C. / Conway, S.J.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM33
D: Histone H3.X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8287
Polymers23,5082
Non-polymers3205
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.13, 52.893, 105.698
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22274.467 Da / Num. of mol.: 1 / Fragment: UNP residues 882-1073
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM33, KIAA1113, RFG7, TIF1G / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UPN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Histone H3.X / Histone H3.Y2


Mass: 1233.463 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide contains an extra lysine on the C-terminus when compared with the wild-type [ARTKQTARK(ac)]
Source: (synth.) Homo sapiens (human) / References: UniProt: P0DPK5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density meas: 1 Mg/m3 / Density % sol: 45.09 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000
PH range: 5

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Data collection

DiffractionMean temperature: 197 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.625→37.385 Å / Num. obs: 16564 / % possible obs: 92.2 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Net I/σ(I): 12
Reflection shellResolution: 1.625→1.776 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 829 / CC1/2: 0.595 / Rpim(I) all: 0.462 / % possible all: 57.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC1.1.7 (20200918)data reduction
STARANISOVersion 2.3.46 (17-Sep-2020data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MR8

5mr8


Resolution: 1.625→37.38 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 841 -RANDOM
Rwork0.2077 ---
obs0.2099 16564 63 %-
Displacement parametersBiso mean: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.3863 Å20 Å20 Å2
2---1.2933 Å20 Å2
3---0.907 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.625→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 11 182 1699
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081573HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862130HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d559SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes261HARMONIC5
X-RAY DIFFRACTIONt_it1553HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion200SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1470SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion16.39
LS refinement shellResolution: 1.625→1.72 Å
RfactorNum. reflection% reflection
Rfree0.3204 16 -
Rwork0.2844 --
obs--9.62 %

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