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- PDB-9gd5: Crystal structure of apo TRIM24 PHD-BRD in C121 space group -

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Basic information

Entry
Database: PDB / ID: 9gd5
TitleCrystal structure of apo TRIM24 PHD-BRD in C121 space group
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION / Transcriptional regulation / Bromodomain / PHD
Function / homology
Function and homology information


perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / : / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / : / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / nuclear receptor binding / male germ cell nucleus / protein catabolic process / euchromatin / response to peptide hormone / RING-type E3 ubiquitin transferase / regulation of protein stability / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / ubiquitin protein ligase activity / p53 binding / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / protein kinase activity / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / chromatin / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol
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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.681 Å
AuthorsPlatt, M.A. / Kot, E. / Conway, S.J. / Koekemoer, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008784/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of apo TRIM24 PHD-BRD in C121 space group
Authors: Platt, M.A. / Kot, E. / Conway, S.J. / Koekemoer, L.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription intermediary factor 1-alpha
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2256
Polymers42,9632
Non-polymers2624
Water2,342130
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6123
Polymers21,4821
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6123
Polymers21,4821
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.9, 36.907, 129.363
Angle α, β, γ (deg.)90, 110.044, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 825 - 1006 / Label seq-ID: 3 - 184

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Transcription intermediary factor 1-alpha / TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / RING-type E3 ubiquitin ...TIF1-alpha / E3 ubiquitin-protein ligase TRIM24 / RING finger protein 82 / RING-type E3 ubiquitin transferase TIF1-alpha / Tripartite motif-containing protein 24


Mass: 21481.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Production host: Escherichia coli (E. coli)
References: UniProt: O15164, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2M ammonium sulfate, 0.1M HEPES (pH 7.9), 2% PEG400, 8% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→44.45 Å / Num. obs: 43525 / % possible obs: 95.7 % / Redundancy: 6.5 % / Rrim(I) all: 0.144 / Net I/σ(I): 1.97
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 1485 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.681→44.45 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.001 / SU ML: 0.094 / Cross valid method: NONE / ESU R: 0.117 / ESU R Free: 0.112 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2402 2124 4.881 %
Rwork0.2104 41390 -
all0.212 --
obs-43514 95.656 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.031 Å20 Å20.051 Å2
2---0.017 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.681→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 4 130 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122950
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.8573994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.763510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32610528
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.08610140
X-RAY DIFFRACTIONr_chiral_restr0.1040.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022256
X-RAY DIFFRACTIONr_nbd_refined0.2050.21234
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2142
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.217
X-RAY DIFFRACTIONr_mcbond_it2.3272.3821412
X-RAY DIFFRACTIONr_mcangle_it3.3494.2651758
X-RAY DIFFRACTIONr_scbond_it3.3892.7581538
X-RAY DIFFRACTIONr_scangle_it5.1714.9092236
X-RAY DIFFRACTIONr_lrange_it6.39828.2214390
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.055577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.108350.05007
12BX-RAY DIFFRACTIONLocal ncs0.108350.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.681-1.7240.3251130.34121800.3433370.9060.80468.71440.296
1.724-1.7710.3511420.31824740.3232680.8930.74880.0490.275
1.771-1.8230.311440.29227130.29331260.9310.93191.39480.248
1.823-1.8790.3151340.27428820.27630240.880.93899.73550.234
1.879-1.940.2591240.25729030.25730270.9470.9451000.212
1.94-2.0080.311460.23127320.23528780.9280.9621000.199
2.008-2.0840.2341440.19726320.19927760.9620.9741000.166
2.084-2.1690.2411270.19625620.19826890.9620.9751000.169
2.169-2.2650.2561370.19424120.19725490.9610.9711000.167
2.265-2.3750.2521450.19323050.19624510.9610.97699.95920.166
2.375-2.5030.2251300.1922340.19223640.970.9781000.16
2.503-2.6540.2341150.19721160.19922310.9660.9761000.174
2.654-2.8370.298960.21320240.21721200.9530.9731000.183
2.837-3.0630.224720.20918520.2119240.9660.9731000.18
3.063-3.3540.27650.20517460.20718110.9480.9741000.189
3.354-3.7470.228780.19515690.19716470.9750.9781000.187
3.747-4.3220.17710.17213830.17214540.9810.9831000.17
4.322-5.2810.174530.18811940.18812470.980.9811000.18
5.281-7.4160.246550.229210.2229760.9820.9761000.203
7.416-44.450.192330.215550.2095880.980.9811000.215

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