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- PDB-3o33: Crystal structure of TRIM24 PHD-Bromo in the free state -

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Basic information

Entry
Database: PDB / ID: 3o33
TitleCrystal structure of TRIM24 PHD-Bromo in the free state
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION / PHD finger / Bromodomain / TRIM24 / breast cancer
Function / homology
Function and homology information


perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / nuclear receptor binding / protein catabolic process / lysine-acetylated histone binding / euchromatin / RING-type E3 ubiquitin transferase / regulation of protein stability / response to peptide hormone / ubiquitin protein ligase activity / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / 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 / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Bromodomain-like / Zinc finger RING-type profile. / Histone Acetyltransferase; Chain A / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z. / Patel, D.J.
CitationJournal: Nature / Year: 2010
Title: TRIM24 links a non-canonical histone signature to breast cancer.
Authors: Tsai, W.W. / Wang, Z. / Yiu, T.T. / Akdemir, K.C. / Xia, W. / Winter, S. / Tsai, C.Y. / Shi, X. / Schwarzer, D. / Plunkett, W. / Aronow, B. / Gozani, O. / Fischle, W. / Hung, M.C. / Patel, D.J. / Barton, M.C.
History
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,79712
Polymers85,2744
Non-polymers5238
Water4,360242
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4493
Polymers21,3181
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4493
Polymers21,3181
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4493
Polymers21,3181
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4493
Polymers21,3181
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 48.498, 122.729
Angle α, β, γ (deg.)86.45, 81.46, 67.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcription intermediary factor 1-alpha / TIF1-alpha / Tripartite motif-containing protein 24 / RING finger protein 82


Mass: 21318.395 Da / Num. of mol.: 4 / Fragment: UNP residues 824-1006
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O15164
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes (pH 7.5), 2.0 M ammonium sulfate and 2% Polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2009
RadiationMonochromator: SI mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52087 / Num. obs: 50497 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.107 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4 / Num. unique all: 5031 / % possible all: 96.8

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2PUY, 2YYN

2puy

2yyn


Resolution: 2→19.69 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 2487 -Random
Rwork0.2207 ---
all-52087 --
obs-50135 96.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 8 242 5989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.2989 235 -
Rwork0.2578 --
obs-4869 93.8 %

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