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- PDB-3o37: Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 p... -

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Basic information

Entry
Database: PDB / ID: 3o37
TitleCrystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide
Components
  • Histone H3.1Histone H3
  • Transcription intermediary factor 1-alpha
KeywordsTRANSCRIPTION/Protein binding / TRIM24 / PHD finger / Bromodomain / unmodified H3K4 / breast cancer / TRANSCRIPTION / TRANSCRIPTION-Protein binding complex
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / Signaling by FGFR1 in disease ...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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / Signaling by FGFR1 in disease / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / Defective pyroptosis / HDACs deacetylate histones / nuclear receptor binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / protein catabolic process / lysine-acetylated histone binding / euchromatin / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / regulation of protein stability / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / response to peptide hormone / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin protein ligase activity / negative regulation of epithelial cell proliferation / nucleosome / Signaling by BRAF and RAF1 fusions / p53 binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / regulation of apoptotic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / protein kinase activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / protein-containing complex / mitochondrion / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Zinc finger RING-type profile. / Histone Acetyltransferase; Chain A / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / 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 / Histone H3.1
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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
E: Histone H3.1
F: Histone H3.1
G: Histone H3.1
H: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,39816
Polymers89,8758
Non-polymers5238
Water4,252236
1
A: Transcription intermediary factor 1-alpha
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6004
Polymers22,4692
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
F: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6004
Polymers22,4692
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription intermediary factor 1-alpha
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6004
Polymers22,4692
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription intermediary factor 1-alpha
H: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6004
Polymers22,4692
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.667, 63.848, 79.299
Angle α, β, γ (deg.)89.92, 89.99, 89.80
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: Protein/peptide
Histone H3.1 / Histone H3


Mass: 1150.332 Da / Num. of mol.: 4 / Fragment: UNP residues 2-11 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , 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 6, 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. obs: 47703 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.092 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 4754 / Rsym value: 0.491 / % possible all: 99.5

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.67 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2339 -RANDOM
Rwork0.227 ---
all-47279 --
obs-46640 98.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 8 236 6308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.304 250 -
Rwork0.269 --
obs-4707 99.5 %

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