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- PDB-5h1u: Complex structure of TRIM24 PHD-bromodomain and inhibitor 2 -

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Basic information

Entry
Database: PDB / ID: 5h1u
TitleComplex structure of TRIM24 PHD-bromodomain and inhibitor 2
ComponentsTranscription intermediary factor 1-alpha
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / TRANSCRIPTION TRANSCRIPTION INHIBITOR / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 / p53 binding / ubiquitin protein ligase activity / Signaling by BRAF and RAF1 fusions / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein kinase activity / protein ubiquitination / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-amino-1,3-benzothiazole-6-carboxamide / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsLiu, J.
CitationJournal: FEBS J. / Year: 2017
Title: The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network
Authors: Liu, J. / Li, F. / Bao, H. / Jiang, Y. / Zhang, S. / Ma, R. / Gao, J. / Wu, J. / Ruan, K.
History
DepositionOct 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transcription intermediary factor 1-alpha
A: 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)86,45619
Polymers84,9254
Non-polymers1,53115
Water3,801211
1
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6335
Polymers21,2311
Non-polymers4024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10390 Å2
MethodPISA
2
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5554
Polymers21,2311
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10460 Å2
MethodPISA
3
C: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6335
Polymers21,2311
Non-polymers4024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10530 Å2
MethodPISA
4
D: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6335
Polymers21,2311
Non-polymers4024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.560, 48.568, 123.374
Angle α, β, γ (deg.)86.720, 81.460, 67.900
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 827 or resseq 829:836 or (resid...
21(chain B and (resseq 827 or resseq 829:840 or (resid...
31(chain C and (resseq 827 or resseq 829:836 or (resid...
41(chain D and (resseq 827 or resseq 829:840 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and (resseq 827 or resseq 829:836 or (resid...AB8274
12CYSCYSGLYGLY(chain A and (resseq 827 or resseq 829:836 or (resid...AB829 - 8366 - 13
13GLUGLUGLUGLU(chain A and (resseq 827 or resseq 829:836 or (resid...AB83714
14ASPASPPROPRO(chain A and (resseq 827 or resseq 829:836 or (resid...AB827 - 10064 - 183
15ASPASPPROPRO(chain A and (resseq 827 or resseq 829:836 or (resid...AB827 - 10064 - 183
16ASPASPPROPRO(chain A and (resseq 827 or resseq 829:836 or (resid...AB827 - 10064 - 183
17ASPASPPROPRO(chain A and (resseq 827 or resseq 829:836 or (resid...AB827 - 10064 - 183
21ASPASPASPASP(chain B and (resseq 827 or resseq 829:840 or (resid...BA8274
22CYSCYSCYSCYS(chain B and (resseq 827 or resseq 829:840 or (resid...BA829 - 8406 - 17
23CYSCYSCYSCYS(chain B and (resseq 827 or resseq 829:840 or (resid...BA84118
24ASPASPPROPRO(chain B and (resseq 827 or resseq 829:840 or (resid...BA827 - 10064 - 183
25ASPASPPROPRO(chain B and (resseq 827 or resseq 829:840 or (resid...BA827 - 10064 - 183
26ASPASPPROPRO(chain B and (resseq 827 or resseq 829:840 or (resid...BA827 - 10064 - 183
31ASPASPASPASP(chain C and (resseq 827 or resseq 829:836 or (resid...CC8274
32CYSCYSGLYGLY(chain C and (resseq 827 or resseq 829:836 or (resid...CC829 - 8366 - 13
33GLUGLUGLUGLU(chain C and (resseq 827 or resseq 829:836 or (resid...CC83714
34PROPROPROPRO(chain C and (resseq 827 or resseq 829:836 or (resid...CC824 - 10061 - 183
35PROPROPROPRO(chain C and (resseq 827 or resseq 829:836 or (resid...CC824 - 10061 - 183
36PROPROPROPRO(chain C and (resseq 827 or resseq 829:836 or (resid...CC824 - 10061 - 183
37PROPROPROPRO(chain C and (resseq 827 or resseq 829:836 or (resid...CC824 - 10061 - 183
41ASPASPASPASP(chain D and (resseq 827 or resseq 829:840 or (resid...DD8274
42CYSCYSCYSCYS(chain D and (resseq 827 or resseq 829:840 or (resid...DD829 - 8406 - 17
43CYSCYSCYSCYS(chain D and (resseq 827 or resseq 829:840 or (resid...DD84118
44GLUGLUPROPRO(chain D and (resseq 827 or resseq 829:840 or (resid...DD826 - 10063 - 183
45GLUGLUPROPRO(chain D and (resseq 827 or resseq 829:840 or (resid...DD826 - 10063 - 183
46GLUGLUPROPRO(chain D and (resseq 827 or resseq 829:840 or (resid...DD826 - 10063 - 183

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Components

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


Mass: 21231.316 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG'
References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-6KT / 2-amino-1,3-benzothiazole-6-carboxamide


Mass: 193.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7N3OS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 2%(v/v) Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 56293 / % possible obs: 92 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.94 Å2 / Rmerge(I) obs: 0.085 / Net I/av σ(I): 8.63 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.972.40.4450.872189.5
1.97-2.052.40.3850.834192.5
2.05-2.142.50.3840.825193.5
2.14-2.252.50.2490.919187.2
2.25-2.392.50.1940.873187.9
2.39-2.582.40.1240.972193.3
2.58-2.842.60.1020.979195.7
2.84-3.252.50.0650.991194.6
3.25-4.092.50.0530.987190.5
4.09-402.50.0380.996194.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H1T

5h1t


Resolution: 1.901→33.552 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.2
RfactorNum. reflection% reflection
Rfree0.2692 2811 5.07 %
Rwork0.2252 --
obs0.2275 55456 90.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.28 Å2 / Biso mean: 34.2598 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.901→33.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 90 211 5950
Biso mean--61.55 31.79 -
Num. residues----701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075858
X-RAY DIFFRACTIONf_angle_d0.9067945
X-RAY DIFFRACTIONf_chiral_restr0.052853
X-RAY DIFFRACTIONf_plane_restr0.0061026
X-RAY DIFFRACTIONf_dihedral_angle_d13.013545
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3189X-RAY DIFFRACTION6.927TORSIONAL
12B3189X-RAY DIFFRACTION6.927TORSIONAL
13C3189X-RAY DIFFRACTION6.927TORSIONAL
14D3189X-RAY DIFFRACTION6.927TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9015-1.93430.72241440.70322210235475
1.9343-1.96940.53211240.52982429255385
1.9694-2.00730.31781370.30962691282893
2.0073-2.04830.34921010.28682710281191
2.0483-2.09280.44121400.36732646278691
2.0928-2.14150.29481540.2572743289796
2.1415-2.1950.30171400.2392761290195
2.195-2.25440.26821140.23382135224983
2.2544-2.32070.32221170.22632431254882
2.3207-2.39560.31471450.21832689283494
2.3956-2.48120.26241410.22242706284793
2.4812-2.58050.29311380.22012751288994
2.5805-2.69790.29431520.21792768292096
2.6979-2.840.29171370.21842840297796
2.84-3.01790.26341510.22462731288296
3.0179-3.25070.28041740.21552700287493
3.2507-3.57750.2521570.19672763292097
3.5775-4.09440.17971320.17752490262284
4.0944-5.15550.17381650.14132710287595
5.1555-33.55730.17271480.15152741288995
Refinement TLS params.Method: refined / Origin x: -0.9318 Å / Origin y: 0.2144 Å / Origin z: 0.1696 Å
111213212223313233
T0.1979 Å2-0.0042 Å2-0.0086 Å2-0.1449 Å2-0.0008 Å2--0.1963 Å2
L0.2444 °2-0.0192 °2-0.1157 °2--0.0059 °2-0.0477 °2--0.3256 °2
S0.0359 Å °-0.0009 Å °0.0201 Å °0.0019 Å °-0.03 Å °-0.0062 Å °0.0439 Å °0.0067 Å °-0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB827 - 1006
2X-RAY DIFFRACTION1allA827 - 1006
3X-RAY DIFFRACTION1allC824 - 1006
4X-RAY DIFFRACTION1allD826 - 1006
5X-RAY DIFFRACTION1allE0 - 4
6X-RAY DIFFRACTION1allG1 - 223
7X-RAY DIFFRACTION1allF1 - 8
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allH2 - 3

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