[English] 日本語
Yorodumi
- PDB-5h1v: Complex structure of TRIM24 PHD-bromodomain and inhibitor 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h1v
TitleComplex structure of TRIM24 PHD-bromodomain and inhibitor 6
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 / male germ cell nucleus ...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 / male germ cell nucleus / nuclear receptor binding / lysine-acetylated histone binding / regulation of protein stability / euchromatin / protein catabolic process / RING-type E3 ubiquitin transferase / response to peptide hormone / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / p53 binding / ubiquitin protein ligase activity / 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 / Zinc finger, RING-type, conserved site ...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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / 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 RING-type profile. / Zinc finger, FYVE/PHD-type / Zinc finger, RING-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
2-Hydrazino-1,3-benzothiazole-6-carbohydrazide / Transcription intermediary factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,2499
Polymers42,4632
Non-polymers7867
Water2,576143
1
A: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6645
Polymers21,2311
Non-polymers4324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription intermediary factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5854
Polymers21,2311
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.028, 36.027, 113.207
Angle α, β, γ (deg.)90.000, 96.880, 90.000
Int Tables number4
Space group name H-MP1211

-
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.: 2 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7FU / 2-Hydrazino-1,3-benzothiazole-6-carbohydrazide


Mass: 223.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N5OS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 27040 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Χ2: 0.931 / Net I/av σ(I): 19.897 / Net I/σ(I): 6.5 / Num. measured all: 126161
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.074.70.39726260.9260.2020.4470.62598.6
2.07-2.154.50.29826660.940.1560.3380.58198.3
2.15-2.254.50.24526840.9450.1290.2780.75998.2
2.25-2.374.80.18127300.9760.0910.2040.67299.7
2.37-2.524.80.13926800.9850.0710.1570.70499.1
2.52-2.714.70.1126910.9880.0560.1240.77798.6
2.71-2.994.60.08526780.9920.0440.0960.93398
2.99-3.424.90.06927500.9940.0350.0781.19199.4
3.42-4.314.50.05626910.9960.0290.0641.50197.2
4.31-404.60.05328440.9970.0270.061.53598.6

-
Processing

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

5h1t


Resolution: 2.002→37.464 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1359 5.03 %
Rwork0.1804 25650 -
obs0.1825 27009 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.54 Å2 / Biso mean: 34.8989 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 2.002→37.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 44 143 2947
Biso mean--51.2 35.67 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062861
X-RAY DIFFRACTIONf_angle_d0.7573868
X-RAY DIFFRACTIONf_chiral_restr0.047415
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d12.911737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0021-2.07360.24521120.17792451256396
2.0736-2.15660.25171380.18752528266698
2.1566-2.25480.25271350.18782549268498
2.2548-2.37360.23171260.186326182744100
2.3736-2.52230.2571400.18462545268599
2.5223-2.7170.23881240.19952566269099
2.717-2.99030.2641350.20642566270198
2.9903-3.42280.24161670.19882580274799
3.4228-4.31130.18071400.1582560270097
4.3113-37.47040.18541420.16522687282998
Refinement TLS params.Method: refined / Origin x: 13.2478 Å / Origin y: -0.6278 Å / Origin z: 13.045 Å
111213212223313233
T0.158 Å20.0035 Å20.0407 Å2-0.1431 Å2-0.012 Å2--0.2219 Å2
L0.2298 °20.0113 °20.2981 °2-0.4077 °20.0926 °2--1.3619 °2
S-0.0083 Å °-0.0324 Å °0.0123 Å °0.0967 Å °0.0247 Å °0.0289 Å °-0.0261 Å °-0.0258 Å °-0.0144 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA825 - 1006
2X-RAY DIFFRACTION1allB825 - 1006
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD0 - 1
5X-RAY DIFFRACTION1allF1 - 54
6X-RAY DIFFRACTION1allF55 - 155
7X-RAY DIFFRACTION1allE2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more