[English] 日本語
Yorodumi
- PDB-3u78: E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u78
TitleE67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 Jumonji demethylase
ComponentsLysine-specific demethylase 7
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / epigenetics / histone lysine demethylation / BIX analogs / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding ...histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / HDMs demethylate histones / Signaling by BRAF and RAF1 fusions / iron ion binding / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Chem-E67 / NICKEL (II) ION / Lysine-specific demethylase 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.689 Å
AuthorsUpadhyay, A.K. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: An Analog of BIX-01294 Selectively Inhibits a Family of Histone H3 Lysine 9 Jumonji Demethylases.
Authors: Upadhyay, A.K. / Rotili, D. / Han, J.W. / Hu, R. / Chang, Y. / Labella, D. / Zhang, X. / Yoon, Y.S. / Mai, A. / Cheng, X.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Sep 13, 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_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_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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0918
Polymers46,0811
Non-polymers1,0107
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.429, 77.429, 289.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-809-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 7 / KIAA1718 / JmjC domain-containing histone demethylation protein 1D


Mass: 46081.043 Da / Num. of mol.: 1 / Fragment: Jumonji domain (UNP residues 92-488)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM1D, KDM7, KIAA1718 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZMT4, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

-
Non-polymers , 7 types, 52 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-E67 / 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine


Mass: 549.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H47N7O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 15-20% v/v PEG5000 MME, 0.2 M calcium chloride, 0.1 M Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2010
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.689→26.593 Å / Num. all: 14476 / Num. obs: 14476 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Biso Wilson estimate: 48.26 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 25.5
Reflection shellResolution: 2.689→2.89 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1324 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_336)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KVA

3kva


Resolution: 2.689→26.593 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1448 10.01 %RANDOM
Rwork0.1984 ---
obs0.2051 14472 95.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.322 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.0184 Å2-0 Å2-0 Å2
2--8.0184 Å20 Å2
3----16.0368 Å2
Refinement stepCycle: LAST / Resolution: 2.689→26.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 52 45 3037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083067
X-RAY DIFFRACTIONf_angle_d1.1954156
X-RAY DIFFRACTIONf_dihedral_angle_d16.3591125
X-RAY DIFFRACTIONf_chiral_restr0.08451
X-RAY DIFFRACTIONf_plane_restr0.006523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.689-2.78550.29191260.21361136X-RAY DIFFRACTION86
2.7855-2.89690.35981320.2381186X-RAY DIFFRACTION91
2.8969-3.02860.30131360.22871227X-RAY DIFFRACTION92
3.0286-3.1880.29121420.21261275X-RAY DIFFRACTION95
3.188-3.38730.28231430.21861286X-RAY DIFFRACTION96
3.3873-3.64830.28831470.19121316X-RAY DIFFRACTION98
3.6483-4.01430.28531490.18911351X-RAY DIFFRACTION99
4.0143-4.59260.20971510.15831361X-RAY DIFFRACTION99
4.5926-5.77640.22131540.16121378X-RAY DIFFRACTION98
5.7764-26.59430.23541680.20071508X-RAY DIFFRACTION98

+
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