[English] 日本語
Yorodumi
- PDB-3u4s: Histone Lysine demethylase JMJD2A in complex with T11C peptide su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u4s
TitleHistone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine
Components
  • HISTONE 3 TAIL ANALOG (T11C Peptide)
  • Lysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE SUBSTRATE / double-stranded beta-helix / demethylase / histone 3 tail / nucleus / OXIDOREDUCTASE-OXIDOREDUCTASE SUBSTRATE complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / negative regulation of autophagy / response to nutrient levels / 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 / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / fibrillar center / 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 / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-(carboxycarbonyl)-D-cysteine / NICKEL (II) ION / Lysine-specific demethylase 4A / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.15 Å
AuthorsMa, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases.
Authors: Woon, E.C. / Tumber, A. / Kawamura, A. / Hillringhaus, L. / Ge, W. / Rose, N.R. / Ma, J.H. / Chan, M.C. / Walport, L.J. / Che, K.H. / Ng, S.S. / Marsden, B.D. / Oppermann, U. / McDonough, M.A. / Schofield, C.J.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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 4A
B: Lysine-specific demethylase 4A
C: HISTONE 3 TAIL ANALOG (T11C Peptide)
D: HISTONE 3 TAIL ANALOG (T11C Peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,98910
Polymers90,3554
Non-polymers6356
Water7,782432
1
A: Lysine-specific demethylase 4A
C: HISTONE 3 TAIL ANALOG (T11C Peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4955
Polymers45,1772
Non-polymers3173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-16 kcal/mol
Surface area15330 Å2
MethodPISA
2
B: Lysine-specific demethylase 4A
D: HISTONE 3 TAIL ANALOG (T11C Peptide)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4955
Polymers45,1772
Non-polymers3173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-15 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.819, 150.060, 55.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, UNP residues 1-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: O75164, 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
#2: Protein/peptide HISTONE 3 TAIL ANALOG (T11C Peptide)


Mass: 851.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P68431

-
Non-polymers , 4 types, 438 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-08P / N-(carboxycarbonyl)-D-cysteine / N-oxalyl-D-cysteine


Type: D-peptide linking / Mass: 193.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7NO5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 46809 / Num. obs: 46669 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.15-2.234.40.449198.5
2.23-2.324.70.3481100
2.32-2.424.90.2641100
2.42-2.554.90.2071100
2.55-2.714.90.1491100
2.71-2.924.90.1081100
2.92-3.214.80.0761100
3.21-3.684.80.0761100
3.68-4.634.70.076199.9
4.63-504.60.036198.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.28 Å
Translation2.5 Å37.28 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
RefinementResolution: 2.15→37.281 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.27 / σ(F): 0 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1779 3.99 %
Rwork0.1811 --
obs0.1828 44595 95.84 %
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.705 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.0966 Å2-0 Å20 Å2
2---4.0892 Å2-0 Å2
3---10.1857 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 28 432 6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135947
X-RAY DIFFRACTIONf_angle_d1.1198076
X-RAY DIFFRACTIONf_dihedral_angle_d14.1032167
X-RAY DIFFRACTIONf_chiral_restr0.081823
X-RAY DIFFRACTIONf_plane_restr0.0061036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20820.27091200.23672846X-RAY DIFFRACTION85
2.2082-2.27310.27521270.22463084X-RAY DIFFRACTION91
2.2731-2.34650.25571240.21583037X-RAY DIFFRACTION90
2.3465-2.43030.2971350.20793229X-RAY DIFFRACTION94
2.4303-2.52760.2861370.21443214X-RAY DIFFRACTION95
2.5276-2.64260.27011320.21453294X-RAY DIFFRACTION97
2.6426-2.78190.29661370.2073354X-RAY DIFFRACTION98
2.7819-2.95610.26291410.20973362X-RAY DIFFRACTION98
2.9561-3.18430.20861400.19533391X-RAY DIFFRACTION99
3.1843-3.50450.21431440.19123435X-RAY DIFFRACTION100
3.5045-4.01110.22021440.16973468X-RAY DIFFRACTION100
4.0111-5.05160.16611470.13223485X-RAY DIFFRACTION100
5.0516-37.28620.18821510.16573617X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4821-0.011-0.62260.96670.33130.37820.141-0.41450.14230.4507-0.05050.2197-0.08430.1048-0.04530.45960.00060.12230.3627-0.06110.23597.1357-48.26533.2227
20.5586-0.1597-0.19420.43710.00540.22120.1041-0.1719-0.0460.2515-0.0792-0.053-0.12580.11810.01520.2621-0.0244-0.09230.24780.0110.166724.9355-52.3979-4.7976
30.26340.12790.28750.3566-0.16120.610.08690.0246-0.0566-0.13020.15160.17980.1082-0.2184-0.1160.23550.0075-0.09280.2644-0.02580.50894.7566-60.8183-16.5962
40.1864-0.1117-0.00050.09340.08680.28760.0257-0.09750.12160.3064-0.1656-0.1852-0.07470.13520.08890.3777-0.0248-0.01140.2192-0.03710.354422.9153-22.3325-19.4349
50.0809-0.1043-0.03210.13380.13990.30180.1985-0.12170.2390.1665-0.04880.176-0.1174-0.44570.11390.15780.06710.33620.2172-0.10930.4007-2.9437-20.3186-26.9872
60.4923-0.15250.0060.5864-0.21350.25840.20560.10720.41860.1546-0.1083-0.1243-0.0997-0.0395-0.06990.260.01510.1240.18150.00670.30612.2227-20.8745-32.2058
70.0637-0.00890.09560.0393-0.02410.16430.10120.1740.14130.0939-0.0499-0.0926-0.1490.25140.04950.0311-0.13310.29860.28970.39450.599128.1746-14.1907-40.6945
80.0278-0.0341-0.0070.08430.08990.18870.025-0.0021-0.070.0105-0.02440.0089-0.00490.04120.00170.3370.0102-0.11970.4237-0.08710.396726.6003-61.2913-11.3992
90.04190.3182-0.15993.133-1.57490.7940.00580.06160.1543-0.023-0.0362-0.0079-0.08510.05070.03380.50470.08220.11920.44410.10230.63867.3405-11.3617-36.4482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 8:53)
2X-RAY DIFFRACTION2chain 'A' and (resseq 54:293)
3X-RAY DIFFRACTION3chain 'A' and (resseq 294:352)
4X-RAY DIFFRACTION4chain 'B' and (resseq 7:58)
5X-RAY DIFFRACTION5chain 'B' and (resseq 59:144)
6X-RAY DIFFRACTION6chain 'B' and (resseq 145:293)
7X-RAY DIFFRACTION7chain 'B' and (resseq 294:354)
8X-RAY DIFFRACTION8chain 'C'
9X-RAY DIFFRACTION9chain 'D'

+
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