[English] 日本語
Yorodumi
- PDB-6h8p: JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h8p
TitleJMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
Components
  • Histone H1.4
  • Lysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / DEMETHYLASE / HISTONE / JMJC DOMAIN / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / cardiac muscle hypertrophy in response to stress / chromosome condensation / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / cardiac muscle hypertrophy in response to stress / chromosome condensation / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / nucleosomal DNA binding / positive regulation of neuron differentiation / methylated histone binding / negative regulation of autophagy / response to nutrient levels / euchromatin / HDMs demethylate histones / chromatin DNA binding / fibrillar center / histone deacetylase binding / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / double-stranded DNA binding / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain ...: / : / : / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H1.4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsChowdhury, R. / Walport, L.J. / Schofield, C.J.
Citation
Journal: FEBS Lett. / Year: 2018
Title: Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.
Authors: Walport, L.J. / Hopkinson, R.J. / Chowdhury, R. / Zhang, Y. / Bonnici, J. / Schiller, R. / Kawamura, A. / Schofield, C.J.
#1: Journal: Nature / Year: 2007
Title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / ...Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / Borowski, T. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4A
B: Lysine-specific demethylase 4A
C: Histone H1.4
D: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,81216
Polymers91,8314
Non-polymers98212
Water8,179454
1
A: Lysine-specific demethylase 4A
C: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4989
Polymers45,9152
Non-polymers5837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-24 kcal/mol
Surface area15080 Å2
MethodPISA
2
B: Lysine-specific demethylase 4A
D: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3147
Polymers45,9152
Non-polymers3995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-26 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.722, 150.146, 57.601
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3
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 H1.4 / Histone H1b / Histone H1s-4


Mass: 1588.978 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10412

-
Non-polymers , 6 types, 466 molecules

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


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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MIB buffer (malonic acid/imidazole/boric acid, pH 6.0) 25% w/v polyethylene glycol 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.98→47.45 Å / Num. obs: 60704 / % possible obs: 99.1 % / Redundancy: 8.1 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.5
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5991 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OX0

2ox0


Resolution: 1.983→47.44 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 2968 4.9 %
Rwork0.192 --
obs0.193 60572 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 48.3 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 56 Å2
Refinement stepCycle: LAST / Resolution: 1.983→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 50 454 6183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055950
X-RAY DIFFRACTIONf_angle_d0.8868079
X-RAY DIFFRACTIONf_dihedral_angle_d15.5333488
X-RAY DIFFRACTIONf_chiral_restr0.049832
X-RAY DIFFRACTIONf_plane_restr0.0081043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9826-2.01510.30221330.31132459X-RAY DIFFRACTION90
2.0151-2.04990.32371470.30222718X-RAY DIFFRACTION100
2.0499-2.08710.32131430.28742721X-RAY DIFFRACTION99
2.0871-2.12730.27061180.27312772X-RAY DIFFRACTION99
2.1273-2.17070.28131410.25962694X-RAY DIFFRACTION100
2.1707-2.21790.30121330.26092767X-RAY DIFFRACTION100
2.2179-2.26950.28081320.25292731X-RAY DIFFRACTION100
2.2695-2.32620.28151740.25632734X-RAY DIFFRACTION100
2.3262-2.38910.27731300.23962756X-RAY DIFFRACTION99
2.3891-2.45940.2371410.23272735X-RAY DIFFRACTION99
2.4594-2.53880.27171580.2262726X-RAY DIFFRACTION100
2.5388-2.62950.25051390.23042786X-RAY DIFFRACTION100
2.6295-2.73480.25371410.2252567X-RAY DIFFRACTION93
2.7348-2.85930.27671320.22422762X-RAY DIFFRACTION99
2.8593-3.010.24321310.20682805X-RAY DIFFRACTION100
3.01-3.19850.20631410.18862774X-RAY DIFFRACTION100
3.1985-3.44540.19861370.17892811X-RAY DIFFRACTION100
3.4454-3.7920.16641330.16312816X-RAY DIFFRACTION100
3.792-4.34040.16391590.14632811X-RAY DIFFRACTION100
4.3404-5.46720.15731510.12972698X-RAY DIFFRACTION95
5.4672-47.4540.1931540.18532961X-RAY DIFFRACTION98
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)
10.04340.01160.00340.0205-0.04230.04770.02890.12030.1987-0.2357-0.1275-0.37590.18860.34240.00010.58520.0510.08180.33350.02340.3765125.90722.6362-8.1191
20.8076-0.2791-0.26810.2881-0.12170.25550.07580.05580.3075-0.31630.10350.12010.2764-0.14360.14810.5475-0.0984-0.10170.32760.07180.2932107.992218.2584-5.5702
30.12010.06610.14990.10880.15440.3236-0.14360.0883-0.0051-0.35770.57380.35640.431-0.29880.2237-0.3385-0.7374-0.74810.3286-0.09010.36994.553918.1451.6877
40.125-0.0760.00090.03550.00270.1850.12640.07650.0616-0.21010.16220.28240.0807-0.52170.18490.3645-0.082-0.19090.52080.22070.520997.774433.6339-3.6537
50.878-0.3291-0.03990.5211-0.55770.83880.0038-0.17820.0143-0.18040.12960.06510.3713-0.19610.06830.3549-0.0921-0.09930.22430.02210.2522111.257220.37453.4087
60.1314-0.21680.16410.1328-0.16310.13740.0421-0.0218-0.0737-0.12480.0035-0.10170.1513-0.018900.34380.0204-0.02770.33070.04180.414127.956612.97612.5177
70.07070.0159-0.02920.0325-0.01440.02630.40910.3974-0.397-0.3775-0.30040.67710.2196-0.1591-0.0020.55530.1175-0.18360.4826-0.12020.4462107.380547.1301-30.0057
80.40870.26360.21690.37040.18090.30130.38280.68650.0478-0.2422-0.4399-0.60340.14860.46020.1580.25190.15090.33920.79060.33930.3892134.695955.7447-28.7339
90.1905-0.1206-0.06040.1150.00420.08280.29730.3386-0.099-0.2516-0.2985-0.17530.1820.42940.07020.48870.24440.16580.57450.02180.3852136.797538.9114-27.4432
100.6359-0.31440.30210.5434-0.06910.11040.16880.1860.062-0.1138-0.315-0.04910.04270.1773-0.00140.26780.06020.04810.33780.04010.2502122.972753.9721-21.0606
110.3474-0.30160.34460.5013-0.36280.2270.12030.15190.0807-0.1981-0.18170.13020.05760.1214-0.00410.28850.05750.0090.3224-0.01830.2522118.300753.2521-19.9604
120.0921-0.0747-0.04340.0825-0.02830.05070.0524-0.0558-0.05840.1555-0.01170.20440.0339-0.2673-00.30590.04120.00760.358-0.00290.5224100.333159.5956-14.2908
130.0040.00220.0030.00270.0030.0016-0.04770.01270.058-0.0433-0.02250.0089-0.02320.0299-00.6314-0.0788-0.01140.6410.04590.5269107.201110.98388.3312
140.00210.0002-0.00160.01220.0030.0011-0.0428-0.0230.0318-0.014-0.0427-0.01370.03290.03190.00010.63280.00850.03820.879-0.19021.215126.141862.6828-18.6713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 291 )
6X-RAY DIFFRACTION6chain 'A' and (resid 292 through 354 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 317 )
12X-RAY DIFFRACTION12chain 'B' and (resid 318 through 355 )
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 29 )
14X-RAY DIFFRACTION14chain 'D' and (resid 24 through 28 )

+
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