[English] 日本語
Yorodumi
- PDB-5tvr: JMJD2A in complex with Ni(II) and alpha-Ketoglutarate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tvr
TitleJMJD2A in complex with Ni(II) and alpha-Ketoglutarate
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / oxidoreductase demethylase monooxygenase epigenetics
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 / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / 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. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsCascella, B. / Lee, S.G. / Jez, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI-097119 United States
Department of Defense (DOD, United States)W81XWH-10-1-0442 United States
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: The small molecule JIB-04 disrupts O2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A.
Authors: Cascella, B. / Lee, S.G. / Singh, S. / Jez, J.M. / Mirica, L.M.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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
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.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4A
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0758
Polymers83,5352
Non-polymers5406
Water6,485360
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0384
Polymers41,7681
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0384
Polymers41,7681
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.143, 101.122, 149.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 41767.543 Da / Num. of mol.: 2 / Fragment: UNP residues 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli (E. coli)
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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.66 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 17.5% PEG-3350 and 0.1 M citrate pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→35.152 Å / Num. obs: 51526 / % possible obs: 99.8 % / Redundancy: 7 % / Rsym value: 0.077 / Net I/σ(I): 23.7
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
PHASERphasing
Cootmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVH

3rvh


Resolution: 2.093→35.152 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 2030 3.97 %
Rwork0.1812 --
obs0.1829 51141 52.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→35.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 24 360 6086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055930
X-RAY DIFFRACTIONf_angle_d0.9288035
X-RAY DIFFRACTIONf_dihedral_angle_d15.7232203
X-RAY DIFFRACTIONf_chiral_restr0.04823
X-RAY DIFFRACTIONf_plane_restr0.0051035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0931-2.14550.25221230.21062993X-RAY DIFFRACTION44
2.1455-2.20340.26511330.21553199X-RAY DIFFRACTION48
2.2034-2.26830.28031340.23043235X-RAY DIFFRACTION48
2.2683-2.34150.26911410.2053396X-RAY DIFFRACTION50
2.3415-2.42510.22621420.19093469X-RAY DIFFRACTION51
2.4251-2.52220.2371450.1943492X-RAY DIFFRACTION52
2.5222-2.6370.26111450.19463512X-RAY DIFFRACTION52
2.637-2.77590.2611460.1963527X-RAY DIFFRACTION52
2.7759-2.94980.23441460.20413528X-RAY DIFFRACTION52
2.9498-3.17740.23461480.18643569X-RAY DIFFRACTION53
3.1774-3.49690.20561460.18063556X-RAY DIFFRACTION53
3.4969-4.00230.18761530.16623614X-RAY DIFFRACTION54
4.0023-5.04010.18621520.14113760X-RAY DIFFRACTION56
5.0401-35.15710.22241760.17444261X-RAY DIFFRACTION63
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)
12.36020.63970.18140.81630.36811.61670.13170.36220.5151-0.0444-0.10330.242-0.6223-0.3416-0.47190.40320.20170.0920.2738-0.01520.1577-8.4734126.089424.865
21.8253-0.6563-0.00192.3891-0.07912.0459-0.01910.3007-0.1321-0.10480.01070.3796-0.1943-0.59050.02760.17790.00630.02050.3356-0.04980.1378-6.1694112.630118.0558
32.11411.20530.82841.36410.62750.8778-0.24080.3492-0.5572-0.2129-0.19520.03770.3131-0.2467-0.47910.1778-0.2684-0.03780.2026-0.31540.36541.832694.49418.4523
42.5787-0.37430.17142.7002-0.02562.6033-0.06180.1732-0.1536-0.0420.0003-0.0648-0.1907-0.16310.02550.1324-0.03420.03560.1449-0.06290.06462.4469109.747122.0032
52.69760.7587-0.70982.304-1.74532.82740.09390.18430.1796-0.2179-0.057-0.1487-0.43360.0577-0.00530.4221-0.06210.06450.22190.0260.218213.2132128.168512.9777
62.3317-1.4155-0.19461.49560.83772.31850.03430.1809-0.7009-0.04530.05190.68850.6911-0.31220.09090.4258-0.2683-0.16530.42340.0550.4512-32.4775108.313546.0578
71.41540.54420.14362.4428-0.28541.08770.0299-0.00190.2173-0.01590.23360.9870.1073-0.585-0.06170.227-0.04590.03930.31220.06140.4398-31.4333121.67253.4265
82.5906-0.7496-1.17620.58770.54930.66270.0205-0.10830.29960.09240.18430.6313-0.3903-0.3229-0.03650.28290.28210.3170.23770.01290.5372-24.0366140.027354.5256
93.2913-1.42840.06012.7056-1.68541.32010.0590.53330.3276-0.78360.28871.0294-0.1818-0.74340.06270.32940.0481-0.11830.39650.16570.5049-27.8405137.582638.4722
102.13811.1481-1.97751.0302-1.24812.99540.00570.0050.19790.12220.29440.73070.1083-0.5421-0.18680.30050.04970.12090.30870.05170.4407-28.6324131.767857.0889
115.9724-2.45732.87871.2512-0.70632.41610.1507-0.6394-0.24830.80350.16040.76690.1582-0.8112-0.23420.4049-0.1350.11340.36640.05560.4058-29.239112.327565.969
121.20280.43970.38172.9687-0.96512.0180.03140.09560.169-0.02680.09470.2430.1622-0.161-0.11090.0573-0.0001-0.00820.13320.0030.1727-20.851123.098951.5953
132.61380.4334-0.59573.8851-0.68153.85420.1261-0.0084-0.0647-0.03040.1072-0.6515-0.21390.5621-0.01670.16050.00550.02710.1588-0.05980.2086-8.7178126.836146.4674
141.17820.6922-0.85463.3056-0.59731.95040.0280.00170.02480.03460.05540.05650.2235-0.1477-0.08360.0967-0.0312-0.02710.1205-0.00280.1657-19.8021118.89552.8596
153.12620.1971-0.22821.9502-0.76934.09550.0908-0.0966-0.7959-0.0228-0.144-0.52760.77030.49050.09640.52170.0253-0.00720.28130.0610.4638-12.6348101.315260.1109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 353 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 144 )
11X-RAY DIFFRACTION11chain 'B' and (resid 145 through 164 )
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 226 )
13X-RAY DIFFRACTION13chain 'B' and (resid 227 through 252 )
14X-RAY DIFFRACTION14chain 'B' and (resid 253 through 317 )
15X-RAY DIFFRACTION15chain 'B' and (resid 318 through 352 )

+
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