[English] 日本語
Yorodumi
- PDB-9gp1: Jumonji domain-containing protein 2A with crystallization epitope... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gp1
TitleJumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / Crystal Epitopes / Jumonji domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / 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. / 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
Similarity search - Domain/homology
NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)168,25912
Polymers167,7634
Non-polymers4968
Water9,674537
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0653
Polymers41,9411
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0653
Polymers41,9411
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0653
Polymers41,9411
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0653
Polymers41,9411
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.03, 101.6, 141.43
Angle α, β, γ (deg.)90, 99.38, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Beg auth comp-ID: LEU / Beg label comp-ID: LEU

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEAA9 - 3549 - 354
211PHEPHEBB9 - 3549 - 354
322PHEPHEAA9 - 3549 - 354
422PHEPHECC9 - 3549 - 354
533PHEPHEAA9 - 3549 - 354
633PHEPHEDD9 - 3549 - 354
744LEULEUBB9 - 3559 - 355
844LEULEUCC9 - 3559 - 355
955PHEPHEBB9 - 3549 - 354
1055PHEPHEDD9 - 3549 - 354
1166PHEPHECC9 - 3549 - 354
1266PHEPHEDD9 - 3549 - 354

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / ...JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / [histone H3]-trimethyl-L-lysine(36) demethylase 4A / [histone H3]-trimethyl-L-lysine(9) demethylase 4A


Mass: 41940.668 Da / Num. of mol.: 4 / Mutation: R913A
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, [histone H3]-trimethyl-L-lysine9 demethylase, [histone H3]-trimethyl-L-lysine36 demethylase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 25% PEG3350, 0.1M bis-tris pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.21→101.6 Å / Num. obs: 77812 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 0.993 / Net I/σ(I): 11.7
Reflection shellResolution: 2.21→2.27 Å / Num. unique obs: 5675 / CC1/2: 0.606

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→82.135 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.469 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.319 / ESU R Free: 0.233 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2589 3949 5.077 %
Rwork0.215 73839 -
all0.217 --
obs-77788 97.613 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å20 Å2-0.303 Å2
2---0.862 Å2-0 Å2
3---1.006 Å2
Refinement stepCycle: LAST / Resolution: 2.21→82.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11115 0 8 537 11660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211467
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.82315600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01551396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.302562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3101765
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.50810533
X-RAY DIFFRACTIONr_chiral_restr0.1290.21634
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029076
X-RAY DIFFRACTIONr_nbd_refined0.2180.25015
X-RAY DIFFRACTIONr_nbtor_refined0.3160.27851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2682
X-RAY DIFFRACTIONr_metal_ion_refined0.2370.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3520.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.218
X-RAY DIFFRACTIONr_mcbond_it4.8144.1955593
X-RAY DIFFRACTIONr_mcangle_it6.9387.5256986
X-RAY DIFFRACTIONr_scbond_it5.4914.2695874
X-RAY DIFFRACTIONr_scangle_it7.6757.7388614
X-RAY DIFFRACTIONr_lrange_it10.10645.12517496
X-RAY DIFFRACTIONr_ncsr_local_group_10.0750.0511000
X-RAY DIFFRACTIONr_ncsr_local_group_20.0830.0510950
X-RAY DIFFRACTIONr_ncsr_local_group_30.0820.0510904
X-RAY DIFFRACTIONr_ncsr_local_group_40.0750.0511451
X-RAY DIFFRACTIONr_ncsr_local_group_50.080.0511421
X-RAY DIFFRACTIONr_ncsr_local_group_60.0590.0511529
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.074960.05009
12BX-RAY DIFFRACTIONLocal ncs0.074960.05009
23AX-RAY DIFFRACTIONLocal ncs0.083090.05009
24CX-RAY DIFFRACTIONLocal ncs0.083090.05009
35AX-RAY DIFFRACTIONLocal ncs0.081880.05009
36DX-RAY DIFFRACTIONLocal ncs0.081880.05009
47BX-RAY DIFFRACTIONLocal ncs0.0750.05009
48CX-RAY DIFFRACTIONLocal ncs0.0750.05009
59BX-RAY DIFFRACTIONLocal ncs0.080430.05009
510DX-RAY DIFFRACTIONLocal ncs0.080430.05009
611CX-RAY DIFFRACTIONLocal ncs0.059240.0501
612DX-RAY DIFFRACTIONLocal ncs0.059240.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.21-2.2670.3343170.28553530.28858420.9240.94297.05580.267
2.267-2.3290.3412550.26753260.2756880.9220.95198.11890.246
2.329-2.3970.3342940.2651420.26456010.9220.95697.05410.236
2.397-2.4710.2612530.22550240.22754150.9540.96797.45150.203
2.471-2.5520.2992450.23548990.23852150.9470.96398.63850.21
2.552-2.6410.3162720.23646890.2450730.9360.96397.79220.214
2.641-2.7410.2942210.22645500.2348910.9390.96597.54650.204
2.741-2.8520.3212420.22943960.23447540.9340.96697.55990.206
2.852-2.9790.2762150.2142360.21345020.950.97198.86720.191
2.979-3.1240.2692250.21639910.21942930.9530.96998.20640.199
3.124-3.2930.2672230.21937980.22241100.9490.96997.83450.209
3.293-3.4920.2421810.22236480.22339230.9630.97297.60390.215
3.492-3.7330.2271770.21133890.21236650.9670.97597.29880.206
3.733-4.0320.2421840.19931370.20134130.9610.97597.30440.197
4.032-4.4150.2251790.18428840.18731620.9690.97796.86910.186
4.415-4.9350.2231410.17925980.18128270.9650.97796.88720.184
4.935-5.6950.1971150.18923700.1925460.9790.97797.60410.193
5.695-6.9660.284950.22119910.22421380.9580.97397.56780.224
6.966-9.8160.202740.20615400.20616700.9810.97896.64670.216
9.816-82.1350.228410.2238780.2239610.9620.9795.62960.24

+
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