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- PDB-9gp1: Jumonji domain-containing protein 2A with crystallization epitope... -

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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 / apoptotic chromosome condensation / 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 / negative regulation of astrocyte differentiation ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / 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 / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / 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 / positive regulation of gene expression / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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