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- PDB-6hgt: Crystal structure of human KDM4A complexed with co-substrate anal... -

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Basic information

Entry
Database: PDB / ID: 6hgt
TitleCrystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation
Components
  • Histone H3.3
  • Lysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / Histone demethylase / Inhibitor / transcription
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / negative regulation of chromosome condensation / Barr body / histone H4K20me2 reader activity / : / histone H3K36 demethylase activity / inner kinetochore ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / negative regulation of chromosome condensation / Barr body / histone H4K20me2 reader activity / : / histone H3K36 demethylase activity / inner kinetochore / pericentric heterochromatin formation / muscle cell differentiation / histone H3K9 demethylase activity / cardiac muscle hypertrophy in response to stress / oocyte maturation / histone demethylase activity / nucleosomal DNA binding / nucleus organization / pericentric heterochromatin / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / embryo implantation / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / negative regulation of autophagy / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / male gonad development / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / regulation of gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / cell population proliferation / chromatin remodeling / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / JmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Tudor domain / Tudor domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / JmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Tudor domain / Tudor domain / A domain family that is part of the cupin metalloenzyme superfamily. / PHD-finger / JmjC domain / JmjC domain profile. / PHD-zinc-finger like domain / jmjN domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H3.1 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMaw, J. / Le Bihan, Y.V. / van Montfort, R.L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC347/A18364 United Kingdom
CitationJournal: To be published
Title: Structure-based design of selective, histone substrate-based inhibitors of histone lysine demethylases 4 (KDM4) subfamily
Authors: Maw, J. / Le Bihan, Y.V. / Bavetsias, V. / Blagg, J.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
E: Histone H3.3
F: Histone H3.3
G: Histone H3.3
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,00920
Polymers173,8988
Non-polymers1,11212
Water8,377465
1
A: Lysine-specific demethylase 4A
E: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7525
Polymers43,4742
Non-polymers2783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
F: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7525
Polymers43,4742
Non-polymers2783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysine-specific demethylase 4A
G: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7525
Polymers43,4742
Non-polymers2783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysine-specific demethylase 4A
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7525
Polymers43,4742
Non-polymers2783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.440, 103.410, 144.520
Angle α, β, γ (deg.)90.00, 99.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41854.617 Da / Num. of mol.: 4
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) / Strain (production host): Rosetta (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 H3.3


Mass: 1619.848 Da / Num. of mol.: 4 / Mutation: K9R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: unidentified (others) / References: UniProt: P84243, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.33→44.27 Å / Num. obs: 72206 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 52.57 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.6
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 7 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5294 / CC1/2: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oq6

2oq6


Resolution: 2.33→43.16 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.86 / SU R Cruickshank DPI: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.378 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3503 4.85 %RANDOM
Rwork0.251 ---
obs0.252 72205 99.7 %-
Displacement parametersBiso mean: 44.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.7905 Å20 Å2-7.6188 Å2
2--3.6331 Å20 Å2
3----6.4236 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.33→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10996 0 48 465 11509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111410HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0515493HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3671SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1915HARMONIC5
X-RAY DIFFRACTIONt_it11410HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion17.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1468SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11947SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.35 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2925 -4.98 %
Rwork0.2456 1373 -
all0.248 1445 -
obs--100 %
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)
1-0.2264-0.81040.64755.5552-3.08950.23120.0350.1373-0.28240.0597-0.0151-0.13890.20840.1518-0.0199-0.04-0.0014-0.0364-0.0096-0.1257-0.039424.29762.627562.1755
22.246-1.30790.09023.119-0.2642.2131-0.02410.32210.1075-0.07830.0787-0.17340.33460.2788-0.0546-0.1824-0.0273-0.0497-0.04590.0132-0.131521.699915.013353.69
34.35191.0574-3.05552.5215-1.24274.3275-0.02260.06470.41070.07890.1541-0.1501-0.13310.2076-0.1316-0.0972-0.0470.006-0.14620.0373-0.012916.280632.342159.9112
41.6009-0.2693-0.00241.98940.00382.0188-0.03230.2312-0.1808-0.27370.10420.21290.3507-0.0432-0.0719-0.096-0.0429-0.0333-0.16450.0256-0.131610.366411.615354.5163
52.03791.7562-0.71925.2095-0.62232.7692-0.00630.03070.23030.0381-0.0735-0.3522-0.29340.29340.0797-0.0482-0.0287-0.0389-0.10350.0521-0.020549.993818.458684.7553
61.3443-0.36220.09431.32710.13050.8862-0.0065-0.0401-0.05350.0265-0.0437-0.1435-0.0130.15040.0502-0.11520.0196-0.0237-0.09550.0188-0.043244.2574-1.75887.7066
71.32970.8761.36721.3663-0.28511.6017-0.03110.0442-0.1364-0.0390.01530.1879-0.0709-0.20590.0158-0.03480.0432-0.03-0.0602-0.0253-0.024333.55194.581681.8836
81.6292-0.5963-1.20350.85950.29392.610.0194-0.1561-0.06020.03960.05970.0185-0.1705-0.142-0.079-0.05640.0116-0.0447-0.1192-0.0061-0.007437.468.334993.2066
90.4773-1.67240.6240.261511.78140.0017-0.08330.1396-0.02610.10260.0014-0.1201-0.2311-0.10430.03810.0281-0.0305-0.1019-0.0311-0.015832.644324.289799.7165
101.24980.33440.2484.0333-0.82911.47510.00850.06330.28890.04880.0218-0.1557-0.38010.1482-0.0303-0.06990.0467-0.0083-0.15950.0493-0.101161.1824-3.581614.239
112.503-0.2831.13062.6192-1.6775.01280.04580.0243-0.3087-0.2931-0.0586-0.02810.140.15880.01290.01780.0282-0.0628-0.2221-0.021-0.034555.5286-24.59399.0406
121.7420.40250.43991.7675-0.03981.7790.0089-0.20220.06710.17460.10090.1865-0.18-0.0495-0.1098-0.04660.04580.0157-0.12930.0144-0.098151.4316-9.071215.5446
132.0052-0.8474-1.19690.0995-0.03562.8350.0593-0.16710.05490.07520.18920.213-0.2083-0.2342-0.2485-0.05780.00840.0156-0.11960.01120.044848.8989-5.103118.973
141.7307-2.81881.63381.20610.88670.50460.0332-0.24380.15980.08760.08130.1113-0.2461-0.2575-0.11450.11990.06220.1756-0.1778-0.1203-0.163243.891310.419524.5848
150.2434-0.0221-0.30082.78-0.07011.9921-0.0117-0.2302-0.0430.05050.0820.26110.3027-0.487-0.0703-0.1616-0.0334-0.0743-0.0117-0.0633-0.002120.612648.333518.1501
161.4842-0.2712-1.9282.96021.27674.9111-0.0294-0.0180.5035-0.23950.16720.1151-0.2854-0.2127-0.1378-0.08990.0316-0.0892-0.19640.00680.006930.587870.422410.5191
171.24120.4213-0.08971.2378-0.22951.5781-0.0116-0.04890.14480.004-0.0226-0.04220.0404-0.1540.0341-0.11140.014-0.0753-0.1209-0.0468-0.020534.002255.611917.867
181.87210.8231-1.19432.3436-0.54352.552-0.0722-0.1654-0.3064-0.0068-0.0979-0.39790.44180.30210.1701-0.12410.0433-0.0661-0.1718-0.0422-0.081937.075844.725718.8638
190.36140.5092-0.79440.6145-1.7253-0.05520.0020.0091-0.0023-0.00660.0080.02380.0016-0.0241-0.010.0833-0.0835-0.03670.03710.1368-0.11856.438320.289247.516
200.4337-0.71860.62020.0309-1.88050.1980.0023-0.0095-0.03120.062-0.03490.040.0221-0.02510.03260.07420.0055-0.0716-0.01130.1535-0.07637.9829-1.590797.0615
210.00180.398-0.00510.0518-0.1472-0.00180.0122-0.0231-0.03140.0128-0.01270.05640.00090.02030.00060.05760.0420.0411-0.04430.0163-0.030448.2362-13.950224.3963
220.0818-0.6876-0.23420.57480.7319-0.08180.00290.00160.0075-0.00570.0078-0.0068-0.00310.0306-0.01070.0490.0427-0.0776-0.0587-0.0593-0.000937.528359.566424.7218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|5 - 26}
2X-RAY DIFFRACTION2{A|27 - 78}
3X-RAY DIFFRACTION3{A|79 - 124}
4X-RAY DIFFRACTION4{A|125 - 354}
5X-RAY DIFFRACTION5{B|7 - 53}
6X-RAY DIFFRACTION6{B|54 - 226}
7X-RAY DIFFRACTION7{B|227 - 274}
8X-RAY DIFFRACTION8{B|275 - 317}
9X-RAY DIFFRACTION9{B|318 - 353}
10X-RAY DIFFRACTION10{C|6 - 78}
11X-RAY DIFFRACTION11{C|79 - 124}
12X-RAY DIFFRACTION12{C|125 - 274}
13X-RAY DIFFRACTION13{C|275 - 311}
14X-RAY DIFFRACTION14{C|312 - 353}
15X-RAY DIFFRACTION15{D|10 - 70}
16X-RAY DIFFRACTION16{D|71 - 124}
17X-RAY DIFFRACTION17{D|125 - 252}
18X-RAY DIFFRACTION18{D|253 - 352}
19X-RAY DIFFRACTION19{E|7 - 13}
20X-RAY DIFFRACTION20{F|7 - 12}
21X-RAY DIFFRACTION21{G|7 - 13}
22X-RAY DIFFRACTION22{H|7 - 12}

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