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- PDB-4tn7: Crystal structure of mouse KDM2A-H3K36ME-NO complex -

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Basic information

Entry
Database: PDB / ID: 4tn7
TitleCrystal structure of mouse KDM2A-H3K36ME-NO complex
Components
  • (Lysine-specific demethylase ...) x 2
  • Peptide
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / Chromatin modifying enzymes / telomere organization ...[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / neuroepithelial cell differentiation / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / neural tube closure / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / circadian regulation of gene expression / 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 / regulation of circadian rhythm / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / neuron differentiation / 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 / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / positive regulation of gene expression / negative regulation of apoptotic process / chromatin / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #250 / PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #250 / PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / F-box domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Helix non-globular / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Special / Leucine-rich repeat domain superfamily / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / 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
: / NITRIC OXIDE / SUCCINIC ACID / Lysine-specific demethylase 2A / Histone H3.1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCheng, Z.
Funding support United States, 4items
OrganizationGrant numberCountry
Lymphoma Society and the STARR foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079641 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM066569 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM097779 United States
CitationJournal: Genes Dev. / Year: 2014
Title: A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36.
Authors: Cheng, Z. / Cheung, P. / Kuo, A.J. / Yukl, E.T. / Wilmot, C.M. / Gozani, O. / Patel, D.J.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
C: Lysine-specific demethylase 2A
D: Lysine-specific demethylase 2A
E: Peptide
F: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,81611
Polymers96,4386
Non-polymers3785
Water7,278404
1
A: Lysine-specific demethylase 2A
B: Lysine-specific demethylase 2A
E: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4236
Polymers48,2193
Non-polymers2043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysine-specific demethylase 2A
D: Lysine-specific demethylase 2A
F: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3935
Polymers48,2193
Non-polymers1742
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.063, 157.928, 48.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Lysine-specific demethylase ... , 2 types, 4 molecules ACBD

#1: Protein Lysine-specific demethylase 2A / F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing ...F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 39031.324 Da / Num. of mol.: 2 / Fragment: UNP residues 36-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3)
References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Protein Lysine-specific demethylase 2A / F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing ...F-box and leucine-rich repeat protein 11 / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 7534.759 Da / Num. of mol.: 2 / Fragment: UNP residues 450-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3)
References: UniProt: P59997, [histone H3]-dimethyl-L-lysine36 demethylase

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Peptide


Mass: 1652.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

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Non-polymers , 4 types, 409 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 % / Description: PLATE-LIKE CRYSTALS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Li-citrate 18-30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40902 / % possible obs: 97.9 % / Redundancy: 2.9 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1760) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YU1

2yu1


Resolution: 2.2→45.166 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.43 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 2067 5.06 %RANDOM SELECTION
Rwork0.2294 ---
obs0.232 40864 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 20 404 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026873
X-RAY DIFFRACTIONf_angle_d0.5329314
X-RAY DIFFRACTIONf_dihedral_angle_d13.1112558
X-RAY DIFFRACTIONf_chiral_restr0.0221000
X-RAY DIFFRACTIONf_plane_restr0.0021194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25440.33131380.27792367X-RAY DIFFRACTION93
2.2544-2.31080.31771240.27192634X-RAY DIFFRACTION98
2.3108-2.37330.32961360.26942596X-RAY DIFFRACTION98
2.3733-2.44310.34241550.27292608X-RAY DIFFRACTION98
2.4431-2.5220.30751330.25262571X-RAY DIFFRACTION98
2.522-2.61210.33661260.252637X-RAY DIFFRACTION98
2.6121-2.71670.30291460.24982584X-RAY DIFFRACTION98
2.7167-2.84030.28221300.24212581X-RAY DIFFRACTION98
2.8403-2.990.31281360.2442564X-RAY DIFFRACTION98
2.99-3.17730.31631400.23652608X-RAY DIFFRACTION98
3.1773-3.42250.28461490.2262586X-RAY DIFFRACTION97
3.4225-3.76680.23851290.20232604X-RAY DIFFRACTION98
3.7668-4.31150.23541380.19862625X-RAY DIFFRACTION98
4.3115-5.43060.23721390.20382612X-RAY DIFFRACTION98
5.4306-45.17570.261480.22442620X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.8096 Å / Origin y: -1.0164 Å / Origin z: 10.9226 Å
111213212223313233
T0.2097 Å20.0113 Å2-0.0055 Å2-0.2252 Å20.0119 Å2--0.191 Å2
L0.0586 °2-0.1748 °2-0.1084 °2-0.466 °20.1921 °2---0.033 °2
S-0.0151 Å °0.0075 Å °0.0036 Å °0.0141 Å °0.0055 Å °0.0292 Å °-0.005 Å °-0.0072 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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