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- PDB-5fyi: Crystal structure of human JMJD2A in complex with pyruvate -

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Basic information

Entry
Database: PDB / ID: 5fyi
TitleCrystal structure of human JMJD2A in complex with pyruvate
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A / TCA INTERMEDIATE
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 / 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 / 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-hydroxyethoxy)acetaldehyde / NICKEL (II) ION / PYRUVIC ACID / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsNowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Jmjd2A in Complex with Pyruvate
Authors: Nowak, R. / Kopec, J. / Johansson, C. / Szykowska, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
History
DepositionMar 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,56930
Polymers88,6532
Non-polymers1,91628
Water5,855325
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,26315
Polymers44,3261
Non-polymers93714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,30515
Polymers44,3261
Non-polymers97914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.450, 148.830, 57.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4A / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JU MONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(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

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Non-polymers , 7 types, 353 molecules

#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-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-1KA / (2-hydroxyethoxy)acetaldehyde


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.64 Å3/Da / Density % sol: 53.44 % / Description: NONE
Crystal growpH: 6
Details: 0.1M BIS-TRIS PH 6.0 -- 0.2M AMMONIUM SULFATE -- 28% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→29.77 Å / Num. obs: 51046 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A7O

5a7o


Resolution: 2.096→29.767 Å / σ(F): 1.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE-CHAINS WERE REMOVED.
RfactorNum. reflection% reflection
Rfree0.2358 2457 4.8 %
Rwork0.1965 --
obs0.1984 50981 99.89 %
Refinement stepCycle: LAST / Resolution: 2.096→29.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 111 325 5992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0963-2.13670.32641390.28652615X-RAY DIFFRACTION99
2.1367-2.18030.31421420.27412660X-RAY DIFFRACTION100
2.1803-2.22770.33311420.26182624X-RAY DIFFRACTION100
2.2277-2.27950.2861290.25992683X-RAY DIFFRACTION100
2.2795-2.33640.31441430.24932653X-RAY DIFFRACTION100
2.3364-2.39960.33961280.24772679X-RAY DIFFRACTION100
2.3996-2.47020.29911310.23592662X-RAY DIFFRACTION100
2.4702-2.54980.27031250.23462666X-RAY DIFFRACTION100
2.5498-2.64090.32381480.24342686X-RAY DIFFRACTION100
2.6409-2.74660.30331330.23292671X-RAY DIFFRACTION100
2.7466-2.87150.28381250.24052707X-RAY DIFFRACTION100
2.8715-3.02280.25581250.22342703X-RAY DIFFRACTION100
3.0228-3.21190.27831390.21152686X-RAY DIFFRACTION100
3.2119-3.45960.24281370.20662706X-RAY DIFFRACTION100
3.4596-3.80710.20961560.18532717X-RAY DIFFRACTION100
3.8071-4.35650.19281470.16272726X-RAY DIFFRACTION100
4.3565-5.48320.15431180.14312785X-RAY DIFFRACTION100
5.4832-29.77020.20881500.1682895X-RAY DIFFRACTION100

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