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- PDB-5fwj: Crystal structure of human JARID1C in complex with KDM5-C49 -

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Basic information

Entry
Database: PDB / ID: 5fwj
TitleCrystal structure of human JARID1C in complex with KDM5-C49
ComponentsHISTONE DEMETHYLASE JARID1C
KeywordsOXIDOREDUCTASE / LYSINE-SPECIFIC / LYSINE-SPECIFIC DEMETHYLASE 5C
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / histone demethylase activity / HDMs demethylate histones / response to toxic substance / rhythmic process / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription ...[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / histone demethylase activity / HDMs demethylate histones / response to toxic substance / rhythmic process / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. ...Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / 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
Chem-MMK / : / Lysine-specific demethylase 5C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSrikannathasan, V. / Szykowska, A. / Strain-Damerell, C. / Kopec, J. / Nowak, R. / Gileadi, C. / Johansson, C. / Kupinska, K. / Burgess-Brown, N.A. / Shrestha, L. ...Srikannathasan, V. / Szykowska, A. / Strain-Damerell, C. / Kopec, J. / Nowak, R. / Gileadi, C. / Johansson, C. / Kupinska, K. / Burgess-Brown, N.A. / Shrestha, L. / Dong, W. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Huber, K. / Oppermann, U.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U.
History
DepositionFeb 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jun 29, 2016Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEMETHYLASE JARID1C
B: HISTONE DEMETHYLASE JARID1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,51915
Polymers108,4142
Non-polymers1,10613
Water10,935607
1
A: HISTONE DEMETHYLASE JARID1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7728
Polymers54,2071
Non-polymers5657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEMETHYLASE JARID1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7487
Polymers54,2071
Non-polymers5416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.960, 67.340, 74.730
Angle α, β, γ (deg.)86.71, 76.56, 70.35
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HISTONE DEMETHYLASE JARID1C


Mass: 54206.812 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, UNP RESIDUES 8-83 AND 384-772
Source method: isolated from a genetically manipulated source
Details: KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL) AMINO)-2-OXOETHYL)AMINO)METHYL) ISONICOTINIC ACID)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P41229, 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 , 5 types, 620 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MMK / 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid


Mass: 306.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.78 Å3/Da / Density % sol: 55.78 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M BIS-TRIS PH 5.5 -- 25% PEG3350 -- 0.25M MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92009
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2016 / Details: MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.1→51.23 Å / Num. obs: 95919 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.24
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.37 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1682)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A1F

5a1f


Resolution: 2.1→51.232 Å / SU ML: 0.18 / σ(F): 1.97 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 3126 5.1 %
Rwork0.1551 --
obs0.1568 61825 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→51.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6958 0 55 607 7620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047243
X-RAY DIFFRACTIONf_angle_d0.9539831
X-RAY DIFFRACTIONf_dihedral_angle_d13.3742680
X-RAY DIFFRACTIONf_chiral_restr0.0351035
X-RAY DIFFRACTIONf_plane_restr0.0051290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.26341230.20422589X-RAY DIFFRACTION95
2.1328-2.16780.26881440.19942663X-RAY DIFFRACTION97
2.1678-2.20520.21481350.18312649X-RAY DIFFRACTION97
2.2052-2.24530.25091450.182680X-RAY DIFFRACTION97
2.2453-2.28850.1981450.16922640X-RAY DIFFRACTION97
2.2885-2.33520.17071360.15872712X-RAY DIFFRACTION98
2.3352-2.38590.20961510.15592652X-RAY DIFFRACTION98
2.3859-2.44140.22411300.16162678X-RAY DIFFRACTION97
2.4414-2.50250.2141420.16392714X-RAY DIFFRACTION98
2.5025-2.57020.22391320.16532649X-RAY DIFFRACTION98
2.5702-2.64580.17931540.16232688X-RAY DIFFRACTION98
2.6458-2.73120.22941310.16262682X-RAY DIFFRACTION98
2.7312-2.82880.19231440.17182674X-RAY DIFFRACTION98
2.8288-2.9420.19571450.16032677X-RAY DIFFRACTION98
2.942-3.07590.20881360.15872697X-RAY DIFFRACTION98
3.0759-3.23810.20711510.15992683X-RAY DIFFRACTION98
3.2381-3.44090.20681490.15952643X-RAY DIFFRACTION97
3.4409-3.70650.19521320.15362668X-RAY DIFFRACTION97
3.7065-4.07940.16121410.13442670X-RAY DIFFRACTION97
4.0794-4.66930.12641560.11932700X-RAY DIFFRACTION99
4.6693-5.88150.15711540.13382634X-RAY DIFFRACTION98
5.8815-51.24770.17571500.15922657X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 18.7757 Å / Origin y: 45.9757 Å / Origin z: 8.5235 Å
111213212223313233
T0.2073 Å20.0009 Å2-0.0306 Å2-0.1878 Å2-0.0198 Å2--0.1471 Å2
L0.022 °20.1575 °2-0.1089 °2-0.507 °2-0.1551 °2---0.1676 °2
S0.0098 Å °-0.0089 Å °-0.0044 Å °0.0443 Å °-0.0063 Å °-0.0044 Å °-0.0249 Å °0.0062 Å °-0.0013 Å °
Refinement TLS groupSelection details: ALL

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