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Basic information

Entry
Database: PDB / ID: 5fz4
TitleCrystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (N10057a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)
ComponentsLYSINE-SPECIFIC DEMETHYLASE 5B
KeywordsOXIDOREDUCTASE / JARID1B / PLU1 / FRAGMENT SCREENING / STRUCTURAL GENOMICS CONSORTIUM / SGC / DIAMOND I04-1 / PANDDA
Function / homology
Function and homology information


regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain ...: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / 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 / 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-P6B / PHOSPHATE ION / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNowak, R. / Krojer, T. / Pearce, N. / Talon, R. / Collins, P. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. ...Nowak, R. / Krojer, T. / Pearce, N. / Talon, R. / Collins, P. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N10057A
Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / ...Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U.
History
DepositionMar 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 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 1.2Jan 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: LYSINE-SPECIFIC DEMETHYLASE 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,63120
Polymers55,2141
Non-polymers1,41719
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.360, 141.360, 151.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2182-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 5B / CANCER/TESTIS ANTIGEN 31 / CT31 / HISTONE DEMETHYLASE JARID1B / JUMONJI/ARID DOMAIN-CONTAINING ...CANCER/TESTIS ANTIGEN 31 / CT31 / HISTONE DEMETHYLASE JARID1B / JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B / PLU-1 / RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1 / RBP2-H1


Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-101,374-770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UGL1, 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 , 8 types, 224 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-P6B / (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol


Mass: 245.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N3O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL ...RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL SEQUENCE Q9UGL1. DELETED RESIDUES WERE LINKED WITH 4 GLYCINE LINKER (GGGG).

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91732
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91732 Å / Relative weight: 1
ReflectionResolution: 2.07→75.98 Å / Num. obs: 55014 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 19.7 % / Biso Wilson estimate: 44.04 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.3
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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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 5A3P

5a3p


Resolution: 2.07→70.68 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.2 / Stereochemistry target values: ML
Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP TO BE PUBLISHED.
RfactorNum. reflection% reflection
Rfree0.2343 2672 4.9 %
Rwork0.1984 --
obs0.2002 54952 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 79 205 3935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093920
X-RAY DIFFRACTIONf_angle_d1.1965315
X-RAY DIFFRACTIONf_dihedral_angle_d15.1211474
X-RAY DIFFRACTIONf_chiral_restr0.048558
X-RAY DIFFRACTIONf_plane_restr0.006683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10770.34421450.32232686X-RAY DIFFRACTION100
2.1077-2.14820.29871340.30742717X-RAY DIFFRACTION100
2.1482-2.1920.29821310.27532696X-RAY DIFFRACTION100
2.192-2.23970.34921320.27812719X-RAY DIFFRACTION100
2.2397-2.29180.31171350.2562707X-RAY DIFFRACTION100
2.2918-2.34910.28211290.24412720X-RAY DIFFRACTION100
2.3491-2.41270.28891460.2432721X-RAY DIFFRACTION100
2.4127-2.48360.26151460.24182713X-RAY DIFFRACTION100
2.4836-2.56380.28891170.23142742X-RAY DIFFRACTION100
2.5638-2.65550.27911490.22272710X-RAY DIFFRACTION100
2.6555-2.76180.2721440.22192723X-RAY DIFFRACTION100
2.7618-2.88750.25681550.21342729X-RAY DIFFRACTION100
2.8875-3.03970.25971250.21312755X-RAY DIFFRACTION100
3.0397-3.23020.20971480.21122751X-RAY DIFFRACTION100
3.2302-3.47960.25721060.2012787X-RAY DIFFRACTION100
3.4796-3.82970.21631590.19052779X-RAY DIFFRACTION100
3.8297-4.38380.20851550.16622780X-RAY DIFFRACTION100
4.3838-5.52280.18981440.15092842X-RAY DIFFRACTION100
5.5228-70.72120.21711720.18023003X-RAY DIFFRACTION100

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