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- PDB-5fyb: Crystal structure of the catalytic domain of human JARID1B in com... -

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Basic information

Entry
Database: PDB / ID: 5fyb
TitleCrystal structure of the catalytic domain of human JARID1B in complex with MC1648
ComponentsLYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
KeywordsOXIDOREDUCTASE / JARID1B / PLU1
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 / histone demethylase activity / single fertilization / response to fungicide / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / cellular response to leukemia inhibitory factor / HDMs demethylate histones / transcription corepressor activity / sequence-specific double-stranded DNA binding / rhythmic process / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / 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 ...: / : / : / 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-77J / : / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsNowak, R. / Srikannathasan, V. / Rotili, D. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. ...Nowak, R. / Srikannathasan, V. / Rotili, D. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc1648
Authors: Nowak, R. / Srikannathasan, V. / Rotili, D. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / ...Authors: Nowak, R. / Srikannathasan, V. / Rotili, D. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U.
History
DepositionMar 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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, LYSINE-SPECIFIC DEMETHYLASE 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,45329
Polymers55,2141
Non-polymers2,23928
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.110, 142.110, 151.670
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-1758-

MN

21A-2248-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 5B, 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 / LYSINE-SPECIFIC DEMETHYLASE 5B / LYSINE-SPECIFIC DEMETHYLASE 5B


Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, UNP RESIDUES 26-101 AND 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 , 6 types, 496 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-77J / N-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide


Mass: 291.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13N3O3S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 41.49 % / 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 / 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: 1.87→64.56 Å / Num. obs: 74172 / % possible obs: 99.4 % / Observed criterion σ(I): 1.2 / Redundancy: 20 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.6
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1682)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A3P

5a3p


Resolution: 1.87→51.851 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 3796 5.1 %
Rwork0.1905 --
obs0.1922 74164 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→51.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 126 468 4254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073929
X-RAY DIFFRACTIONf_angle_d1.0825310
X-RAY DIFFRACTIONf_dihedral_angle_d13.5771458
X-RAY DIFFRACTIONf_chiral_restr0.046558
X-RAY DIFFRACTIONf_plane_restr0.006708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8701-1.89380.37691620.34112524X-RAY DIFFRACTION99
1.8938-1.91870.37441540.31732503X-RAY DIFFRACTION99
1.9187-1.9450.37931430.29472548X-RAY DIFFRACTION99
1.945-1.97280.29991370.28562569X-RAY DIFFRACTION99
1.9728-2.00220.2971470.27642542X-RAY DIFFRACTION99
2.0022-2.03350.28251270.26592567X-RAY DIFFRACTION99
2.0335-2.06680.31811370.25672551X-RAY DIFFRACTION99
2.0668-2.10250.30271350.25852568X-RAY DIFFRACTION99
2.1025-2.14070.28491080.24722589X-RAY DIFFRACTION99
2.1407-2.18190.28721270.23862598X-RAY DIFFRACTION99
2.1819-2.22640.24771440.23082567X-RAY DIFFRACTION99
2.2264-2.27480.26051300.22442573X-RAY DIFFRACTION99
2.2748-2.32770.27251520.22352587X-RAY DIFFRACTION99
2.3277-2.3860.24831500.2142569X-RAY DIFFRACTION99
2.386-2.45050.27551390.21332595X-RAY DIFFRACTION99
2.4505-2.52260.25661480.20322574X-RAY DIFFRACTION100
2.5226-2.6040.22341310.20752618X-RAY DIFFRACTION99
2.604-2.69710.25961380.20572608X-RAY DIFFRACTION99
2.6971-2.8050.25261490.20382597X-RAY DIFFRACTION99
2.805-2.93270.23551530.19692611X-RAY DIFFRACTION100
2.9327-3.08730.21351470.19352625X-RAY DIFFRACTION100
3.0873-3.28070.22771350.18982638X-RAY DIFFRACTION100
3.2807-3.53390.18951320.1792662X-RAY DIFFRACTION100
3.5339-3.88950.19931300.15692675X-RAY DIFFRACTION100
3.8895-4.4520.16961580.13972691X-RAY DIFFRACTION100
4.452-5.6080.17181430.14472731X-RAY DIFFRACTION100
5.608-51.87090.18891400.17822888X-RAY DIFFRACTION99

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