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- PDB-6eiy: Crystal structure of KDM5B in complex with KDOPZ000034a. -

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Basic information

Entry
Database: PDB / ID: 6eiy
TitleCrystal structure of KDM5B in complex with KDOPZ000034a.
ComponentsLysine-specific demethylase 5B,Lysine-specific demethylase 5B
KeywordsOXIDOREDUCTASE / KDM5B Lysine specific demethylase
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 / 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
Similarity search - Domain/homology
Chem-B6W / : / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSrikannathasan, V. / Newman, J.A. / Szykowska, A. / Wright, M. / Ruda, G.F. / Vazquez-Rodriguez, S.A. / Kupinska, K. / Strain-Damerell, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. ...Srikannathasan, V. / Newman, J.A. / Szykowska, A. / Wright, M. / Ruda, G.F. / Vazquez-Rodriguez, S.A. / Kupinska, K. / Strain-Damerell, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Huber, K. / von Delft, F.
CitationJournal: to be published
Title: Crystal structure of KDM5B in complex with KDOPZ000034a.
Authors: srikannathasan, v.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)54,13811
Polymers53,1541
Non-polymers98410
Water3,333185
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint4 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.380, 142.380, 152.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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


Mass: 53154.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5B, JARID1B, PLU1, RBBP2H1 / Plasmid: PFB-LIC-BSE / Cell (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, 195 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-B6W / 2-chloranyl-~{N}-[2-[4-(3-cyano-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidin-5-yl)pyrazol-1-yl]ethyl]ethanamide


Mass: 387.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18ClN7O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.8M Pottassium 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→51.983 Å / Num. obs: 49958 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 18.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 19 % / Rmerge(I) obs: 2.524 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3615 / CC1/2: 0.586 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a1f

5a1f


Resolution: 2.15→51.983 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.2154 2501 5.01 %
Rwork0.1861 --
obs0.1876 49896 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.63 Å2 / Biso mean: 55.6744 Å2 / Biso min: 28.84 Å2
Refinement stepCycle: final / Resolution: 2.15→51.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 54 185 3865
Biso mean--55.81 56.44 -
Num. residues----456
Refinement TLS params.Method: refined / Origin x: 76.6588 Å / Origin y: 66.4016 Å / Origin z: 11.7505 Å
111213212223313233
T0.2994 Å2-0.0341 Å20.0478 Å2-0.4992 Å2-0.021 Å2--0.3104 Å2
L2.5233 °20.0741 °20.263 °2-0.4517 °20.016 °2---0.3563 °2
S0.0113 Å °-0.0265 Å °0.1557 Å °-0.0337 Å °0.0165 Å °-0.0186 Å °-0.0051 Å °0.0177 Å °-0.0303 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 754
2X-RAY DIFFRACTION1allA800 - 801
3X-RAY DIFFRACTION1allB1 - 2
4X-RAY DIFFRACTION1allB3
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allC3
7X-RAY DIFFRACTION1allE1
8X-RAY DIFFRACTION1allF1
9X-RAY DIFFRACTION1allS1 - 189

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