SASDE37: Lysine-specific demethylase 5B, KDM5B, in HEPES buffer

Basic information

• Entry: Database: SASBDB / ID: SASDE37

Sample

Lysine-specific demethylase 5B, KDM5B, in HEPES buffer

• Lysine-specific demethylase 5B (protein), KDM5B, Homo sapiens

Function / homology

Function:

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 / Chromatin modifications during the maternal to zygotic transition (MZT) / post-embryonic development / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol

Domain/homology:

: / : / : / : / 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 / 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

Component:

Lysine-specific demethylase 5B

• Biological species: Homo sapiens (human)
• Citation: Journal: Sci Rep / Year: 2019; Title: Molecular architecture of the Jumonji C family histone demethylase KDM5B.; Authors: Jerzy Dorosz / Line Hyltoft Kristensen / Nanda G Aduri / Osman Mirza / Rikke Lousen / Saskia Bucciarelli / Ved Mehta / Selene Sellés-Baiget / Sara Marie Øie Solbak / Anders Bach / Pablo Mesa / Pablo Alcon Hernandez / Guillermo Montoya / Tam T T N Nguyen / Kasper D Rand / Thomas Boesen / Michael Gajhede / ; Abstract: The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.

Contact author

• Saskia Bucciarelli (University of Copenhagen, Copenhagen, Denmark)

Models

• Model #2573: ; Type: dummy / Radius of dummy atoms: 4.75 A / Symmetry: P1 / Comment: Averaged Spatial Repersentation / Chi-square value: 2.098 / P-value: 0.736543; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2592: ; Type: dummy / Software: (r9988) / Radius of dummy atoms: 2.40 A / Symmetry: P1 / Comment: Individual model / Chi-square value: 2.098 / P-value: 0.736543; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Lysine-specific demethylase 5B, KDM5B, in HEPES buffer; Specimen concentration: 0.75-1.80
• Buffer: Name: 50 mM HEPES, 300 mM NaCl, 5% (v/v) glycerol, 1mM DTT / pH: 7.7

Entity #1355

Name: KDM5B / Type: protein / Description: Lysine-specific demethylase 5B / Formula weight: 175.81 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q9UGL1
Sequence:

MEAATTLHPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK LNFLDQIAKY WELQGSTLKI PHVERKILDL FQLNKLVAEE GGFAVVCKDR KWTKIATKMG FAPGKAVGSH IRGHYERILN PYNLFLSGDS LRCLQKPNLT TDTKDKEYKP HDIPQRQSVQ PSETCPPARR AKRMRAEAMN IKIEPEETTE ARTHNLRRRM GCPTPKCENE KEMKSSIKQE PIERKDYIVE NEKEKPKSRS KKATNAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLI PPLHDVPKGD WRCPKCLAQE CSKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM VPTELVEKEF WRLVSTIEED VTVEYGADIA SKEFGSGFPV RDGKIKLSPE EEEYLDSGWN LNNMPVMEQS VLAHITADIC GMKLPWLYVG MCFSSFCWHI EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE LFVSQPDLLH QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST VQKDMAIMIE DEKALRETVR KLGVIDSERM DFELLPDDER QCVKCKTTCF MSAISCSCKP GLLVCLHHVK ELCSCPPYKY KLRYRYTLDD LYPMMNALKL RAESYNEWAL NVNEALEAKI NKKKSLVSFK ALIEESEMKK FPDNDLLRHL RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN ELRQFVTQLY ALPCVLSQTP LLKDLLNRVE DFQQHSQKLL SEETPSAAEL QDLLDVSFEF DVELPQLAEM RIRLEQARWL EEVQQACLDP SSLTLDDMRR LIDLGVGLAP YSAVEKAMAR GPLQELLTVS EHWDDKAKSL LKARPRHSLN SLATAVKEIE EIPAYLPNGA ALKDSVQRAR DWLQDVEGLQ AGGRVPVLDT LIELVTRGRS IPVHLNSLPR LETLVAEVQA WKECAVNTFL TENSPYSLLE VLCPRCDIGL LGLKRKQRKL KEPLPNGKKK STKLESLSDL ERALTESKET ASAMATLGEA RLREMEALQS LRLANEGKLL SPLQDVDIKI CLCQKAPAAP MIQCELCRDA FHTSCVAVPS ISQGLRIWLC PHCRRSEKPP LEKILPLLAS LQRIRVRLPE GDALRYMIER TVNWQHRAQQ LLSSGNLKFV QDRVGSGLLY SRWQASAGQV SDTNKVSQPP GTTSFSLPDD WDNRTSYLHS PFSTGRSCIP LHGVSPEVNE LLMEAQLLQV SLPEIQELYQ TLLAKPSPAQ QTDRSSPVRP SSEKNDCCRG KRDGINSLER KLKRRLEREG LSSERWERVK KMRTPKKKKI KLSHPKDMNN FKLERERSYE LVRSAETHSL PSDTSYSEQE DSEDEDAICP AVSCLQPEGD EVDWVQCDGS CNQWFHQVCV GVSPEMAEKE DYICVRCTVK DAPSRK

Experimental information

• Beam: Instrument name: University of Copenhagen, Department of Drug Design and Pharmacology Xenocs / BioXolver L with GeniX3D; City: Copenhagen / 国: Denmark / Type of source: X-ray in house / Wavelength: 0.154 Å
• Detector: Name: Pilatus3 R 300K / Type: pixel counting / Pixsize x: 172 mm

Scan

Title: Lysine-specific demethylase 5B, KDM5B, in HEPES buffer
Measurement date: Oct 24, 2018 / Storage temperature: 7 °C / Cell temperature: 7 °C / Unit: 1/A /

	Min	Max
Q	0.0056	0.4829

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 167 /

	Min	Max
Q	0.00558563	0.19892
P(R) point	1	167
R	0	269

Result

Type of curve: other
Comments: KDM5B at concentrations of 0.75, 1, 1.5 and 1.8 mg/ml were measured with two different sample-detector distances (d1 = 571 mm, d2 = 1382 mm) using a sample volume of 7 µl per concentration. After background correction, the scattering curves were brought to absolute scale using water as a secondary standard and subsequently normalized by concentration. As no concentration-dependence was observed, all four curves were then averaged to produce the current data set. Measurement times were: 0.75 mg/ml: d1: 90 min, d2: 120 min; 1 mg/ml: d1: 60 min, d2: 120 min; 1.5 mg/ml: d1: 60 min, d2: 100 min; 1.8 mg/ml: d1: 30 min, d2: 40 min. The dummy atom model (top) represents the spatially aligned and volume occupancy corrected low resolution structure obtained from multiple shape reconstructions (DAMFILT model) that are available in the full entry zip archive. An individual model example (bottom) and the corresponding fit to the data are also displayed.

	Experimental	Standard
MW	121 kDa	152 kDa

	P(R)	Guinier	Guinier error
Forward scattering, I0	0.06685	0.08391	0.0113
Radius of gyration, Rg	8.53 nm	8.841 nm	3.342

	Min	Max
D	-	26.9
Guinier point	1	10