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- EMDB-3982: Molecular Architecture of the Jumonji C histone demethylase KDM5B. -

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Basic information

Entry
Database: EMDB / ID: EMD-3982
TitleMolecular Architecture of the Jumonji C histone demethylase KDM5B.
Map data
Sample
  • Organelle or cellular component: KDM5B
    • Protein or peptide: KDM5B
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsAduri NA / Gajhede M
CitationJournal: 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 ...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- ...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.
History
DepositionNov 9, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseMar 27, 2019-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0279
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0279
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3982.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.15 Å
Density
Contour LevelBy AUTHOR: 0.0279 / Movie #1: 0.0279
Minimum - Maximum-0.038809728 - 0.11967578
Average (Standard dev.)0.000055093136 (±0.003127656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 567.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z567.000567.000567.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0390.1200.000

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Supplemental data

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Sample components

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Entire : KDM5B

EntireName: KDM5B
Components
  • Organelle or cellular component: KDM5B
    • Protein or peptide: KDM5B

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Supramolecule #1: KDM5B

SupramoleculeName: KDM5B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: KDM5B

MacromoleculeName: KDM5B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MEAATTLHPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG ICKVRPPPD WQPPFACDVD KLHFTPRIQR LNELEAQTRV KLNFLDQIAK YWELQGSTLK I PHVERKIL DLFQLNKLVA EEGGFAVVCK DRKWTKIATK MGFAPGKAVG ...String:
MEAATTLHPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG ICKVRPPPD WQPPFACDVD KLHFTPRIQR LNELEAQTRV KLNFLDQIAK YWELQGSTLK I PHVERKIL DLFQLNKLVA EEGGFAVVCK DRKWTKIATK MGFAPGKAVG SHIRGHYERI LN PYNLFLS GDSLRCLQKP NLTTDTKDKE YKPHDIPQRQ SVQPSETCPP ARRAKRMRAE AMN IKIEPE ETTEARTHNL RRRMGCPTPK CENEKEMKSS IKQEPIERKD YIVENEKEKP KSRS KKATN AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQE CSKP QEAFGFEQAA RDYTLRTFGE MADAFKSDYF NMPVHMVPTE LVEKEFWRLV STIEED VTV EYGADIASKE FGSGFPVRDG KIKLSPEEEE YLDSGWNLNN MPVMEQSVLA HITADIC GM KLPWLYVGMC FSSFCWHIED HWSYSINYLH WGEPKTWYGV PGYAAEQLEN VMKKLAPE L FVSQPDLLHQ LVTIMNPNTL MTHEVPVYRT NQCAGEFVIT FPRAYHSGFN QGFNFAEAV NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST VQKDMAIMIE DEKALRETV RKLGVIDSER MDFELLPDDE RQCVKCKTTC FMSAISCSCK PGLLVCLHHV K ELCSCPPY KYKLRYRYTL DDLYPMMNAL KLRAESYNEW ALNVNEALEA KINKKKSLVS FK ALIEESE MKKFPDNDLL RHLRLVTQDA EKCASVAQQL LNGKRQTRYR SGGGKSQNQL TVN ELRQFV TQLYALPCVL SQTPLLKDLL NRVEDFQQHS QKLLSEETPS AAELQDLLDV SFEF DVELP QLAEMRIRLE QARWLEEVQQ ACLDPSSLTL DDMRRLIDLG VGLAPYSAVE KAMAR LQEL LTVSEHWDDK AKSLLKARPR HSLNSLATAV KEIEEIPAYL PNGAALKDSV QRARDW LQD VEGLQAGGRV PVLDTLIELV TRGRSIPVHL NSLPRLETLV AEVQAWKECA VNTFLTE NS PYSLLEVLCP RCDIGLLGLK RKQRKLKEPL PNGKKKSTKL ESLSDLERAL TESKETAS A MATLGEARLR EMEALQSLRL ANEGKLLSPL QDVDIKICLC QKAPAAPMIQ CELCRDAFH TSCVAVPSIS QGLRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD ALRYMIERTV NWQHRAQQL LSSGNLKFVQ DRVGSGLLYS RWQASAGQVS DTNKVSQPPG TTSFSLPDDW D NRTSYLHS PFSTGRSCIP LHGVSPEVNE LLMEAQLLQV SLPEIQELYQ TLLAKPSPAQ QT DRSSPVR PSSEKNDCCR GKRDGINSLE RKLKRRLERE GLSSERWERV KKMRTPKKKK IKL SHPKDM NNFKLERERS YELVRSAETH SLPSDTSYSE QEDSEDEDAI CPAVSCLQPE GDEV DWVQC DGSCNQWFHQ VCVGVSPEMA EKEDYICVRC TVKDAPSRK

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.7
StainingType: NEGATIVE / Material: Uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 10.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9599

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