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- EMDB-0800: Abo1 structure with AAA+ and bromodomains in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-0800
TitleAbo1 structure with AAA+ and bromodomains in apo state
Map dataapo-Abo1 with bromodomain
Sample
  • Complex: apo-Abo1
    • Protein or peptide: Abo1
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsCho C / Jang J
Funding support Korea, Republic Of, 5 items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1A2B3006293 Korea, Republic Of
National Research Foundation (Korea)2018R1A6A7052113 Korea, Republic Of
National Research Foundation (Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (Korea)NRF-2018R1D1A1B07047345 Korea, Republic Of
National Research Foundation (Korea)NRF-2015H1D3A1066116 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone.
Authors: Carol Cho / Juwon Jang / Yujin Kang / Hiroki Watanabe / Takayuki Uchihashi / Seung Joong Kim / Koichi Kato / Ja Yil Lee / Ji-Joon Song /
Abstract: The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate ...The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3-H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3-H4 loading by utilizing ATP.
History
DepositionSep 30, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseDec 25, 2019-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0800.png

Downloads & links

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Map

FileDownload / File: emd_0800.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationapo-Abo1 with bromodomain
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.0097145485 - 0.026930096
Average (Standard dev.)0.00008021694 (±0.0013738818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0100.0270.000

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Supplemental data

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Sample components

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Entire : apo-Abo1

EntireName: apo-Abo1
Components
  • Complex: apo-Abo1
    • Protein or peptide: Abo1

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Supramolecule #1: apo-Abo1

SupramoleculeName: apo-Abo1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Abo1

MacromoleculeName: Abo1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKEEASEHGG SADETQELSP VSDSSDEMPN NAKRRRRSQS MIANKRIHQA FQEDEGDEDW EEEEHKPKA KRRYNTRSNE SFSEGDDEPF EVSESSALED ELSDSEDSFI RSVRSKPKYK P GTRRSTRL RNRRSQDEEE SEEEHRPILR ERTSRINYSV PLAFPPVDEM ...String:
MKEEASEHGG SADETQELSP VSDSSDEMPN NAKRRRRSQS MIANKRIHQA FQEDEGDEDW EEEEHKPKA KRRYNTRSNE SFSEGDDEPF EVSESSALED ELSDSEDSFI RSVRSKPKYK P GTRRSTRL RNRRSQDEEE SEEEHRPILR ERTSRINYSV PLAFPPVDEM DGDPSSQVNQ SR SRKTHSE LAITKLLRQQ VSSFMPYIDS SGSESESDNT RIKKSSAKTI KALTDPANSG GPP DFGRIR EKSDLADSDP LGVDSSLSFE SVGGLDNYIN QLKEMVMLPL LYPEIFQRFN MQPP RGVLF HGPPGTGKTL MARALAAACS SENKKVSFYM RKGADCLSKW VGEAERQLRL LFEEA KSTQ PSIIFFDEID GLAPVRSSKQ EQIHASIVST LLALMDGMES RGQVIIIGAT NRPDAV DPA LRRPGRFDRE FYFPLPDRDA RKKIIEIHTR NWDPPVPEWL CSMLAEKSKG YGGADLR AL CTEAALNSIK RTYPQLYRST KRLQIDPKTI KVKVKDFVMS MKRMIPSSER SSISPSKP L SPELKPLLNE AFQDIEKTLQ KLMPVASKLN PLEEVMYDDP KENDFEYQQR LETFETLRI YKPRFLICGR KGLGQTALGP AILQQYEGVH VQSFDMSTLL QDSTQSIETS IIHLFLEVRR HTPSIIYIP DIDNWLNVLP LTAITTFSSM LERLDFSDQI LFLALSSSPL SELHPQLREW F SSKQSVYS LQYPTRDSII AFFQPILELI KASPTELPGG IPRKRRVLPE LPLAPDPPPF TS QKITLKQ TKQADMRLLN KLKIKLNALL GSLRARYRKF KKPLIDFNDI YCVDPETGHS YRS REECHY EFVDDVVKQI GSDQKFSMMS LEEIEKRTWD NCYCTPKQFV HDIKLILRDA LQLE DSETI KRAQEMYANV LLGVEDMEDD QFSQRCERMA LREAERRKLR HGKLQKHLDE TKADM QFTS EKPSVDESIT EVDDAIKDGP PVLAETLTNS LMEDVGPENV DMDIEDNEIF TNQSTM SVP SMLVENEESP KPDEYIDQKD KVQSPLLNGK SPVGVPSEAA LRVSTDVSTN ISSNGRA DI PVDTLITSPA DVPNNAPTDA HNITSADGHI ENIEQEVVFP DLVFDEDRLT PLKQLLID S TTGFTVDQLL HLHSFLYQII WNTKSEWNRN SVVDECERAV KEFMINALQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.015 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23581
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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