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- EMDB-15165: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module... -

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Basic information

Entry
Database: EMDB / ID: EMD-15165
TitleStructure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80
Map datamain map
Sample
  • Complex: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Ino80 ATPase
    • Protein or peptide: Actin-related protein 8
    • Protein or peptide: Actin
    • Protein or peptide: Actin related protein 4 (Arp4)
    • Protein or peptide: Ies4
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordschromatin remodeler / INO80 / Actin-related protein / DNA binding protein
Function / homology
Function and homology information


Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding ...Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP binding
Similarity search - Function
INO80 complex, subunit Ies4 / INO80 complex subunit Ies4 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin-related protein 8 / Actin-related protein 4 / INO80 complex subunit 4 / Actin
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKunert F / Metzner FJ / Eustermann S / Jung J / Woike S / Schall K / Kostrewa D / Hopfner KP
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)833613 INO3DEuropean Union
German Research Foundation (DFG)CRC1064 Germany
German Research Foundation (DFG)CRC1361 Germany
German Research Foundation (DFG)RTG1721 Germany
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Prize Germany
CitationJournal: Sci Adv / Year: 2022
Title: Structural mechanism of extranucleosomal DNA readout by the INO80 complex.
Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian ...Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian Eustermann / Karl-Peter Hopfner /
Abstract: The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which ...The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
History
DepositionJun 14, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15165.png

Downloads & links

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Map

FileDownload / File: emd_15165.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0959293 - 0.20795052
Average (Standard dev.)0.00023553464 (±0.004032985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_15165_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15165_half_map_2.map
Annotationhalf map B
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-In...

EntireName: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
Components
  • Complex: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Ino80 ATPase
    • Protein or peptide: Actin-related protein 8
    • Protein or peptide: Actin
    • Protein or peptide: Actin related protein 4 (Arp4)
    • Protein or peptide: Ies4
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-In...

SupramoleculeName: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Ino80 ATPase

MacromoleculeName: Ino80 ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 37.445441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RKRRREKSMA ATLEQQAAAL QKASQAEDEA ERLKYIREAE RANKKVQQTK YILQKGIKGP ARNLPPIEPN LEGGTMATFS AENMEPGKV KGKGRGGRLK KSKEQKQAEK EQAELAQAAI DAGEEPPSKE ETKIRIKLSK AKASAKEEAE KDKENKEPKQ P KEPEKPVE ...String:
RKRRREKSMA ATLEQQAAAL QKASQAEDEA ERLKYIREAE RANKKVQQTK YILQKGIKGP ARNLPPIEPN LEGGTMATFS AENMEPGKV KGKGRGGRLK KSKEQKQAEK EQAELAQAAI DAGEEPPSKE ETKIRIKLSK AKASAKEEAE KDKENKEPKQ P KEPEKPVE EPKDPLELKF QSKGYNQIYD QIWRDLARKD VSKVFRLATD SYATKASNLK KTAILASKEA KRWQLRTNKG TK DLQARAK RVMRDMMGFW KRNEREERDL RKAAERLELE NARKEEADRE AARQRRKLNF LISQTELYSD YKDDDDKGTD YKD DDDK

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Macromolecule #2: Actin-related protein 8

MacromoleculeName: Actin-related protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 84.139266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVGKVSERVL AREGLERTDN GMRQTSWPEV QPINQKNYYT DYMKRDDQIL SLRLQNEANR ERLVKTAQDR DRALNTNTNG EVPLPLDEL QEDAPPAPSA AMDPSKIIVI HPGSQNLRIG FASDALPKTI PMVLGTQYSQ TESEMHEALP RRQFEGRTME Q QYGEEWVK ...String:
MVGKVSERVL AREGLERTDN GMRQTSWPEV QPINQKNYYT DYMKRDDQIL SLRLQNEANR ERLVKTAQDR DRALNTNTNG EVPLPLDEL QEDAPPAPSA AMDPSKIIVI HPGSQNLRIG FASDALPKTI PMVLGTQYSQ TESEMHEALP RRQFEGRTME Q QYGEEWVK KYQKMCSDLK VTMRANKLKV LPNSKDLVVN FNRRTEPEII SQHNDPLQVE WTNVNKAPED GTTQKVFIGQ QA LRIAEDS SPKYKLWWPI QHGWLNEDDY PTRAHLFDDL EMLLDRALRR ELGLTKKADW KQYSCVIVIP DLYDKRYVEL LLH LCIEFF DLSRVAFIQE SMAATFGAGY TQACVVDVGA QKTSISCVED GLVIEDSRVN LKYGGYDVTE TFIKMMLYDN FPYQ DINLR RRHDFLLAEE LKMKYCTLSQ ANISVQAFDF HLRAPNQPTR KYQFKFYDEV ILAPMGFYDP SIFDNSTKLR GRRKL IDRS YNAYDVDMPD DPTSSAQLAI LAMVQPSLAA PTATASFNGD PTATPSKERT QPFNFLSRPD ATGTPGTSKA PSPAPD GAS TPVPGPYIFG ASSREANGGS PAPSGRNGGT PAPANGTTVL PATSFDNPTS QQPQQRSAKE IAAERDAVLP IAPLDVA IL TSIQHAAKGD EKKVRELVGS IMVVGGGAKI PHFAPFLEEK LKIRRPDLAD RILVSRSARE MDEQVVVWKG ASVFAKLS T NDSWVTNYEY KMLGSRCIYM KLLWHY

UniProtKB: Actin-related protein 8

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Macromolecule #3: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 41.735512 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEEEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH HGIMIGMGQK DSYVGDEAQS KRGILTLRYP IEHGVVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP INPKSNREKM TQIVFETFNA PAFYVSIQAV LSLYASGRTT GIVLDSGDGV T HVVPIYEG ...String:
MEEEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH HGIMIGMGQK DSYVGDEAQS KRGILTLRYP IEHGVVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP INPKSNREKM TQIVFETFNA PAFYVSIQAV LSLYASGRTT GIVLDSGDGV T HVVPIYEG FSLPHAIARL DMAGRDLTDY LMKILAERGY TFSTTAEREI VRDIKEKLCY VALDFEQEIQ TAAQSSHLEK SY ELPDGQV ITIGNERFRA PEALFQPSVL GLESGGIHVT TFNSIMKCDV DVRKDLYGNI VMSGGTTMYP GLSDRMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin

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Macromolecule #4: Actin related protein 4 (Arp4)

MacromoleculeName: Actin related protein 4 (Arp4) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 51.761199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSQQPLSSSV QPADIYGGDE VSALVLDPGY CNTRAGFAGE EMPKQVIPSF YGHVDGRDLF GDEVIVPRAG FEVRNYMNRD SMVEDWDAA TRVWEYLLVQ RLQPPRPTPA SKNGLNVSDD GDVQMEDSAP NEDALDALEK PLTENPLLMT EAPWNTPKAR E KAIEVVME ...String:
MSQQPLSSSV QPADIYGGDE VSALVLDPGY CNTRAGFAGE EMPKQVIPSF YGHVDGRDLF GDEVIVPRAG FEVRNYMNRD SMVEDWDAA TRVWEYLLVQ RLQPPRPTPA SKNGLNVSDD GDVQMEDSAP NEDALDALEK PLTENPLLMT EAPWNTPKAR E KAIEVVME NWGTPAFWLS RTPVLAAFAA GKATALVIDV GGANTSVTAI HDGMVLKRSI QRSPAAGVWL SGQIRSMWKS QD PPVNVVP TFMVENKKPV EAGAPPDCRL RNFGFPIHDS FRAFEEERVL TEFKESVVEV WRGPGKYLNP GNEDFAKTQP GRV FEFPDG SNQMWREQRY RVAEGMWDET AAYPSLNPDE AAITKAQTIP ALIKAALDGV DVDLRPNLLG NVVVTGSTSL LNGF NDRLN HELTNMYPGL KIKLHAAGLT SERRFGAWIG GSILASLGTF HQMWISRKEY EENGAGIVEK RCK

UniProtKB: Actin-related protein 4

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Macromolecule #5: Ies4

MacromoleculeName: Ies4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 29.015457 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPSSKNATP SNKDRRKSGI AAAGNGNAAA SSKIVTLKVT PERLRAIFDP DILMEDAPAS KASPAAANSN TENATESNPN SPSASTPAG QSVMGPPAEG PKKKGVKRGA AALGPNGEPK PRGKPGPKKK QRLEDGTIVE EPSRKLGPKA NQGAINAGLR A LDRSGKPC ...String:
MAPSSKNATP SNKDRRKSGI AAAGNGNAAA SSKIVTLKVT PERLRAIFDP DILMEDAPAS KASPAAANSN TENATESNPN SPSASTPAG QSVMGPPAEG PKKKGVKRGA AALGPNGEPK PRGKPGPKKK QRLEDGTIVE EPSRKLGPKA NQGAINAGLR A LDRSGKPC RKWTRGTFQM KSFTGVVWEI PRWTAPPRPK PETAAPDDAA ATVAVNGNGA TPASTAADNN SNKENNNPSI AA AKVEDAS SQTAVKSEMS TGSGDIEMQS VAPSIAPSPA PVPIAVA

UniProtKB: INO80 complex subunit 4

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Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
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: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 343000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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