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- EMDB-15163: Cryo-EM reconstruction of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomp... -

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Basic information

Entry
Database: EMDB / ID: EMD-15163
TitleCryo-EM reconstruction of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80
Map datasharpened map
Sample
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: Actin-like protein ARP8
    • Protein or peptide: Actin
    • Protein or peptide: Actin-related protein 4
    • Protein or peptide: Ino eighty subunit 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordschromatin remodeler / INO80 / Actin-related protein / DNA binding protein
Function / homology
Function and homology information


RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic recombination / regulation of TOR signaling / Swr1 complex ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic recombination / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / kinetochore assembly / Ino80 complex / regulation of metabolic process / SWI/SNF complex / DNA duplex unwinding / ATP-dependent chromatin remodeler activity / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / chromosome, centromeric region / protein secretion / subtelomeric heterochromatin formation / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / double-strand break repair / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / cytoskeleton / chromatin remodeling / DNA repair / mRNA binding / DNA-templated transcription / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actins signature 1. ...DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / : / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromatin-remodeling ATPase INO80 / Actin / Actin-related protein 4 / Ino eighty subunit 4 / Actin-like protein ARP8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 14, 2022-
Map releaseDec 14, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15163.png

Downloads & links

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Map

FileDownload / File: emd_15163.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.735
Minimum - Maximum-4.7337427 - 7.520875
Average (Standard dev.)0.005667613 (±0.15742645)
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_15163_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15163_half_map_2.map
Annotationhalf map B
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)

EntireName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
Components
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: Actin-like protein ARP8
    • Protein or peptide: Actin
    • Protein or peptide: Actin-related protein 4
    • Protein or peptide: Ino eighty subunit 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)

SupramoleculeName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 72.170648 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQ QSKDWQFDNT NDSQDLHFKK LYRDMSMINK EWAEYQSFKN ANLSDIINEK DADEDEEDDE DELEDGEEDM E EDEASTGR ...String:
MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQ QSKDWQFDNT NDSQDLHFKK LYRDMSMINK EWAEYQSFKN ANLSDIINEK DADEDEEDDE DELEDGEEDM E EDEASTGR HTNGKSMRGN GIQKSRKKDA AAAAAIGKAI KDDQTHADTV VTVNGDENED GNNGEDEDND NDNENNNDND ND NENENDN DSDNDDEEEN GEEDEEEEEI EDLDEEDFAA FEEQDDNDDE DFNPDVEKRR KRSSSSSSST KLSMNSLSLI TSK KINKNI TINSDRPKIV RELIKMCNKN KHQKIKKRRF TNCIVTDYNP IDSKLNIKIT LKQYHVKRLK KLINDAKRER EREE ALKNN VGLDGNDLDN DEDGSESHKR RKLNNNTANG ADDANKRKFN TRHGLPTYGM KMNAKEARAI QRHYDNTYTT IWKDM ARKD STKMSRLVQQ IQSIRSTNFR KTSSLCAREA KKWQSKNFKQ IKDFQTRARR GIREMSNFWK KNEREERDLK KKIEKE AME QAKKEEEEKE SKRQAKKLNF LLTQTELYSH FIGRKDYKDD DDKGTDYKDD DDK

UniProtKB: Chromatin-remodeling ATPase INO80

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Macromolecule #2: Actin-like protein ARP8

MacromoleculeName: Actin-like protein ARP8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.322688 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSQEEAESSI IYEEPIDIPL EDDDDEDELE EENSVPLSSQ ADQENAENES DDSVDNVVGS ETPRSVTGLS VDPRDVADEE DEDEEGEDE DEDEDDNDVD NEDENDNDNA NENENELGSS RDKRAPPAVQ TSKRYKKYPK LDPAKAPPGK KVPLHLLEKR R LGRIKAAE ...String:
MSQEEAESSI IYEEPIDIPL EDDDDEDELE EENSVPLSSQ ADQENAENES DDSVDNVVGS ETPRSVTGLS VDPRDVADEE DEDEEGEDE DEDEDDNDVD NEDENDNDNA NENENELGSS RDKRAPPAVQ TSKRYKKYPK LDPAKAPPGK KVPLHLLEKR R LGRIKAAE EFAKTLKKIG IEKVETTTLP ATGLFQPLML INQKNYSSDY LKKDDQIFAL RDRKFLRNNN TSQISSTNTP DV IDLKSLP HSEASAAPLN DEIDLNDPTA TIVIHPGSNS IKIGFPKDDH PVVVPNCVAV PKKWLDLENS EHVENVCLQR EQS EEFNNI KSEMEKNFRE RMRYYKRKVP GNAHEQVVSF NENSKPEIIS EKNDPSPIEW IFDDSKLYYG SDALRCVDEK FVIR KPFRG GSFNVKSPYY KSLAELISDV TKLLEHALNS ETLNVKPTKF NQYKVVLVIP DIFKKSHVET FIRVLLTELQ FQAVA IIQE SLATCYGAGI STSTCVVNIG AAETRIACVD EGTVLEHSAI TLDYGGDDIT RLFALFLLQS DFPLQDWKID SKHGWL LAE RLKKNFTTFQ DADVAVQLYN FMNRSPNQPT EKYEFKLFDE VMLAPLALFF PQIFKLIRTS SHKNSSLEFQ LPESRDL FT NELNDWNSLS QFESKEGNLY CDLNDDLKIL NRILDAHNII DQLQDKPENY GNTLKENFAP LEKAIVQSIA NASITADV T RMNSFYSNIL IVGGSSKIPA LDFILTDRIN IWRPSLLSSA SFPQFYKKLT KEIKDLEGHY VNAPDKTEDE NKQILQAQI KEKIVEELEE QHQNIEHQNG NEHIFPVSII PPPRDMNPAL IIWKGASVLA QIKLVEELFI TNSDWDVHGS RILQYKCIFT Y

UniProtKB: Actin-like protein ARP8

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Macromolecule #3: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 41.735547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG ...String:
MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP MNPKSNREKM TQIMFETFNV PAFYVSIQAV LSLYSSGRTT GIVLDSGDGV T HVVPIYAG FSLPHAILRI DLAGRDLTDY LMKILSERGY SFSTTAEREI VRDIKEKLCY VALDFEQEMQ TAAQSSSIEK SY ELPDGQV ITIGNERFRA PEALFHPSVL GLESAGIDQT TYNSIMKCDV DVRKELYGNI VMSGGTTMFP GIAERMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLTTFQQMW ISKQEYDESG PSIVHHKCF

UniProtKB: Actin

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Macromolecule #4: Actin-related protein 4

MacromoleculeName: Actin-related protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 54.894684 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQ WQWALQNELY LNSNSGIPAL LTEPVWNSTE NRKKSLEVLL EGMQFEACYL APTSTCVSFA AGRPNCLVVD I GHDTCSVS ...String:
MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQ WQWALQNELY LNSNSGIPAL LTEPVWNSTE NRKKSLEVLL EGMQFEACYL APTSTCVSFA AGRPNCLVVD I GHDTCSVS PIVDGMTLSK STRRNFIAGK FINHLIKKAL EPKEIIPLFA IKQRKPEFIK KTFDYEVDKS LYDYANNRGF FQ ECKETLC HICPTKTLEE TKTELSSTAK RSIESPWNEE IVFDNETRYG FAEELFLPKE DDIPANWPRS NSGVVKTWRN DYV PLKRTK PSGVNKSDKK VTPTEEKEQE AVSKSTSPAA NSADTPNETG KRPLEEEKPP KENNELIGLA DLVYSSIMSS DVDL RATLA HNVVLTGGTS SIPGLSDRLM TELNKILPSL KFRILTTGHT IERQYQSWLG GSILTSLGTF HQLWVGKKEY EEVGV ERLL NDRFR

UniProtKB: Actin-related protein 4

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Macromolecule #5: Ino eighty subunit 4

MacromoleculeName: Ino eighty subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.111197 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSQESSVLSE SQEQLANNPK IEDTSPPSAN SRDNSKPVLP WDYKNKAIEI KSFSGYKVNF TGWIRRDVRE ERQRGSEFTA SDVKGSDDK ATRKKEPADE DPEVKQLEKE GEDGLDS

UniProtKB: Ino eighty subunit 4

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: 44.68 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 327293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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