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- EMDB-15186: Cryo-EM reconstruction of DNA bound Arp4-Ies4-N-actin-Arp8-Ino80H... -

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Basic information

Entry
Database: EMDB / ID: EMD-15186
TitleCryo-EM reconstruction of DNA bound Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80
Map datamap
Sample
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) bound to DNA
    • Protein or peptide: Ino80
    • Protein or peptide: Arp8
    • Protein or peptide: Actin
    • Protein or peptide: Arp4
    • Protein or peptide: Ies4
    • DNA: DNA
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 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 15, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15186.png

Downloads & links

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Map

FileDownload / File: emd_15186.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.0082
Minimum - Maximum-0.00870377 - 0.04151663
Average (Standard dev.)0.0002483973 (±0.0021668721)
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_15186_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15186_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) bound to DNA
Components
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) bound to DNA
    • Protein or peptide: Ino80
    • Protein or peptide: Arp8
    • Protein or peptide: Actin
    • Protein or peptide: Arp4
    • Protein or peptide: Ies4
    • DNA: DNA

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

SupramoleculeName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) bound to DNA
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Ino80

MacromoleculeName: Ino80 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQQ SKDWQFDNTN DSQDLHFKKL YRDMSMINKE WAEYQSFKNA NLSDIINEKD ADEDEEDDED ELEDGEEDME EDEASTGRHT ...String:
MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQQ SKDWQFDNTN DSQDLHFKKL YRDMSMINKE WAEYQSFKNA NLSDIINEKD ADEDEEDDED ELEDGEEDME EDEASTGRHT NGKSMRGNGI QKSRKKDAAA AAAIGKAIKD DQTHADTVVT VNGDENEDGN NGEDEDNDND NENNNDNDND NENENDNDSD NDDEEENGEE DEEEEEIEDL DEEDFAAFEE QDDNDDEDFN PDVEKRRKRS SSSSSSTKLS MNSLSLITSK KINKNITINS DRPKIVRELI KMCNKNKHQK IKKRRFTNCI VTDYNPIDSK LNIKITLKQY HVKRLKKLIN DAKREREREE ALKNNVGLDG NDLDNDEDGS ESHKRRKLNN NTANGADDAN KRKFNTRHGL PTYGMKMNAK EARAIQRHYD NTYTTIWKDM ARKDSTKMSR LVQQIQSIRS TNFRKTSSLC AREAKKWQSK NFKQIKDFQT RARRGIREMS NFWKKNEREE RDLKKKIEKE AMEQAKKEEE EKESKRQAKK LNFLLTQTEL YSHFIGRKDY KDDDDKGTDY KDDDDK

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Macromolecule #2: Arp8

MacromoleculeName: Arp8 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSQEEAESSI IYEEPIDIPL EDDDDEDELE EENSVPLSSQ ADQENAENES DDSVDNVVGS ETPRSVTGLS VDPRDVADEE DEDEEGEDED EDEDDNDVDN EDENDNDNAN ENENELGSSR DKRAPPAVQT SKRYKKYPKL DPAKAPPGKK VPLHLLEKRR LGRIKAAEEF ...String:
MSQEEAESSI IYEEPIDIPL EDDDDEDELE EENSVPLSSQ ADQENAENES DDSVDNVVGS ETPRSVTGLS VDPRDVADEE DEDEEGEDED EDEDDNDVDN EDENDNDNAN ENENELGSSR DKRAPPAVQT SKRYKKYPKL DPAKAPPGKK VPLHLLEKRR LGRIKAAEEF AKTLKKIGIE KVETTTLPAT GLFQPLMLIN QKNYSSDYLK KDDQIFALRD RKFLRNNNTS QISSTNTPDV IDLKSLPHSE ASAAPLNDEI DLNDPTATIV IHPGSNSIKI GFPKDDHPVV VPNCVAVPKK WLDLENSEHV ENVCLQREQS EEFNNIKSEM EKNFRERMRY YKRKVPGNAH EQVVSFNENS KPEIISEKND PSPIEWIFDD SKLYYGSDAL RCVDEKFVIR KPFRGGSFNV KSPYYKSLAE LISDVTKLLE HALNSETLNV KPTKFNQYKV VLVIPDIFKK SHVETFIRVL LTELQFQAVA IIQESLATCY GAGISTSTCV VNIGAAETRI ACVDEGTVLE HSAITLDYGG DDITRLFALF LLQSDFPLQD WKIDSKHGWL LAERLKKNFT TFQDADVAVQ LYNFMNRSPN QPTEKYEFKL FDEVMLAPLA LFFPQIFKLI RTSSHKNSSL EFQLPESRDL FTNELNDWNS LSQFESKEGN LYCDLNDDLK ILNRILDAHN IIDQLQDKPE NYGNTLKENF APLEKAIVQS IANASITADV TRMNSFYSNI LIVGGSSKIP ALDFILTDRI NIWRPSLLSS ASFPQFYKKL TKEIKDLEGH YVNAPDKTED ENKQILQAQI KEKIVEELEE QHQNIEHQNG NEHIFPVSII PPPRDMNPAL IIWKGASVLA QIKLVEELFI TNSDWDVHGS RILQYKCIFT Y

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Macromolecule #3: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPM NPKSNREKMT QIMFETFNVP AFYVSIQAVL SLYSSGRTTG IVLDSGDGVT HVVPIYAGFS ...String:
MDSEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGIMVGMGQK DSYVGDEAQS KRGILTLRYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPM NPKSNREKMT QIMFETFNVP AFYVSIQAVL SLYSSGRTTG IVLDSGDGVT HVVPIYAGFS LPHAILRIDL AGRDLTDYLM KILSERGYSF STTAEREIVR DIKEKLCYVA LDFEQEMQTA AQSSSIEKSY ELPDGQVITI GNERFRAPEA LFHPSVLGLE SAGIDQTTYN SIMKCDVDVR KELYGNIVMS GGTTMFPGIA ERMQKEITAL APSSMKVKII APPERKYSVW IGGSILASLT TFQQMWISKQ EYDESGPSIV HHKCF

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Macromolecule #4: Arp4

MacromoleculeName: Arp4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQW QWALQNELYL NSNSGIPALL TEPVWNSTEN RKKSLEVLLE GMQFEACYLA PTSTCVSFAA GRPNCLVVDI GHDTCSVSPI ...String:
MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQW QWALQNELYL NSNSGIPALL TEPVWNSTEN RKKSLEVLLE GMQFEACYLA PTSTCVSFAA GRPNCLVVDI GHDTCSVSPI VDGMTLSKST RRNFIAGKFI NHLIKKALEP KEIIPLFAIK QRKPEFIKKT FDYEVDKSLY DYANNRGFFQ ECKETLCHIC PTKTLEETKT ELSSTAKRSI ESPWNEEIVF DNETRYGFAE ELFLPKEDDI PANWPRSNSG VVKTWRNDYV PLKRTKPSGV NKSDKKVTPT EEKEQEAVSK STSPAANSAD TPNETGKRPL EEEKPPKENN ELIGLADLVY SSIMSSDVDL RATLAHNVVL TGGTSSIPGL SDRLMTELNK ILPSLKFRIL TTGHTIERQY QSWLGGSILT SLGTFHQLWV GKKEYEEVGV ERLLNDRFR

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Macromolecule #5: Ies4

MacromoleculeName: Ies4 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
MSQESSVLSE SQEQLANNPK IEDTSPPSAN SRDNSKPVLP WDYKNKAIEI KSFSGYKVNF TGWIRRDVRE ERQRGSEFTA SDVKGSDDKA TRKKEPADED PEVKQLEKEG EDGLDS

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Macromolecule #6: DNA

MacromoleculeName: DNA / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString:
CTTACCCTGC GTGCCCGCGC ACCCTGGCGA CTTCGCCTCG TTTTGGCGAT TTTCTTAG

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.68 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69226

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