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- EMDB-4277: CryoEM Structure INO80core Nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4277
TitleCryoEM Structure INO80core Nucleosome complex
Map data
Sample
  • Complex: INO80core Nucleosome Complex
    • Complex: INO80core
      • Protein or peptide: x 6 types
    • Complex: Histone octamer
      • Protein or peptide: x 4 types
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: x 2 types
  • Ligand: x 2 types
Function / homology
Function and homology information


RMTs methylate histone arginines / DASH complex / heterochromatin formation => GO:0031507 / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / chromatin => GO:0000785 ...RMTs methylate histone arginines / DASH complex / heterochromatin formation => GO:0031507 / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / chromatin => GO:0000785 / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / negative regulation of megakaryocyte differentiation / ATP-dependent activity, acting on DNA / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / helicase activity / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / mitotic spindle / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA repair / enzyme binding / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
DASH complex subunit Dad4 / DASH complex subunit Dad4 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / PAPA-1-like conserved region / PAPA-1 / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain ...DASH complex subunit Dad4 / DASH complex subunit Dad4 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / PAPA-1-like conserved region / PAPA-1 / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Histone-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INO80 complex subunit B-like conserved region domain-containing protein / RuvB-like helicase / RuvB-like helicase / Uncharacterized protein / Vps72/YL1 C-terminal domain-containing protein / Histone H2A type 1 / Histone H2A type 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Homo sapiens (human) / synthetic construct (others) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.34 Å
AuthorsEustermann S / Schall K / Kostrewa D / Strauss M / Hopfner K
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Molecular Biology OrganizationEMBO ALTF 1098-2012 Germany
German Research FoundationCRC1064, GRK1721 Germany
European Research CouncilATMMACHINE Germany
CitationJournal: Nature / Year: 2018
Title: Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.
Authors: Sebastian Eustermann / Kevin Schall / Dirk Kostrewa / Kristina Lakomek / Mike Strauss / Manuela Moldt / Karl-Peter Hopfner /
Abstract: In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone ...In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers such as the 15-subunit INO80 complex . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA. The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange.
History
DepositionJan 31, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseApr 25, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fml
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4277.png

Downloads & links

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Map

FileDownload / File: emd_4277.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.078898385 - 0.14019749
Average (Standard dev.)0.00019601843 (±0.004939095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 360.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0790.1400.000

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Supplemental data

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Sample components

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Entire : INO80core Nucleosome Complex

EntireName: INO80core Nucleosome Complex
Components
  • Complex: INO80core Nucleosome Complex
    • Complex: INO80core
      • Protein or peptide: RuvB-like helicase
      • Protein or peptide: RuvB-like helicase
      • Protein or peptide: Ino80
      • Protein or peptide: les2
      • Protein or peptide: Ies6
      • Protein or peptide: Actin related protein 5
    • Complex: Histone octamer
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Nucleosomal DNA Strand 1
      • DNA: Nucleosomal DNA Strand 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: INO80core Nucleosome Complex

SupramoleculeName: INO80core Nucleosome Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Molecular weightTheoretical: 1 MDa

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Supramolecule #2: INO80core

SupramoleculeName: INO80core / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#12
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Synthetic deoxyribonucleic acid

SupramoleculeName: Synthetic deoxyribonucleic acid / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: RuvB-like helicase

MacromoleculeName: RuvB-like helicase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 50.451848 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVQISEVRGN TRDHRTAAHT HIKGLGLNSS GIAEKQAAGF VGQCAAREAC GVVVDLIKAH KMAGRGVLLA GGPGTGKTAL ALAISQELG TKIPFCPITG SEIYSTEVKK TEVLMENFRR AIGLRVRETK DVYEGEVTEM TPEEAENPLG GYGKTISTLL I GLKSARGQ ...String:
MVQISEVRGN TRDHRTAAHT HIKGLGLNSS GIAEKQAAGF VGQCAAREAC GVVVDLIKAH KMAGRGVLLA GGPGTGKTAL ALAISQELG TKIPFCPITG SEIYSTEVKK TEVLMENFRR AIGLRVRETK DVYEGEVTEM TPEEAENPLG GYGKTISTLL I GLKSARGQ KKLRLDPSIY EAIQKERVQV GDVIYIETNT GACKRVGRSD AYATEFDLEA EEYVPIPKGE VHKKKEIVQD VT LHDLDVA NARPQGGQDI ISMMGQLMKP KMTEITDKLR MEINKVVQKY INQGVAELIP GVLFIDEAHM LDIECFTYLN KAL ESPIAP IVVLASNRGI ATIRGADDLK AAHGIPPDFL QRLLIIPTHP YEPDEIRRIV RIRAQTEGVQ LTDAAVDRVA EHGV RISLR YCLQLLAPAS ILARVNGRTQ VDVQDIAEAE ELFLDARRSA NILTSTGESG GLHGFIS

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Macromolecule #2: RuvB-like helicase

MacromoleculeName: RuvB-like helicase / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 53.212746 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAPLVTSVT ETKELRGLNL IAAHSHIRGL GVDADTLEPR PSSQGLVGQE KARKAAAVVL EMIKQGKIAG RAVLIAGPPS TGKTAIAMG MAQSLGQDVP FTTLAASEIF SLEMSKTEAL TQAFRKSIGV RIKEESEIME GEVVEIQIDR SVTGGAKQGK L TIKTTDME ...String:
MAAPLVTSVT ETKELRGLNL IAAHSHIRGL GVDADTLEPR PSSQGLVGQE KARKAAAVVL EMIKQGKIAG RAVLIAGPPS TGKTAIAMG MAQSLGQDVP FTTLAASEIF SLEMSKTEAL TQAFRKSIGV RIKEESEIME GEVVEIQIDR SVTGGAKQGK L TIKTTDME AIYDMGSKMI DAMTKERVMA GDIISIDKSS GKITKLGRSY ARSRDYDAMG VDTKFLQCPE GELQKRKEVV HT VSLHEID VINSRTQGFL ALFSGDTGEI RSEIRDQINT KVAEWKEEGK AEIVPGVLFI DEVHMLDIEC FSYINRALES DLA PIVIMA SNRGVSRIRG TDYKSPHGLP LDFLDRVVII NTHPYTPDEL RQILSIRAQE EEVDLTPDAL ALLTKIGQEA GLRY ASNLI TTSQLIAAKR RAKQVGVEDV QRSFKLFYDP ARSVRFVQES EKRLIGNDGV VDFSYQGAAE AAAPTLPAAA PVDPV GGEK MDMS

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Macromolecule #3: Ino80

MacromoleculeName: Ino80 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 210.443344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDHFPTVLQR PPHFDEDGSA GTGRMRSNVV GNGSSNGARD DRGLRGGLRD ILNPVGSASQ TMPSASHGGT HSTPGTPGAP APPRPHSSF SLRSPTQTGN HHASPYSAPT SSAAATSSQQ PAGACSMLNN PFVTASTPFP PPPLQAPPSL ASSRTSPSGL Q HPPRSPLH ...String:
MDHFPTVLQR PPHFDEDGSA GTGRMRSNVV GNGSSNGARD DRGLRGGLRD ILNPVGSASQ TMPSASHGGT HSTPGTPGAP APPRPHSSF SLRSPTQTGN HHASPYSAPT SSAAATSSQQ PAGACSMLNN PFVTASTPFP PPPLQAPPSL ASSRTSPSGL Q HPPRSPLH APPVYYPSDV RDRDLVRDQQ TSLSFYDPTT DSKRDRDRER DRERERTGSD PESGAWSTST QNSPPKIRDS YN YSRSPSF NNSGNYPSAT GSYPPRSPVV RPHPAPPAGS MSPSAGSRTV TSPSLRHLAM PSTHSSQSAS TVLPPLARTE TPA PSARAT PASNTPSRAS GVMSFSNILS SSEPISKPRP TSPISLDNNP AMVARTEPAE RPDKGEKDKK QSRKIIKTRV SDIK SAEST PKMTRKSAVK PETPTMLRIP TKRTANGSMK HKAFSADKEK TIRDIMDQFD YESIDETEFE DELLAWKERA RRRRQ EMNR RDFIHRQSRR SDFAETEALK LQIHANLGKA RYSDLHYDEA LQEVREQELW AEKERKKDMQ RKRRREKSMA ATLEQQ AAA LQKASQAEDE AERLKYIREA ERANKKVQQT KYILQKGIKG PARNLPPIEP NLEGGTMATF SAENMEPGKV KGKGRGG RL KKSKEQKQAE KEQAELAQAA IDAGEEPPSK EETKIRIKLS KAKASAKEEA EKDKENKEPK QPKEPEKPVE EPKDPLEL K FQSKGYNQIY DQIWRDLARK DVSKVFRLAT DSYATKASNL KKTAILASKE AKRWQLRTNK GTKDLQARAK RVMRDMMGF WKRNEREERD LRKAAERLEL ENARKEEADR EAARQRRKLN FLISQTELYS HFISKKIKTH EVERSTDHPD VATDEKDKIP EPTLNINVP EPTGPIAPKV TDFNSLDFDN EDESALQAAA MANAQNAIAE AQKKAREFNK DETKLDEDGE MNFQHPELTE F EVAQPKLL NCQLKEYQLK GLNWLVNLYE QGINGILADE MGLGKTVQSI SVMAYLAERY DIWGPFLVVA PASTLHNWQQ EV SKFVPDF KVLPYWGTAA DRKVLRKFWD RKHTTYKKDS PFHVMITSYQ LVVSDVAYFQ KMKWQYMILD EAQAIKSSQS SRW KCLLGF HCRNRLLLTG TPIQNNMQEL WALLHFIMPS LFDSHDEFSE WFSKDIESHA QSNTKLNEDQ LKRLHMILKP FMLR RVKKH VQKELGDKIE IDVFCELSYR QRAMYQSLRN QISIMDLIEK ATVGDNEDSA TLMNLVMQFR KVCNHPDLFE RADTS SPFF CGHFAETGSF LREGTNVALG YSTRSLVEYR LPRLIWCDGG RLDKPGPGNL VAGFRSKYLN HMMNIWTPEN IRSSLE GIE NFTWLRFVDT SLQEAYRASH TDVFARAVDL ASKQNRLGHM QIVYDEPEDK KWTPVHALFQ ICERENPKAV AEITTEG VL RDLMNIARVK YRELGLCRLE KAARPRASAP PIEVVCDSRS AVIERENIMF HPAMRKALFG PTPSEIKEAS FGPRPVTL Y PPRALLPAPD HDKQRFTNIT VPSMARFVTD SGKLAKLDEL LRELKEGGHR VLLYFQMTRM IDLMEEYLTY RNYKYCRLD GSTKLEDRRD TVADFQTRPE IFIFLLSTRA GGLGINLTTA DTVIFYDSDW NPTIDSQAMD RAHRLGQTKQ VTVYRLITRG TIEERIRKR ALQKEEVQRV VITGTGSVDF SGRRPPENRN RDIAMWLADD EQAEMIERRE KELIESGEYD KIMQQRRKGG K RKRGAANG DTVPSLEDMY HEGEGHFDDN KGSGAATPVD ADSLGRGGKR KKAGGSKKAK TTKQRLAIAD GEIDDGEIDI DY KDDDDKG TDYKDDDDK

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Macromolecule #4: les2

MacromoleculeName: les2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 52.018512 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSTRPRRHAA QRASQAITDL ADRDRESDHS HGPISSRMSS FNSSSRSRLP GKGIASVSRS EAGGASDPEH IHLTVKLPSS KLRQATSSS GIKKAGSVGS SSSSSGGGKA AVKRARGGKR SRVLESSEEE EEENEVEVLG DEDEEEEEEE DEIEVREGEG Y DEDEEDVE ...String:
MSTRPRRHAA QRASQAITDL ADRDRESDHS HGPISSRMSS FNSSSRSRLP GKGIASVSRS EAGGASDPEH IHLTVKLPSS KLRQATSSS GIKKAGSVGS SSSSSGGGKA AVKRARGGKR SRVLESSEEE EEENEVEVLG DEDEEEEEEE DEIEVREGEG Y DEDEEDVE DEDEEMQDLG EEDADGEDDE MDVDAEGEED ADGDVNMDAG VVGARATTVR AVPPAIKVTK PPKESPSNGK AA TASKAND NAVPVKRPAP DSDDESLSSL ESEPEEEVNV AGGEDAEGED DDAEGEVDAE GEEEEEEEEI EVADEDAEGE DVE QDEDED EEEEDDDDEM ISRAQTPDMS RLTARQRARL GEASGEYLKL SDEVQSKKHF TAEELS(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)KQ APRTTRRAAQ AAAAAEEAEE AAK QPKRPD PMMIRWVNNK MGSVVAVPEE LLGTHAGVVF GAGPGKGLPA GKMVEEVS

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Macromolecule #5: Ies6

MacromoleculeName: Ies6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 23.127523 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNPDAQSAQ AAHQALVEQL DLHSIHKTFR NPNWRPNQRR NKTIKAILGE SQRKEASSTS AVATPRADDN GGGSGADTPA NNDNNDGLS TSGTSTPANG NGSGAGTPAS NGQPNLAQAS RSLQKLVLEK SLASAQAPDK KAANGFASSA PTATYTNIES A PSLAPMKH ...String:
MSNPDAQSAQ AAHQALVEQL DLHSIHKTFR NPNWRPNQRR NKTIKAILGE SQRKEASSTS AVATPRADDN GGGSGADTPA NNDNNDGLS TSGTSTPANG NGSGAGTPAS NGQPNLAQAS RSLQKLVLEK SLASAQAPDK KAANGFASSA PTATYTNIES A PSLAPMKH YCDVTGLPAP YLDPKTRLRY HNKEIFAMIR NLPQGMGEQF LEARGAHTVL K

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Macromolecule #6: Actin related protein 5

MacromoleculeName: Actin related protein 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 85.996453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPSAVAEPP PIPQRDEPWK RLPPPTVYPV KEARFEKYIP PQLDGRERAL AQPPGQVAIV IDNGSHSVRA GWNFEDKPRL AIPPIMSKY RDRKMGKTFS FAGSDCYADT TARSHIRNAF EAGTGIVSNW DVMEHVLDYV FVKLGMNECD GAIDMPIVMT E AVANLPYS ...String:
MAPSAVAEPP PIPQRDEPWK RLPPPTVYPV KEARFEKYIP PQLDGRERAL AQPPGQVAIV IDNGSHSVRA GWNFEDKPRL AIPPIMSKY RDRKMGKTFS FAGSDCYADT TARSHIRNAF EAGTGIVSNW DVMEHVLDYV FVKLGMNECD GAIDMPIVMT E AVANLPYS RKSMSEIIFE CYGAPSLVYG IDSLFSFRHN QGQTGLVVSS SYSATHVIPV YNRKALLSQA IRLNWGGWHM AE YMLKLLK LKYYTGFPGK LNSSQTEHMV RDFCYVSLDY DRELAGYLDW TGLEDRERIV QYPYTEEVVV QKTEEELARI AER KKESGR RLQEQAAKMR LERLMKKEQE LEYYKDIQRR MQGESKKEIK RLLDEAELKD EAALERVIRD LERSIKRARQ KDLG EPEEE EVPDFSLLDV PDDQLDEAGL RQKRQQRLLK SNWEARQRAK AEKEAEKARL AEEARLDEER RKNDL(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)GNRKS (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)NP TGSGSRKRRR GGAGADQD D DFGADDADWG VYRSVAIGAN KGDDSDDEEG (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)LRYD KTFSYDMTLD AQRDWSKSLL HAFRYGPRPF DPSSQAETHR VHLNVE RIR VPEVLFQPAA IAGVDQAGLV EIAGDILCQR LPSLPGIQDA PDAFLRDVFL TGGNTLFQNF DERLRQGLMA LLPVGAP LR VRRAQDAILD AWRGAAGWAC TEEAKAAWIT REEYLEKGGE YIKEHDLGNA FA

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Macromolecule #9: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #10: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #11: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.990342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #12: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

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Macromolecule #7: Nucleosomal DNA Strand 1

MacromoleculeName: Nucleosomal DNA Strand 1 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 60.652645 KDa
SequenceString: (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DT)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA) (DA)(DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT) (DT) (DC)(DA)(DA)(DT)(DA)(DC) ...String:
(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DT)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA) (DA)(DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT) (DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT) (DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG) (DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG) (DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG) (DC)(DT)(DT)(DG)(DC)(DT)(DA) (DC)(DG) (DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG) (DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG) (DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DA)

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Macromolecule #8: Nucleosomal DNA Strand 2

MacromoleculeName: Nucleosomal DNA Strand 2 / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 60.376426 KDa
SequenceString: (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DC) (DA)(DA)(DG)(DC)(DT)(DC) ...String:
(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DC) (DA)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC) (DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA) (DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG)(DC) (DG)(DA)(DC)(DC)(DT)(DT)(DG)(DC)(DC)(DG) (DG)(DT)(DG)(DC)(DC)(DA)(DG)(DT) (DC) (DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT)(DT) (DC)(DC)(DG)(DA)(DG)

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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

Concentration1 mg/mL
BufferpH: 8
Details: 20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP
DetailsMonodisperse sample: INO80core complex reconstituted with nucleosomal substrate was purified by gelfiltration. Addition of nucleotides or crosslinking was not required.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 1.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3992 / Average electron dose: 59.6 e/Å2
Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 251692
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: An initial ab initio model was generated using CryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Details: An initial ab initio model was generated using CryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1.1b)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.1b) / Number images used: 33937
FSC plot (resolution estimation)

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