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- EMDB-3954: Cryo-EM structure of the human INO80 complex bound to nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3954
TitleCryo-EM structure of the human INO80 complex bound to nucleosome
Map datamap of human INO80 bound to nucleosome
Sample
  • Complex: Complex of core human INO80 with nucleosome
    • Complex: nucleosome
      • Protein or peptide: x 5 types
    • Complex: human INO80
      • Protein or peptide: x 1 types
      • DNA: x 2 types
    • Complex: Histone subunits
      • Protein or peptide: x 3 types
  • Ligand: x 2 types
Function / homology
Function and homology information


: / : / chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / promoter-enhancer loop anchoring activity / positive regulation of nuclear cell cycle DNA replication / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex ...: / : / chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / promoter-enhancer loop anchoring activity / positive regulation of nuclear cell cycle DNA replication / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / Swr1 complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / UV-damage excision repair / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / DNA duplex unwinding / regulation of chromosome organization / positive regulation of double-strand break repair via homologous recombination / protein deubiquitination / regulation of G1/S transition of mitotic cell cycle / mitotic sister chromatid segregation / regulation of DNA replication / MLL1 complex / TFIID-class transcription factor complex binding / regulation of embryonic development / alpha-tubulin binding / Telomere Extension By Telomerase / negative regulation of tumor necrosis factor-mediated signaling pathway / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / regulation of DNA repair / protein localization to CENP-A containing chromatin / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 / positive regulation of DNA repair / Inhibition of DNA recombination at telomere / Meiotic synapsis / DNA helicase activity / telomere organization / telomere maintenance / TBP-class protein binding / 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 / Defective pyroptosis / cellular response to estradiol stimulus / ADP binding / HDACs deacetylate histones / cellular response to ionizing radiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / negative regulation of canonical Wnt signaling pathway / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / spindle / chromatin DNA binding / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / beta-catenin binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly
Similarity search - Function
Actin-related protein 5 / DNA helicase Ino80 / HIT zinc finger / DBINO domain profile. / DBINO domain / DNA-binding domain / Zinc finger, HIT-type / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region ...Actin-related protein 5 / DNA helicase Ino80 / HIT zinc finger / DBINO domain profile. / DBINO domain / DNA-binding domain / Zinc finger, HIT-type / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / 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 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin, conserved site / Actins signature 2. / 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 / Helicase conserved C-terminal 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 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / INO80 complex subunit B / Actin-related protein 5 / Chromatin-remodeling ATPase INO80 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsAyala R / Willhoft O / Aramayo RJ / Wilkinson M / McCormack EA / Ocloo L / Wigley DB / Zhang X
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust098412/Z/12/Z United Kingdom
Cancer Research UKC6913/A21608 United Kingdom
Wellcome Trust095519/Z/11/Z United Kingdom
CitationJournal: Nature / Year: 2018
Title: Structure and regulation of the human INO80-nucleosome complex.
Authors: Rafael Ayala / Oliver Willhoft / Ricardo J Aramayo / Martin Wilkinson / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley / Xiaodong Zhang /
Abstract: Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. ...Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines . Biochemical studies have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding , histone exchange and nucleosome spacing remain poorly understood. Although some remodellers work as monomers , others work as highly cooperative dimers. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.
History
DepositionOct 27, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseApr 25, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hts
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3954.png

Downloads & links

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Map

FileDownload / File: emd_3954.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of human INO80 bound to nucleosome
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.0155 / Movie #1: 0.035
Minimum - Maximum-0.068371326 - 0.19655794
Average (Standard dev.)0.0019386741 (±0.010966605)
SymmetrySpace group: 0
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 294.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z270270270
origin x/y/z0.0120.0120.012
length x/y/z294.300294.300294.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0680.1970.002

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Supplemental data

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Additional map: blurred map (with a factor applied of 250)...

Fileemd_3954_additional.map
Annotationblurred map (with a factor applied of 250) to help visualise the nucleosome and flexible regions of the complex that have not been modelled
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of core human INO80 with nucleosome

EntireName: Complex of core human INO80 with nucleosome
Components
  • Complex: Complex of core human INO80 with nucleosome
    • Complex: nucleosome
      • Protein or peptide: RuvB-like 1
      • Protein or peptide: RuvB-like 2
      • Protein or peptide: DNA helicase INO80
      • Protein or peptide: Actin-related protein 5
      • Protein or peptide: Histone H3.1Histone H3
    • Complex: human INO80
      • Protein or peptide: INO80 complex subunit B
      • DNA: DNA (142-MER)
      • DNA: DNA (142-MER)
    • Complex: Histone subunits
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Complex of core human INO80 with nucleosome

SupramoleculeName: Complex of core human INO80 with nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: human INO80

SupramoleculeName: human INO80 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9-#11
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #3: Histone subunits

SupramoleculeName: Histone subunits / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

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Macromolecule #3: DNA helicase INO80

MacromoleculeName: DNA helicase INO80 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 146.390703 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HLSIEQLNAR RRKVWLSIVK KELPKANKQK ASARNLFLTN SRKLAHQCMK EVRRAALQAQ KNCKETLPRA RRLTKEMLLY WKKYEKVEK EHRKRAEKEA LEQRKLDEEM REAKRQQRKL NFLITQTELY AHFMSRKRDM GHDGIQEEIL RKLEDSSTQR Q IDIGGGVV ...String:
HLSIEQLNAR RRKVWLSIVK KELPKANKQK ASARNLFLTN SRKLAHQCMK EVRRAALQAQ KNCKETLPRA RRLTKEMLLY WKKYEKVEK EHRKRAEKEA LEQRKLDEEM REAKRQQRKL NFLITQTELY AHFMSRKRDM GHDGIQEEIL RKLEDSSTQR Q IDIGGGVV VNITQEDYDS NHFKAQALKN AENAYHIHQA RTRSFDEDAK ESRAAALRAA NKSGTGFGES YSLANPSIRA GE DIPQPTI FNGKLKGYQL KGMNWLANLY EQGINGILAD EMGLGKTVQS IALLAHLAER ENIWGPFLII SPASTLNNWH QEF TRFVPK FKVLPYWGNP HDRKVIRRFW SQKTLYTQDA PFHVVITSYQ LVVQDVKYFQ RVKWQYMVLD EAQALKSSSS VRWK ILLQF QCRNRLLLTG TPIQNTMAEL WALLHFIMPT LFDSHEEFNE WFSKDIESHA ENKSAIDENQ LSRLHMILKP FMLRR IKKD VENELSDKIE ILMYCQLTSR QKLLYQALKN KISIEDLLQS SMGSTQQAQN TTSSLMNLVM QFRKVCNHPE LFERQE TWS PFHISLKPYH ISKFIYRHGQ IRVFNHSRDR WLRVLSPFAP DYIQRSLFHR KGINEESCFS FLRFIDISPA EMANLML QG LLARWLALFL SLKASYRLHQ LRSWGAPEGE SHQRYLRNKD FLLGVNFPLS FPNLCSCPLL KSLVFSSHCK AVSGYSDQ V VHQRRSATSS LRRCLLTELP SFLCVASPRV TAVPLDSYCN DRSAEYERRV LKEGGSLAAK QCLLNGAPEL AADWLNRRS QFFPEPAGGL WSIRPQNGWS FIRIPGKESL ITDSGKLYAL DVLLTRLKSQ GHRVLIYSQM TRMIDLLEEY MVYRKHTYMR LDGSSKISE RRDMVADFQN RNDIFVFLLS TRAGGLGINL TAADTVIFYD SDWNPTVDQQ AMDRAHRLGQ TKQVTVYRLI C KGTIEERI LQRAKEKSEI QRMVISGGNF KPDTLKPKEV VSLLLDDEEL EKKLRLRQEE KRQQEETNRV KERKRKREKY AE KKKKEDE LDGKRRKEGV NLVIPFVPSA DNSNLSADGD DSFISVDSAM PSPFSEISIS SELHTGSIPL DESSSDMLVI VDD PASSAP QSRATNSPAS ITGSVSDTVN GISIQEMPAA GRGHSARSRG RPKGSGSTAK GAGKGRSRKS TAGSAAAMAG AKAG AAAAS AAAYAAYGYN VSKGISASSP LQTSLVRPAG LADFGPSSAS SPLSSPLSKG NNVPGNPKNL HMTSSLAPDS LVRKQ GKGT NPSGGR

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Macromolecule #4: Actin-related protein 5

MacromoleculeName: Actin-related protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.372336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAANVFPFRD ARAAPDPVLE AGPVAHGPLP VPLVLDNGSF QVRAGWACPG QDPGPEPRLQ FRAVCARGRG GARGASGPQV GNALGSLEP LRWMLRSPFD RNVPVNLELQ ELLLDYSFQH LGVSSQGCVD HPIVLTEAVC NPLYSRQMMS ELLFECYGIP K VAYGIDSL ...String:
MAANVFPFRD ARAAPDPVLE AGPVAHGPLP VPLVLDNGSF QVRAGWACPG QDPGPEPRLQ FRAVCARGRG GARGASGPQV GNALGSLEP LRWMLRSPFD RNVPVNLELQ ELLLDYSFQH LGVSSQGCVD HPIVLTEAVC NPLYSRQMMS ELLFECYGIP K VAYGIDSL FSFYHNKPKN SMCSGLIISS GYQCTHVLPI LEGRLDAKNC KRINLGGSQA AGYLQRLLQL KYPGHLAAIT LS RMEEILH EHSYIAEDYV EELHKWRCPD YYENNVHKMQ LPFSSKLLGS TLTSEEKQER RQQQLRRLQE LNARRREEKL QLD QERLDR LLYVQELLED GQMDQFHKAL IELNMDSPEE LQSYIQKLSI AVEQAKQKIL QAEVNLEVDV VDSKPETPDL EQLE PSLED VESMNDFDPL FSEETPGVEK PVTTVQPVFN LAAYHQLFVG TERIRAPEII FQPSLIGEEQ AGIAETLQYI LDRYP KDIQ EMLVQNVFLT GGNTMYPGMK ARMEKELLEM RPFRSSFQVQ LASNPVLDAW YGARDWALNH LDDNEVWITR KEYEEK GGE YLKEHCASNI YVPIRLPKQA SRSSDAQASS KGSAAGGGGA GEQA

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Macromolecule #5: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #7: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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Macromolecule #8: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

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Macromolecule #9: INO80 complex subunit B

MacromoleculeName: INO80 complex subunit B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 38.704172 KDa
SequenceString: MSKLWRRGST SGAMEAPEPG EALELSLAGA HGHGVHKKKH KKHKKKHKKK HHQEEDAGPT QPSPAKPQLK LKIKLGGQVL GTKSVPTFT VIPEGPRSPS PLMVVDNEEE PMEGVPLEQY RAWLDEDSNL SPSPLRDLSG GLGGQEEEEE QRWLDALEKG E LDDNGDLK ...String:
MSKLWRRGST SGAMEAPEPG EALELSLAGA HGHGVHKKKH KKHKKKHKKK HHQEEDAGPT QPSPAKPQLK LKIKLGGQVL GTKSVPTFT VIPEGPRSPS PLMVVDNEEE PMEGVPLEQY RAWLDEDSNL SPSPLRDLSG GLGGQEEEEE QRWLDALEKG E LDDNGDLK KEINERLLTA RQRALLQKAR SQPSPMLPLP VAEGCPPPAL TEEMLLKREE RARKRRLQAA RRAEEHKNQT IE RLTKTAA TSGRGGRGGA RGERRGGRAA APAPMVRYCS GAQGSTLSFP PGVPAPTAVS QRPSPSGPPP RCSVPGCPHP RRY ACSRTG QALCSLQCYR INLQMRLGGP EGPGSPLLAT

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Macromolecule #10: DNA (142-MER)

MacromoleculeName: DNA (142-MER) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 62.533809 KDa
SequenceString: (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)(DA)(DC)(DA)(DG)(DC) (DT) (DC)(DT)(DA)(DG)(DC)(DA) ...String:
(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)(DA)(DC)(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)(DC)(DT)(DC)(DG)(DG) (DG)(DG)(DT)(DG)(DG)(DC)(DG) (DA)(DT) (DA)(DA)(DG)(DT)(DC)(DG)(DT)(DG)(DT)(DC) (DT)(DT)(DA)(DC)(DC)(DG)(DG)(DG) (DT) (DT)(DG)(DG)(DA)(DC)(DT)(DC)(DA)(DA)(DG) (DA)(DC)(DG)(DA)(DT)(DA)(DG)(DT)(DT) (DA)(DC)(DC)

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Macromolecule #11: DNA (142-MER)

MacromoleculeName: DNA (142-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 61.897449 KDa
SequenceString: (DG)(DG)(DT)(DA)(DA)(DC)(DT)(DA)(DT)(DC) (DG)(DT)(DC)(DT)(DT)(DG)(DA)(DG)(DT)(DC) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DG)(DT) (DA)(DA)(DG)(DA)(DC)(DA)(DC)(DG)(DA)(DC) (DT) (DT)(DA)(DT)(DC)(DG)(DC) ...String:
(DG)(DG)(DT)(DA)(DA)(DC)(DT)(DA)(DT)(DC) (DG)(DT)(DC)(DT)(DT)(DG)(DA)(DG)(DT)(DC) (DC)(DA)(DA)(DC)(DC)(DC)(DG)(DG)(DT) (DA)(DA)(DG)(DA)(DC)(DA)(DC)(DG)(DA)(DC) (DT) (DT)(DA)(DT)(DC)(DG)(DC)(DC)(DA) (DC)(DC)(DC)(DC)(DG)(DA)(DG)(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)(DG)(DT)(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)

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Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / 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 #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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 / Chamber humidity: 100 % / Chamber temperature: 277 K

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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 / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 0.5.6)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1.B1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.B1) / Number images used: 58145
FSC plot (resolution estimation)

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