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- EMDB-14737: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-14737
TitleCryo-EM structure of the human INO80 complex bound to a WT nucleosome
Map data
Sample
  • Complex: Complex of human INO80core bound to a WT nucleosome
    • Protein or peptide: x 10 types
    • DNA: x 2 types
  • Ligand: x 3 types
Keywordschromatin remodeler / transcription / replication / DNA repair / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex ...positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / UV-damage excision repair / box C/D snoRNP assembly / protein folding chaperone complex / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / TFIID-class transcription factor complex binding / four-way junction helicase activity / mitotic sister chromatid segregation / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / negative regulation of tumor necrosis factor-mediated signaling pathway / alpha-tubulin binding / ATP-dependent activity, acting on DNA / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / spindle assembly / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / cellular response to ionizing radiation / telomere maintenance / DNA helicase activity / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / positive regulation of DNA repair / DNA methylation / TBP-class protein binding / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / double-strand break repair via homologous recombination / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA Damage Recognition in GG-NER / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / cellular response to estradiol stimulus / lipopolysaccharide binding / Transcriptional regulation by small RNAs / chromatin DNA binding / negative regulation of canonical Wnt signaling pathway / 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 / euchromatin / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / ADP binding / beta-catenin binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines
Similarity search - Function
HIT zinc finger / DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 ...HIT zinc finger / DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / Zinc finger, HIT-type / : / 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 / : / 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 C / 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: 3.2 Å
AuthorsVance NR / Ayala R / Willhoft O / Tvardovskiy A / McCormack EA / Bartke T / Zhang X / Wigley DB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust209327/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
Authors: Vance NR / Ayala R / Willhoft O / Tvardovskiy A / McCormack EA / Bartke T / Zhang X / Wigley DB
History
DepositionApr 7, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14737.png

Downloads & links

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Map

FileDownload / File: emd_14737.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 368 pix.
= 404.8 Å		1.1 Å/pix.
x 368 pix.
= 404.8 Å		1.1 Å/pix.
x 368 pix.
= 404.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-26.213028000000001 - 51.823680000000003
Average (Standard dev.)0.0031996632 (±1.1331027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 404.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_14737_additional_1.map
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Additional map: #2

Fileemd_14737_additional_2.map
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Additional map: #1

Fileemd_14737_additional_3.map
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Half map: #1

Fileemd_14737_half_map_1.map
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Half map: #2

Fileemd_14737_half_map_2.map
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Sample components

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Entire : Complex of human INO80core bound to a WT nucleosome

EntireName: Complex of human INO80core bound to a WT nucleosome
Components
  • Complex: Complex of human INO80core bound to a WT nucleosome
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: Histone H4
    • Protein or peptide: INO80 complex subunit B
    • Protein or peptide: Actin-related protein 5
    • Protein or peptide: INO80 complex subunit C
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (158-MER)
    • DNA: DNA (158-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ZINC ION

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Supramolecule #1: Complex of human INO80core bound to a WT nucleosome

SupramoleculeName: Complex of human INO80core bound to a WT nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.0 MDa

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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

UniProtKB: RuvB-like 1

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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

UniProtKB: RuvB-like 2

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Macromolecule #3: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 3 / 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: Homo sapiens (human)
Molecular weightTheoretical: 177.032812 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASELGARDD GGCTELAKPL YLQYLERALR LDHFLRQTSA IFNRNISSDD SEDGLDDSNP LLPQSGDPLI QVKEEPPNSL LGETSGAGS SGMLNTYSLN GVLQSESKCD KGNLYNFSKL KKSRKWLKSI LLSDESSEAD SQSEDDDEEE LNLSREELHN M LRLHKYKK ...String:
MASELGARDD GGCTELAKPL YLQYLERALR LDHFLRQTSA IFNRNISSDD SEDGLDDSNP LLPQSGDPLI QVKEEPPNSL LGETSGAGS SGMLNTYSLN GVLQSESKCD KGNLYNFSKL KKSRKWLKSI LLSDESSEAD SQSEDDDEEE LNLSREELHN M LRLHKYKK LHQNKYSKDK ELQQYQYYSA GLLSTYDPFY EQQRHLLGPK KKKFKEEKKL KAKLKKVKKK RRRDEELSSE ES PRRHHHQ TKVFAKFSHD APPPGTKKKH LSIEQLNARR RKVWLSIVKK ELPKANKQKA SARNLFLTNS RKLAHQCMKE VRR AALQAQ KNCKETLPRA RRLTKEMLLY WKKYEKVEKE HRKRAEKEAL EQRKLDEEMR EAKRQQRKLN FLITQTELYA HFMS RKRDM GHDGIQEEIL RKLEDSSTQR QIDIGGGVVV NITQEDYDSN HFKAQALKNA ENAYHIHQAR TRSFDEDAKE SRAAA LRAA NKSGTGFGES YSLANPSIRA GEDIPQPTIF NGKLKGYQLK GMNWLANLYE QGINGILADE MGLGKTVQSI ALLAHL AER ENIWGPFLII SPASTLNNWH QEFTRFVPKF KVLPYWGNPH DRKVIRRFWS QKTLYTQDAP FHVVITSYQL VVQDVKY FQ RVKWQYMVLD EAQALKSSSS VRWKILLQFQ CRNRLLLTGT PIQNTMAELW ALLHFIMPTL FDSHEEFNEW FSKDIESH A ENKSAIDENQ LSRLHMILKP FMLRRIKKDV ENELSDKIEI LMYCQLTSRQ KLLYQALKNK ISIEDLLQSS MGSTQQAQN TTSSLMNLVM QFRKVCNHPE LFERQETWSP FHISLKPYHI SKFIYRHGQI RVFNHSRDRW LRVLSPFAPD YIQRSLFHRK GINEESCFS FLRFIDISPA EMANLMLQGL LARWLALFLS LKASYRLHQL RSWGAPEGES HQRYLRNKDF LLGVNFPLSF P NLCSCPLL KSLVFSSHCK AVSGYSDQVV HQRRSATSSL RRCLLTELPS FLCVASPRVT AVPLDSYCND RSAEYERRVL KE GGSLAAK QCLLNGAPEL AADWLNRRSQ FFPEPAGGLW SIRPQNGWSF IRIPGKESLI TDSGKLYALD VLLTRLKSQG HRV LIYSQM TRMIDLLEEY MVYRKHTYMR LDGSSKISER RDMVADFQNR NDIFVFLLST RAGGLGINLT AADTVIFYDS DWNP TVDQQ AMDRAHRLGQ TKQVTVYRLI CKGTIEERIL QRAKEKSEIQ RMVISGGNFK PDTLKPKEVV SLLLDDEELE KKLRL RQEE KRQQEETNRV KERKRKREKY AEKKKKEDEL DGKRRKEGVN LVIPFVPSAD NSNLSADGDD SFISVDSAMP SPFSEI SIS SELHTGSIPL DESSSDMLVI VDDPASSAPQ SRATNSPASI TGSVSDTVNG ISIQEMPAAG RGHSARSRGR PKGSGST AK GAGKGRSRKS TAGSAAAMAG AKAGAAAASA AAYAAYGYNV SKGISASSPL QTSLVRPAGL ADFGPSSASS PLSSPLSK G NNVPGNPKNL HMTSSLAPDS LVRKQGKGTN PSGGR

UniProtKB: Chromatin-remodeling ATPase INO80

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / 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

UniProtKB: Histone H4

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Macromolecule #5: INO80 complex subunit B

MacromoleculeName: INO80 complex subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.704172 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

UniProtKB: INO80 complex subunit B

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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: 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

UniProtKB: Actin-related protein 5

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Macromolecule #7: INO80 complex subunit C

MacromoleculeName: INO80 complex subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.672553 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAQIPIVAT TSTPGIVRNS KKRPASPSHN GSSGGGYGAS KKKKASASSF AQGISMEAMS ENKMVPSEFS TGPVEKAAKP LPFKDPNFV HSGHGGAVAG KKNRTWKNLK QILASERALP WQLNDPNYFS IDAPPSFKPA KKYSDVSGLL ANYTDPQSKL R FSTIEEFS ...String:
MAAQIPIVAT TSTPGIVRNS KKRPASPSHN GSSGGGYGAS KKKKASASSF AQGISMEAMS ENKMVPSEFS TGPVEKAAKP LPFKDPNFV HSGHGGAVAG KKNRTWKNLK QILASERALP WQLNDPNYFS IDAPPSFKPA KKYSDVSGLL ANYTDPQSKL R FSTIEEFS YIRRLPSDVV TGYLALRKAT SIVP

UniProtKB: INO80 complex subunit C

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Macromolecule #8: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #9: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 9 / 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

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #10: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 10 / 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

UniProtKB: Histone H2B type 1-J

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Macromolecule #11: DNA (158-MER)

MacromoleculeName: DNA (158-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.569934 KDa
SequenceString: (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) ...String:
(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)(DA)(DT)(DA) (DT)(DT)(DG)(DA)(DT)

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Macromolecule #12: DNA (158-MER)

MacromoleculeName: DNA (158-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.97523 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(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) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(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)

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #14: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / 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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationName
25.0 mMHEPES
50.0 mMNaCl
1.0 mMTCEP
3.0 mMADP
3.0 mMBeCl2
15.0 mMNaF
5.0 mMMgCl2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.15 K / Max: 77.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 9760 / Average exposure time: 5.1 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 88000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 88000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3647005
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hts

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 156300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 2 / Avg.num./class: 148566 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6hts


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-7zi4:
Cryo-EM structure of the human INO80 complex bound to a WT nucleosome

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