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

Basic information

Entry

Database: EMDB / ID: EMD-14737

• Title: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome

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

• Keywords: chromatin remodeler / transcription / replication / DNA repair / DNA BINDING PROTEIN

Function / homology

Function:

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 / ATP-dependent chromatin remodeler activity / regulation of double-strand break repair / box C/D snoRNP assembly / UV-damage excision repair / protein folding chaperone complex / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / TFIID-class transcription factor complex binding / mitotic sister chromatid segregation / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / negative regulation of tumor necrosis factor-mediated signaling pathway / ATP-dependent activity, acting on DNA / alpha-tubulin binding / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / regulation of DNA repair / Chromatin modifying enzymes / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / DNA helicase activity / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / telomere maintenance / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / positive regulation of DNA repair / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / cellular response to ionizing radiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / double-strand break repair via homologous recombination / euchromatin / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage Recognition in GG-NER / NoRC negatively regulates rRNA expression / beta-catenin binding / ADP binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / PKMTs methylate histone lysines / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / spindle / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events

Domain/homology:

DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / HIT zinc finger / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / 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 H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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

Component:

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

• Biological species: Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Vance NR / Ayala R / Willhoft O / Tvardovskiy A / McCormack EA / Bartke T / Zhang X / Wigley DB

Funding support

United Kingdom, 1 items

Organization	Grant number	Country
Wellcome Trust	209327/Z/17/Z	United Kingdom

• Citation: Journal: 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

Deposition	Apr 7, 2022	-
Header (metadata) release	Apr 19, 2023	-
Map release	Apr 19, 2023	-
Update	Jul 24, 2024	-
Current status	Jul 24, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_14737.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.1 Å

Density

Contour Level	By AUTHOR: 4.5
Minimum - Maximum	-26.213028000000001 - 51.823680000000003
Average (Standard dev.)	0.0031996632 (±1.1331027)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 368 368 368 Spacing 368 368 368
Cell	A=B=C: 404.80002 Å α=β=γ: 90.0 °

Supplemental data

Additional map: #3

• File: emd_14737_additional_1.map

Additional map: #2

• File: emd_14737_additional_2.map

Additional map: #1

• File: emd_14737_additional_3.map

Half map: #1

• File: emd_14737_half_map_1.map

Half map: #2

• File: emd_14737_half_map_2.map

Sample components

Entire : Complex of human INO80core bound to a WT nucleosome

• Entire: Name: 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

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

• Supramolecule: Name: 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 weight: Theoretical: 1.0 MDa

Macromolecule #1: RuvB-like 1

• Macromolecule: Name: 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 weight: Theoretical: 50.296914 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #2: RuvB-like 2

• Macromolecule: Name: 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 weight: Theoretical: 51.222465 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #3: Chromatin-remodeling ATPase INO80

• Macromolecule: Name: 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 weight: Theoretical: 177.032812 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #4: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.394426 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

Macromolecule #5: INO80 complex subunit B

• Macromolecule: Name: INO80 complex subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 38.704172 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #6: Actin-related protein 5

• Macromolecule: Name: Actin-related protein 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 68.372336 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #7: INO80 complex subunit C

• Macromolecule: Name: INO80 complex subunit C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 20.672553 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

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

Macromolecule #8: Histone H3.1

• Macromolecule: Name: Histone H3.1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.437167 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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

• Macromolecule: Name: 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 weight: Theoretical: 14.165551 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

Macromolecule #10: Histone H2B type 1-J

• Macromolecule: Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.935239 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

Macromolecule #11: DNA (158-MER)

• Macromolecule: Name: DNA (158-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 48.569934 KDa

Sequence

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)

Macromolecule #12: DNA (158-MER)

• Macromolecule: Name: DNA (158-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 48.97523 KDa

Sequence

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)

Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 8 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #14: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Macromolecule #15: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.25 mg/mL

Buffer

pH: 8
Component:

Concentration	Name
25.0 mM	HEPES
50.0 mM	NaCl
1.0 mM	TCEP
3.0 mM	ADP
3.0 mM	BeCl2
15.0 mM	NaF
5.0 mM	MgCl2

• Grid: Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300
• Vitrification: Cryogen 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.

Electron microscopy

• Microscope: TFS KRIOS
• Temperature: Min: 77.15 K / Max: 77.15 K
• Image recording: Film 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/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 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 stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 3647005

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

6hts

• Final reconstruction: Number 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 assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
• Final 3D classification: Number classes: 2 / Avg.num./class: 148566 / Software - Name: RELION (ver. 4)

Atomic model buiding 1

Initial model

PDB ID:

6hts

Chain - Source name: PDB / Chain - Initial model type: experimental model

• Refinement: Space: REAL

Output model

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