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- EMDB-51229: CryoEM structure of the human INO80 core- H2A.Z nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51229
TitleCryoEM structure of the human INO80 core- H2A.Z nucleosome complex
Map data
Sample
  • Complex: Human INO80 remodeller with H2A.Z containing nucleosomes
    • Complex: Human INO80 remodeller
      • Protein or peptide: x 6 types
    • Complex: Histone Octamer
      • Protein or peptide: x 5 types
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: x 2 types
  • Ligand: x 3 types
KeywordsHomo sapiens / ATP-dependent chromatin remodeller / 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 / ATP-dependent chromatin remodeler activity / regulation of double-strand break repair / UV-damage excision repair / box C/D snoRNP assembly / protein folding chaperone complex / nucleosomal DNA binding / regulation of chromosome organization / NuA4 histone acetyltransferase complex / TFIID-class transcription factor complex binding / regulation of DNA replication / mitotic sister chromatid segregation / regulation of G1/S transition of mitotic cell cycle / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / ATP-dependent activity, acting on DNA / alpha-tubulin binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / negative regulation of megakaryocyte differentiation / heterochromatin / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / spindle assembly / 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 / telomere maintenance / telomere organization / DNA helicase activity / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / TBP-class protein binding / positive regulation of DNA repair / 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 / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / cellular response to ionizing radiation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to estradiol stimulus / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / euchromatin / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / DNA Damage Recognition in GG-NER / G2/M DNA damage checkpoint / ADP binding / beta-catenin binding / NoRC negatively regulates rRNA expression / chromatin DNA binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events
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 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.Z / Histone H4 / Histone H3.1 / Histone H2B type 2-E / 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: 3.43 Å
AuthorsAggarwal P / Sharma M / Hopfner KP
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)833613 INO3DEuropean Union
German Research Foundation (DFG)HO 2489/9-1 Germany
CitationJournal: To Be Published
Title: Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex
Authors: Aggarwal P / Sharma M / Hopfner KP
History
DepositionAug 1, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51229.png

Downloads & links

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Map

FileDownload / File: emd_51229.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 440 pix.
= 414.92 Å		0.94 Å/pix.
x 440 pix.
= 414.92 Å		0.94 Å/pix.
x 440 pix.
= 414.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.943 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.26807985 - 0.59248126
Average (Standard dev.)0.00092375773 (±0.015893376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 414.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51229_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51229_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human INO80 remodeller with H2A.Z containing nucleosomes

EntireName: Human INO80 remodeller with H2A.Z containing nucleosomes
Components
  • Complex: Human INO80 remodeller with H2A.Z containing nucleosomes
    • Complex: Human INO80 remodeller
      • Protein or peptide: RuvB-like 1
      • Protein or peptide: RuvB-like 2
      • Protein or peptide: INO80 complex subunit C
      • Protein or peptide: Chromatin-remodeling ATPase INO80
      • Protein or peptide: INO80 complex subunit B
      • Protein or peptide: Actin-related protein 5
    • Complex: Histone Octamer
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.Z
      • Protein or peptide: Histone H2B type 2-E
      • Protein or peptide: Histone H2A.Z
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Nucleosomal DNA Strand 1 (152-MER)
      • DNA: Nucleosomal DNA Strand 2 (152-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Human INO80 remodeller with H2A.Z containing nucleosomes

SupramoleculeName: Human INO80 remodeller with H2A.Z containing nucleosomes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13

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Supramolecule #2: Human INO80 remodeller

SupramoleculeName: Human INO80 remodeller / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone Octamer

SupramoleculeName: Histone Octamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#13
Source (natural)Organism: Homo sapiens (human)

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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)

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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: Trichoplusia ni (cabbage looper)
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: Trichoplusia ni (cabbage looper)
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: INO80 complex subunit C

MacromoleculeName: INO80 complex subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.672553 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #4: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 4 / 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: Trichoplusia ni (cabbage looper)
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 #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: Trichoplusia ni (cabbage looper)
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: Trichoplusia ni (cabbage looper)
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 #9: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 9 / 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 #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

UniProtKB: Histone H4

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Macromolecule #11: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #12: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.820045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 2-E

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Macromolecule #13: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV LPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #7: Nucleosomal DNA Strand 1 (152-MER)

MacromoleculeName: Nucleosomal DNA Strand 1 (152-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.121051 KDa
SequenceString: (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) ...String:
(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)

+
Macromolecule #8: Nucleosomal DNA Strand 2 (152-MER)

MacromoleculeName: Nucleosomal DNA Strand 2 (152-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.715758 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 7 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

+
Macromolecule #15: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / 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
Component:
ConcentrationFormulaName
30.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
50.0 mMNaClSodium Chloride
0.5 mMDTTDithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Details: Negative Polarity
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12419217
Details: Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zi4

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94892
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 134.96 / Target criteria: MAXIMUM LIKELIHOOD WITH PHASES
Output model

PDB-9gcg:
CryoEM structure of the human INO80 core- H2A.Z nucleosome complex

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