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- EMDB-51290: CryoEM structure of the human INO80-Hexasome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51290
TitleCryoEM structure of the human INO80-Hexasome complex
Map data
Sample
  • Complex: CryoEM structure of the human INO80-Hexasome complex
    • Complex: Histone Hexamer
      • Protein or peptide: x 4 types
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: x 2 types
    • Protein or peptide: x 6 types
  • Protein or peptide: x 1 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 / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / establishment of protein localization to chromatin ...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 / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / establishment of protein localization to chromatin / Ino80 complex / regulation of double-strand break repair / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / UV-damage excision repair / regulation of chromosome organization / NuA4 histone acetyltransferase complex / MLL1 complex / regulation of DNA replication / TFIID-class transcription factor complex binding / mitotic sister chromatid segregation / regulation of embryonic development / Telomere Extension By Telomerase / protein folding chaperone complex / ATP-dependent activity, acting on DNA / RNA polymerase II core promoter sequence-specific DNA binding / alpha-tubulin binding / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / negative regulation of megakaryocyte differentiation / 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 / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / telomere maintenance / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / TBP-class protein binding / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / DNA helicase activity / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / cellular response to ionizing radiation / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / cellular response to estradiol stimulus / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / negative regulation of canonical Wnt signaling pathway / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / euchromatin / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / chromatin DNA binding / ADP binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / double-strand break repair via homologous recombination / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / beta-catenin binding / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / fibrillar center / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / Transcriptional regulation of granulopoiesis / nuclear matrix / RMTs methylate histone arginines / Metalloprotease DUBs / HCMV Early Events / positive regulation of canonical Wnt signaling pathway
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 H2A conserved site / Histone H2A signature. / Histone H2B 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. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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 type 1-B/E / Histone H2B type 1-B / 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: 3.35 Å
AuthorsSharma M / Aggarwal P / 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: Nucleic Acids Res / Year: 2026
Title: Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex.
Authors: Priyanka Aggarwal / Manmohan Sharma / Stephan Woike / Franziska Kunert / Annika Brem / Manuela Moldt / Karl-Peter Hopfner /
Abstract: The ATP-dependent INO80 chromatin remodeller slides and repositions nucleosomes to shape and maintain chromatin around gene regulatory elements and replication origins. Recent work uncovered ...The ATP-dependent INO80 chromatin remodeller slides and repositions nucleosomes to shape and maintain chromatin around gene regulatory elements and replication origins. Recent work uncovered capabilities of yeast and fungal INO80 to bind and slide hexasomes, but whether this is a universal feature is unknown. Here, we show that human INO80 also slides hexasomes as efficiently as H2A and H2A.Z nucleosomes. By determining a variety of structures of human INO80 bound to canonical and H2A.Z nucleosomes as well as hexasomes, we reveal a predominantly topological sensing of nucleosomal species with at least three positions depending on entry DNA unwrapping. INO80 spin-rotates around the nucleosomal core particle as a function of entry DNA unwrapping. Different degrees of unwrapped entry DNA lead to two different nucleosomal and one hexasomal locations of INO80, determined by binding of the Snf2 ATPase to entry point of extranucleosomal DNA at the nucleosome/hexasome core. Acidic patch binding by the INO80 subunit IES2 can differentiate between (sub)nucleosomal species, is important for nucleosome but not hexasome sliding, and may sense unwrapped exit DNA. These findings provide structural and mechanistic insights into how human INO80 remodels diverse chromatin substrates in a topology driven manner.
History
DepositionAug 7, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51290.png

Downloads & links

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Map

FileDownload / File: emd_51290.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 290.8 Å		0.73 Å/pix.
x 400 pix.
= 290.8 Å		0.73 Å/pix.
x 400 pix.
= 290.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6755798 - 1.1556392
Average (Standard dev.)0.0048896484 (±0.05289871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 290.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51290_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51290_half_map_2.map
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Sample components

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Entire : CryoEM structure of the human INO80-Hexasome complex

EntireName: CryoEM structure of the human INO80-Hexasome complex
Components
  • Complex: CryoEM structure of the human INO80-Hexasome complex
    • Complex: Histone Hexamer
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-B
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Hexasomal DNA Strand 1
      • DNA: Hexasomal DNA strand 2
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: INO80 complex subunit B
    • Protein or peptide: INO80 complex subunit C
    • Protein or peptide: Actin-related protein 5
  • Protein or peptide: Histone H4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: CryoEM structure of the human INO80-Hexasome complex

SupramoleculeName: CryoEM structure of the human INO80-Hexasome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10, #12-#13
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histone Hexamer

SupramoleculeName: Histone Hexamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #9-#10, #12-#13
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Synthetic deoxyribonucleic acid

SupramoleculeName: Synthetic deoxyribonucleic acid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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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: 49.90534 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: KIEEVKSTTK TQRIASHSHV KGLGLDESGL AKQAASGLVG QENAREACGV IVELIKSKKM AGRAVLLAGP PGTGKTALAL AIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG L KTAKGTKQ ...String:
KIEEVKSTTK TQRIASHSHV KGLGLDESGL AKQAASGLVG QENAREACGV IVELIKSKKM AGRAVLLAGP PGTGKTALAL AIAQELGSK VPFCPMVGSE VYSTEIKKTE VLMENFRRAI GLRIKETKEV YEGEVTELTP CETENPMGGY GKTISHVIIG L KTAKGTKQ LKLDPSIFES LQKERVEAGD VIYIEANSGA VKRQGRCDTY ATEFDLEAEE YVPLPKGDVH KKKEIIQDVT LH DLDVANA RPQGGQDILS MMGQLMKPKK TEITDKLRGE INKVVNKYID QGIAELVPGV LFVDEVHMLD IECFTYLHRA LES SIAPIV IFASNRGNCV IRGTEDITSP HGIPLDLLDR VMIIRTMLYT PQEMKQIIKI RAQTEGINIS EEALNHLGEI GTKT TLRYS VQLLTPANLL AKINGKDSIE KEHVEEISEL FYDAKSSAKI LADQQDKY

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: 48.6275 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DVTRIERIGA HSHIRGLGLD DALEPRQASQ GMVGQLAARR AAGVVLEMIR EGKIAGRAVL IAGQPGTGKT AIAMGMAQAL GPDTPFTAI AGSEIFSLEM SKTEALTQAF RRSIGVRIKE ETEIIEGEVV EIQIDRPATG TGSKVGKLTL KTTEMETIYD L GTKMIESL ...String:
DVTRIERIGA HSHIRGLGLD DALEPRQASQ GMVGQLAARR AAGVVLEMIR EGKIAGRAVL IAGQPGTGKT AIAMGMAQAL GPDTPFTAI AGSEIFSLEM SKTEALTQAF RRSIGVRIKE ETEIIEGEVV EIQIDRPATG TGSKVGKLTL KTTEMETIYD L GTKMIESL TKDKVQAGDV ITIDKATGKI SKLGRSFTRA RDYDAMGSQT KFVQCPDGEL QKRKEVVHTV SLHEIDVINS RT QGFLALF SGDTGEIKSE VREQINAKVA EWREEGKAEI IPGVLFIDEV HMLDIESFSF LNRALESDMA PVLIMATNRG ITR IRGTSY QSPHGIPIDL LDRLLIVSTT PYSEKDTKQI LRIRCEEEDV EMSEDAYTVL TRIGLETSLR YAIQLITAAS LVCR KRKGT EVQVDDIKRV YSLFLDESRS TQYMKEYQDA FLFN

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: 85.303375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LKGYQLKGMN WLANLYEQGI NGILADEMGL GKTVQSIALL AHLAERENIW GPFLIISPAS TLNNWHQEFT RFVPKFKVLP YWGNPHDRK VIRRFWSQKT LYTQDAPFHV VITSYQLVVQ DVKYFQRVKW QYMVLDEAQA LKSSSSVRWK ILLQFQCRNR L LLTGTPIQ ...String:
LKGYQLKGMN WLANLYEQGI NGILADEMGL GKTVQSIALL AHLAERENIW GPFLIISPAS TLNNWHQEFT RFVPKFKVLP YWGNPHDRK VIRRFWSQKT LYTQDAPFHV VITSYQLVVQ DVKYFQRVKW QYMVLDEAQA LKSSSSVRWK ILLQFQCRNR L LLTGTPIQ NTMAELWALL HFIMPTLFDS HEEFNEWFSK DIESHAENKS AIDENQLSRL HMILKPFMLR RIKKDVENEL SD KIEILMY CQLTSRQKLL YQALKNKISI EDLLQSSMGS TQQAQNTTSS LMNLVMQFRK VCNHPELFER QETWSPFHIS LKP YHISKF IYRHGQIRVF NHSRDRWLRV LSPFAPDYIQ RSLFHRKGIN EESCFSFLRF IDISPAEMAN LMLQGLLARW LALF LSLKA SYRLHQLRSW GAPEGESHQR YLRNKDFLLG VNFPLSFPNL CSCPLLKSLV FSSHCKAVSG YSDQVVHQRR SATSS LRRC LLTELPSFLC VASPRVTAVP LDSYCNDRSA EYERRVLKEG GSLAAKQCLL NGAPELAADW LNRRSQFFPE PAGGLW SIR PQNGWSFIRI PGKESLITDS GKLYALDVLL TRLKSQGHRV LIYSQMTRMI DLLEEYMVYR KHTYMRLDGS SKISERR DM VADFQNRNDI FVFLLSTRAG GLGINLTAAD TVIFYDSDWN PTVDQQAMDR AHRLGQTKQV TVYRLICKGT IEERILQR A KEKSEIQRMV IS

UniProtKB: Chromatin-remodeling ATPase INO80

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Macromolecule #4: INO80 complex subunit B

MacromoleculeName: INO80 complex subunit B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.692893 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
LTEEMLLKRE ERARKRRLQA ARRAEEHKNQ TIERLTKTAA TSGRGGRGGA RGERRGGRAA APAPMVRYCS GAQGSTLSFP PGVPAPTAV SQRPSPSGPP PRCSVPGCPH PRRYACSRTG QALCSLQCYR INLQMR

UniProtKB: INO80 complex subunit B

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Macromolecule #5: INO80 complex subunit C

MacromoleculeName: INO80 complex subunit C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.064693 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
KDPNFVHSGH GGAVAGKKNR TWKYLKQILA SERALPWQLN DPNYFSIDAP PSFKPAKKYS DVSGLLANYT DPQSKLRFST IEEFSYIRR LPSDVVTGYL ALRKATSI

UniProtKB: INO80 complex subunit C

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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: 65.589383 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: PFRDARAAPD PVLEAGPVAH GPLPVPLVLD NGSFQVRAGW ACPGQDPGPE PRLQFRAVCA RGRGGARGAS GPQVGNALGS LEPLRWMLR SPFDRNVPVN LELQELLLDY SFQHLGVSSQ GCVDHPIVLT EAVCNPLYSR QMMSELLFEC YGIPKVAYGI D SLFSFYHN ...String:
PFRDARAAPD PVLEAGPVAH GPLPVPLVLD NGSFQVRAGW ACPGQDPGPE PRLQFRAVCA RGRGGARGAS GPQVGNALGS LEPLRWMLR SPFDRNVPVN LELQELLLDY SFQHLGVSSQ GCVDHPIVLT EAVCNPLYSR QMMSELLFEC YGIPKVAYGI D SLFSFYHN KPKNSMCSGL IISSGYQCTH VLPILEGRLD AKNCKRINLG GSQAAGYLQR LLQLKYPGHL AAITLSRMEE IL HEHSYIA EDYVEELHKW RCPDYYENNV HKMQLPFSSK LLGSTLTSEE KQERRQQQLR RLQELNARRR EEKLQLDQER LDR LLYVQE LLEDGQMDQF HKALIELNMD SPEELQSYIQ KLSIAVEQAK QKILQAEVNL EVDVVDSKPE TPDLEQLEPS LEDV ESMND FDPLFSEETP GVEKPVTTVQ PVFNLAAYHQ LFVGTERIRA PEIIFQPSLI GEEQAGIAET LQYILDRYPK DIQEM LVQN VFLTGGNTMY PGMKARMEKE LLEMRPFRSS FQVQLASNPV LDAWYGARDW ALNHLDDNEV WITRKEYEEK GGEYLK EHC ASNIYVPIRL PKQ

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: 10.948846 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RPGTVALREI RRYQKSTELL IRKLPFQRLV REIAQDFKTD LRFQSSAVMA LQEACEAYLV GLFEDTNLCA IHAKRVTIMP KDIQLARRI RGERA

UniProtKB: Histone H3.1

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Macromolecule #10: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.180745 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG G

UniProtKB: Histone H4

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Macromolecule #11: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.795306 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NIQGITKPAI RRLARRGGVK RISGLIYEET RGVLKVFLEN VIRDAVTYTE HAKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

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Macromolecule #12: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.865871 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGR VTIAQGGVLP NIQAVLLPK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #13: Histone H2B type 1-B

MacromoleculeName: Histone H2B type 1-B / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.26375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SRKESYSIYV YKVLKQVHPD TGISSKAMGI MNSFVNDIFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTS

UniProtKB: Histone H2B type 1-B

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Macromolecule #7: Hexasomal DNA Strand 1

MacromoleculeName: Hexasomal DNA Strand 1 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 35.098379 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #8: Hexasomal DNA strand 2

MacromoleculeName: Hexasomal DNA strand 2 / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 34.64009 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

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

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

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Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 7 / 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 #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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15713359
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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 34444
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)

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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-9ge5:
CryoEM structure of the human INO80-Hexasome complex

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