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- EMDB-32996: Cryo-EM structure of N1 nucleosome-RA -

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Basic information

Entry
Database: EMDB / ID: EMD-32996
TitleCryo-EM structure of N1 nucleosome-RA
Map dataN1-RA
Sample
  • Complex: IOC3-N2 nucleosome
    • Complex: N2 nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
    • Complex: IOC3
      • Protein or peptide: ISWI chromatin-remodeling complex ATPase ISW1
KeywordsPROTEIN BINDING-DNA COMPLEX
Function / homology
Function and homology information


Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of chromatin organization / DNA-templated transcription elongation / rDNA binding / ATP-dependent chromatin remodeler activity / sister chromatid cohesion ...Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of chromatin organization / DNA-templated transcription elongation / rDNA binding / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / response to heat / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily ...Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / ISWI chromatin-remodeling complex ATPase ISW1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLifei L / Kangjing C / Chen Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the ISW1a complex bound to the dinucleosome.
Authors: Lifei Li / Kangjing Chen / Youyang Sia / Pengjing Hu / Youpi Ye / Zhucheng Chen /
Abstract: Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin ...Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
History
DepositionMar 1, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32996.png

Downloads & links

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Map

FileDownload / File: emd_32996.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN1-RA
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.016775671 - 0.052212432
Average (Standard dev.)0.00021667518 (±0.0018236109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : IOC3-N2 nucleosome

EntireName: IOC3-N2 nucleosome
Components
  • Complex: IOC3-N2 nucleosome
    • Complex: N2 nucleosome
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
    • Complex: IOC3
      • Protein or peptide: ISWI chromatin-remodeling complex ATPase ISW1

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Supramolecule #1: IOC3-N2 nucleosome

SupramoleculeName: IOC3-N2 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 392 kDa/nm

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Supramolecule #2: N2 nucleosome

SupramoleculeName: N2 nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Synthetically produced: Yes

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Supramolecule #4: IOC3

SupramoleculeName: IOC3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
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 #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: ISWI chromatin-remodeling complex ATPase ISW1

MacromoleculeName: ISWI chromatin-remodeling complex ATPase ISW1 / type: protein_or_peptide / ID: 7 / 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: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 123.301703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MENLKPFQVG LPPHDPESNK KRYLLKDANG KKFDLEGTTK RFEHLLSLSG LFKHFIESKA AKDPKFRQVL DVLEENKANG KGKGKHQDV RRRKTEHEED AELLKEEDSD DDESIEFQFR ESPAYVNGQL RPYQIQGVNW LVSLHKNKIA GILADEMGLG K TLQTISFL ...String:
MENLKPFQVG LPPHDPESNK KRYLLKDANG KKFDLEGTTK RFEHLLSLSG LFKHFIESKA AKDPKFRQVL DVLEENKANG KGKGKHQDV RRRKTEHEED AELLKEEDSD DDESIEFQFR ESPAYVNGQL RPYQIQGVNW LVSLHKNKIA GILADEMGLG K TLQTISFL GYLRYIEKIP GPFLVIAPKS TLNNWLREIN RWTPDVNAFI LQGDKEERAE LIQKKLLGCD FDVVIASYEI II REKSPLK KINWEYIIID EAHRIKNEES MLSQVLREFT SRNRLLITGT PLQNNLHELW ALLNFLLPDI FSDAQDFDDW FSS ESTEED QDKIVKQLHT VLQPFLLRRI KSDVETSLLP KKELNLYVGM SSMQKKWYKK ILEKDLDAVN GSNGSKESKT RLLN IMMQL RKCCNHPYLF DGAEPGPPYT TDEHLVYNAA KLQVLDKLLK KLKEEGSRVL IFSQMSRLLD ILEDYCYFRN YEYCR IDGS TAHEDRIQAI DDYNAPDSKK FVFLLTTRAG GLGINLTSAD VVVLYDSDWN PQADLQAMDR AHRIGQKKQV KVFRLV TDN SVEEKILERA TQKLRLDQLV IQQNRTSLKK KENKADSKDA LLSMIQHGAA DVFKSGTSTG SAGTPEPGSG EKGDDID LD ELLLKSENKT KSLNAKYETL GLDDLQKFNQ DSAYEWNGQD FKKKIQRDII SPLLLNPTKR ERKENYSIDN YYKDVLNT G RSSTPSHPRM PKPHVFHSHQ LQPPQLKVLY EKERMWTAKK TGYVPTMDDV KAAYGDISDE EEKKQKLELL KLSVNNSQP LTEEEEKMKA DWESEGFTNW NKLEFRKFIT VSGKYGRNSI QAIARELAPG KTLEEVRAYA KAFWSNIERI EDYEKYLKII ENEEEKIKR VKMQQEALRR KLSEYKNPFF DLKLKHPPSS NNKRTYSEEE DRFILLMLFK YGLDRDDVYE LVRDEIRDCP L FELDFYFR SRTPVELARR GNTLLQCLEK EFNAGIVLDD ATKDRMKKED ENGKRIREEF ADQTANEKEN VDGVESKKAK IE DTSNVGT EQLVAEKIPE NETTH

UniProtKB: ISWI chromatin-remodeling complex ATPase ISW1

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Macromolecule #5: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.15477 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DA)

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Macromolecule #6: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.265824 KDa
SequenceString: (DT)(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) ...String:
(DT)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMNaClSodium chloridesodium chloride
10.0 mMTristris
2.0 mMMgCl2magnesium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Relion3.0
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170126

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