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- EMDB-32992: Cryo-EM structure of ISW1a-dinucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-32992
TitleCryo-EM structure of ISW1a-dinucleosome
Map dataISW1a-dinuclesome
Sample
  • Complex: ISW1a-dinucleosome
    • Protein or peptide: x 6 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsIoc3 binding / PROTEIN BINDING
Function / homology
Function and homology information


Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / negative regulation of RNA export from nucleus / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding ...Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / negative regulation of RNA export from nucleus / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / nucleosome array spacer activity / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / mRNA 3'-UTR binding / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / response to heat / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Isw1/2, N-terminal / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain ...Isw1/2, N-terminal / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / 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 / 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. / Homeobox-like domain superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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 / ISWI one complex protein 3 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 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_32992.png

Downloads & links

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Map

FileDownload / File: emd_32992.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationISW1a-dinuclesome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0048
Minimum - Maximum-0.010158123 - 0.030327283
Average (Standard dev.)0.0001436729 (±0.0010906338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1

Fileemd_32992_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_32992_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ISW1a-dinucleosome

EntireName: ISW1a-dinucleosome
Components
  • Complex: ISW1a-dinucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (343-MER)
    • DNA: DNA(343-MER)
    • Protein or peptide: ISWI one complex protein 3
    • Protein or peptide: ISWI chromatin-remodeling complex ATPase ISW1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ISW1a-dinucleosome

SupramoleculeName: ISW1a-dinucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 392 kDa/nm

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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: 4 / 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: 4 / 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: 4 / 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 one complex protein 3

MacromoleculeName: ISWI one complex protein 3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 72.422539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVAPKPKPAH EQVEPALIPS NWTSVIPLLT SDFKNQYSVI SRLKNPNMKP VPYAGDIIKL MAFINKFSSF FHSDLQNLSF QDFEVGLDL YPGDPNGSAA GIVKGPEDTS LLLYPDFMAI KDIVYCQDKM NLLFLSLLDL TFTENFDGKS AKKKGPLTTW E NLKSSSKK ...String:
MVAPKPKPAH EQVEPALIPS NWTSVIPLLT SDFKNQYSVI SRLKNPNMKP VPYAGDIIKL MAFINKFSSF FHSDLQNLSF QDFEVGLDL YPGDPNGSAA GIVKGPEDTS LLLYPDFMAI KDIVYCQDKM NLLFLSLLDL TFTENFDGKS AKKKGPLTTW E NLKSSSKK VFSNPLYRLR LVAREWGYPR EWRQQLPSDQ DISKPKTALF EQDEQTPVVD PSHPEILTPN IYTWNANEPL PL ESNPLYN REMDKNGILA LKPMDRVVLL RALTDWCASH SSAIHDEIYK LTHGKKDPVF GIQTQQVPRY TIEGVDNTIN QFK KLCSLI QSRYEIRSKK KHFVKQLKEG KKPDLSRKLE ILKEIKAELK NAVKSEKDEL LFSLYDKWVP LFEGELPDQP LANP FSERL YKLRLQEFFL GRVPHIGDFY MPRLHSYGDS LEMSTFTDLR NLQALLSKFK NNEYNAFTLF ENDGQSMSAQ FKLFY HDTP SLAHDVARGR NTSGKVYWYE LCHDSATLLE FLEFLDYKIV KPQDEKKEGN EKEKEALNNE AHILEQKSTT DNNPSI NTN PLPKDAKYNT ARKKLQILKE FLSDYYFILR QFEQMKVQFA DMKPGKRQLR RIQRQTVNYN T

UniProtKB: ISWI one complex protein 3

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Macromolecule #8: ISWI chromatin-remodeling complex ATPase ISW1

MacromoleculeName: ISWI chromatin-remodeling complex ATPase ISW1 / type: protein_or_peptide / ID: 8 / 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) / Strain: S288c
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 (343-MER)

MacromoleculeName: DNA (343-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 108.890133 KDa
SequenceString: (DC)(DC)(DG)(DC)(DG)(DG)(DT)(DA)(DC)(DC) (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) ...String:
(DC)(DC)(DG)(DC)(DG)(DG)(DT)(DA)(DC)(DC) (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)(DA)(DG)(DC) (DT)(DT) (DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DG)(DC) (DT)(DC)(DG)(DA)(DC)(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) (DG)(DC)(DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT) (DG)(DG)(DT)(DC)(DA)(DT) (DA)(DG)(DC) (DT)(DG)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DT) (DG)

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Macromolecule #6: DNA(343-MER)

MacromoleculeName: DNA(343-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 109.775656 KDa
SequenceString: (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DC) (DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG) (DC)(DT)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DC) (DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG) (DC)(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)(DG)(DG)(DT)(DC) (DG) (DA)(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DG)(DA) (DC)(DA)(DA)(DG)(DC)(DT)(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) (DG)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DC)(DG) (DG)

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / 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 #10: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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 chloride
10.0 mMTristris
2.0 mMMgCl2magnesium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER / Details: Relion3.0
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66852
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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