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- EMDB-22688: cryo-EM map of di-chromatosome containing H1.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-22688
Titlecryo-EM map of di-chromatosome containing H1.4
Map datacryo-EM map of di-chromatosome containing human linker histone H1.4
Sample
  • Complex: di-chromatosome containing human linker histone H1.4
    • Protein or peptide: human histone H3.1Histone H3
    • Protein or peptide: human histone H4
    • Protein or peptide: human histone H2A1
    • Protein or peptide: human histone H2B1J
    • Protein or peptide: DNA (394-MER)
    • Protein or peptide: DNA(394-MER)
    • Protein or peptide: scFv20
    • Protein or peptide: human histone H1.4
Biological specieshuman (human) / Homo sapiens (human) / Mougeotia scalaris (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.73 Å
AuthorsZhou B-R / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Mol Cell / Year: 2021
Title: Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.
Authors: Bing-Rui Zhou / Hanqiao Feng / Seyit Kale / Tara Fox / Htet Khant / Natalia de Val / Rodolfo Ghirlando / Anna R Panchenko / Yawen Bai /
Abstract: The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they ...The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
History
DepositionSep 18, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22688.png

Downloads & links

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Map

FileDownload / File: emd_22688.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of di-chromatosome containing human linker histone H1.4
Voxel sizeX=Y=Z: 4.75 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.48836753 - 2.4284444
Average (Standard dev.)-0.00044692206 (±0.05986313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 608.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.754.754.75
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z608.000608.000608.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ180180180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.4882.428-0.000

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Supplemental data

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Sample components

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Entire : di-chromatosome containing human linker histone H1.4

EntireName: di-chromatosome containing human linker histone H1.4
Components
  • Complex: di-chromatosome containing human linker histone H1.4
    • Protein or peptide: human histone H3.1Histone H3
    • Protein or peptide: human histone H4
    • Protein or peptide: human histone H2A1
    • Protein or peptide: human histone H2B1J
    • Protein or peptide: DNA (394-MER)
    • Protein or peptide: DNA(394-MER)
    • Protein or peptide: scFv20
    • Protein or peptide: human histone H1.4

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Supramolecule #1: di-chromatosome containing human linker histone H1.4

SupramoleculeName: di-chromatosome containing human linker histone H1.4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: human (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: human histone H3.1

MacromoleculeName: human histone H3.1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRK Q LATKAARK SA PATGGVK KPH RYRPGT VALR EIRRY QKSTE LLIR KLPFQR LVR EIAQDFK TD LRFQSSAV M ALQEACEAY LVGLFEDTNL CAIHAKRVT I MPKDIQLA RR IRGERA

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Macromolecule #2: human histone H4

MacromoleculeName: human histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MSGRGKGGKG LGKGGAKRH R KVLRDNIQ GI TKPAIRR LAR RGGVKR ISGL IYEET RGVLK VFLE NVIRDA VTY TEHAKRK TV TAMDVVYA L KRQGRTLYG FGG

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Macromolecule #3: human histone H2A1

MacromoleculeName: human histone H2A1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRS S RAGLQFPV GR VHRLLRK GNY SERVGA GAPV YLAAV LEYLT AEIL ELAGNA ARD NKKTRII PR HLQLAIRN D EELNKLLGR VTIAQGGVLP NIQAVLLPK K TESHHKAK GK

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Macromolecule #4: human histone H2B1J

MacromoleculeName: human histone H2B1J / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAP A PKKGSKKA VT KAQKKDG KKR KRSRKE SYSI YVYKV LKQVH PDTG ISSKAM GIM NSFVNDI FE RIAGEASR L AHYNKRSTI TSREIQTAVR LLLPGELAK H AVSEGTKA VT KYTSAK

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Macromolecule #5: DNA (394-MER)

MacromoleculeName: DNA (394-MER) / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGGCTGGACC CTATACGCGG CCGCCCTGGA GAATCCCGGT GCCGAGGCCG CTCAATTGGT CGTAGACAGC TCTAGCACCG CTTAAACGCA CGTACGCGCT GTCCCCCGCG TTTTAACCGC CAAGGGGATT ACTCCCTAGT CTCCAGGCAC GTGTCAGATA TATACATCCT ...String:
GGGCTGGACC CTATACGCGG CCGCCCTGGA GAATCCCGGT GCCGAGGCCG CTCAATTGGT CGTAGACAGC TCTAGCACCG CTTAAACGCA CGTACGCGCT GTCCCCCGCG TTTTAACCGC CAAGGGGATT ACTCCCTAGT CTCCAGGCAC GTGTCAGATA TATACATCCT GTGCATGTAT TGAACAGCGA CCACAGTACT CTGGACCCTA TACGCGGCCG CCCTGGAGAA TCCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCCTGTG CATGTATTGA ACAGCGACCA CCCC

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Macromolecule #6: DNA(394-MER)

MacromoleculeName: DNA(394-MER) / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGGGTGGTCG CTGTTCAATA CATGCACAGG ATGTATATAT CTGACACGTG CCTGGAGACT AGGGAGTAAT CCCCTTGGCG GTTAAAACGC GGGGGACAGC GCGTACGTGC GTTTAAGCGG TGCTAGAGCT GTCTACGACC AATTGAGCGG CCTCGGCACC GGGATTCTCC ...String:
GGGGTGGTCG CTGTTCAATA CATGCACAGG ATGTATATAT CTGACACGTG CCTGGAGACT AGGGAGTAAT CCCCTTGGCG GTTAAAACGC GGGGGACAGC GCGTACGTGC GTTTAAGCGG TGCTAGAGCT GTCTACGACC AATTGAGCGG CCTCGGCACC GGGATTCTCC AGGGCGGCCG CGTATAGGGT CCAGAGTACT GTGGTCGCTG TTCAATACAT GCACAGGATG TATATATCTG ACACGTGCCT GGAGACTAGG GAGTAATCCC CTTGGCGGTT AAAACGCGGG GGACAGCGCG TACGTGCGTT TAAGCGGTGC TAGAGCTGTC TACGACCAAT TGAGCGGCCT CGGCACCGGG ATTCTCCAGG GCGGCCGCGT ATAGGGTCCA GCCC

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Macromolecule #7: scFv20

MacromoleculeName: scFv20 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mougeotia scalaris (plant)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQD FSLTINNLES DDTATYYCLQ HGESPYTFGS GTKLEIKRAG GGGSGGGGSG GGGSGGGGSM EVQLQQSGPE LVEPGTSVKM ...String:
MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQD FSLTINNLES DDTATYYCLQ HGESPYTFGS GTKLEIKRAG GGGSGGGGSG GGGSGGGGSM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKATL TSDKSSSTVY MELSSLTSED SAVYYCARKS SRLRSTLDYW GQGTSVTVSS

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Macromolecule #8: human histone H1.4

MacromoleculeName: human histone H1.4 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSETAPAAPA APAPAEKTP V KKKARKSA GA AKRKASG PPV SELITK AVAA SKERS GVSLA ALKK ALAAAG YDV EKNNSRI KL GLKSLVSK G TLVQTKGTG ASGSFKLNKK AASGEAKPK A KKAGAAKA KK PAGAAKK PKK ATGAAT PKKS AKKTP ...String:
MSETAPAAPA APAPAEKTP V KKKARKSA GA AKRKASG PPV SELITK AVAA SKERS GVSLA ALKK ALAAAG YDV EKNNSRI KL GLKSLVSK G TLVQTKGTG ASGSFKLNKK AASGEAKPK A KKAGAAKA KK PAGAAKK PKK ATGAAT PKKS AKKTP KKAKK PAAA AGAKKA KSP KKAKAAK PK KAPKSPAK A KAVKPKAAK PKTAKPKAAK PKKAAAKKK

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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: 7.4
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: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 10876

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