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- EMDB-22683: Cryo-EM structure of a chromatosome containing human linker histo... -

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Basic information

Entry
Database: EMDB / ID: EMD-22683
TitleCryo-EM structure of a chromatosome containing human linker histone H1.0
Map datasharpened cryo-EM map for structure model building
Sample
  • Complex: chromatosome containing human linker histone H1.0
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (197-MER)
    • DNA: DNA (197-MER)
    • Protein or peptide: scFv20
    • Protein or peptide: Histone H1.0
Function / homology
Function and homology information


negative regulation of DNA recombination / positive regulation of transcription regulatory region DNA binding / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...negative regulation of DNA recombination / positive regulation of transcription regulatory region DNA binding / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / minor groove of adenine-thymine-rich DNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin formation / epigenetic regulation of gene expression / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / transcription repressor complex / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / chromatin DNA binding / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin / Golgi apparatus / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H1.0 / Histone H4 / Histone H3.1
Similarity search - Component
Biological specieshuman (human) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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 17, 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: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k5x
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22683.png

Downloads & links

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Map

FileDownload / File: emd_22683.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened cryo-EM map for structure model building
Voxel sizeX=Y=Z: 1.3125 Å
Density
Contour LevelBy EMDB: 3.0 / Movie #1: 4
Minimum - Maximum-19.435028 - 40.489586
Average (Standard dev.)-7.1725906e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31251.31251.3125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-19.43540.490-0.000

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Supplemental data

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Sample components

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Entire : chromatosome containing human linker histone H1.0

EntireName: chromatosome containing human linker histone H1.0
Components
  • Complex: chromatosome containing human linker histone H1.0
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (197-MER)
    • DNA: DNA (197-MER)
    • Protein or peptide: scFv20
    • Protein or peptide: Histone H1.0

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Supramolecule #1: chromatosome containing human linker histone H1.0

SupramoleculeName: chromatosome containing human linker histone H1.0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: human (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3.1

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

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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: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

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Macromolecule #7: scFv20

MacromoleculeName: scFv20 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.34542 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...String:
MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS

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Macromolecule #8: Histone H1.0

MacromoleculeName: Histone H1.0 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.927182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGA SGSFRLAKSD EPKKSVAFKK TKKEIKKVAT PKKASKPKKA ASKAPTKKPK ATPVKKAKKK LAATPKKAKK P KTVKAKPV ...String:
MTENSTSAPA AKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV GENADSQIKL SIKRLVTTGV LKQTKGVGA SGSFRLAKSD EPKKSVAFKK TKKEIKKVAT PKKASKPKKA ASKAPTKKPK ATPVKKAKKK LAATPKKAKK P KTVKAKPV KASKPKKAKP VKPKAKSSAK RAGKKK

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Macromolecule #5: DNA (197-MER)

MacromoleculeName: DNA (197-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.510484 KDa
SequenceString: (DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(DC)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT) (DG)(DC)(DC)(DG)(DA)(DG) ...String:
(DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG) (DC)(DC)(DG)(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)(DT) (DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT) (DT) (DG)(DA)(DA)(DC)(DA)(DG)(DC)(DG)(DA)(DC) (DC)(DA)(DC)(DC)(DC)(DC)

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Macromolecule #6: DNA (197-MER)

MacromoleculeName: DNA (197-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.141883 KDa
SequenceString: (DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(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) ...String:
(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DT)(DC)(DG) (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(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)(DC)(DC) (DG)(DG) (DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC) (DG)(DT)(DA)(DT)(DA)(DG)(DG)(DG)(DT)(DC) (DC)(DA)(DG)(DC)(DC)(DC)

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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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4qlc


Details: input pdb models: 4QLC, 6DZT, 5NL0 5Y0C
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 133758
FSC plot (resolution estimation)

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