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- PDB-8aag: H1-bound palindromic nucleosome, state 1 -

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Basic information

Entry
Database: PDB / ID: 8aag
TitleH1-bound palindromic nucleosome, state 1
Components
  • (DNA/RNA (185- ...) x 2
  • Histone H1.0-B
  • Histone H2A type 1
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3.2
  • Histone H4
KeywordsGENE REGULATION / linker histone H1 / nucleosome
Function / homology
Function and homology information


chromosome condensation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...chromosome condensation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / 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 / telomere organization / RNA Polymerase I Promoter Opening / 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 / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / 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 / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...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 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-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA/RNA hybrid (> 100) / Histone H1.0-B / Histone H4
Similarity search - Component
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsAlegrio Louro, J. / Beinsteiner, B. / Cheng, T.C. / Patel, A.K.M. / Boopathi, R. / Angelov, D. / Hamiche, A. / Bednar, J. / Kale, S. / Dimitrov, S. / Klaholz, B.
Funding support France, European Union, 8items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR) France
French Infrastructure for Integrated Structural Biology (FRISBI) France
Instruct-ERIC Center (Strasbourg Centre) France
Foundation for Medical Research (France) France
Institut National du Cancer (inCA)
European Regional Development FundepiRNA - (Region Grand Est; Competitivite Alsace 2014-2020)European Union
European Molecular Biology Organization (EMBO)EMBO IG 5056European Union
CitationJournal: Structure / Year: 2023
Title: Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms.
Authors: Jaime Alegrio Louro / Ramachandran Boopathi / Brice Beinsteiner / Abdul Kareem Mohideen Patel / Tat Cheung Cheng / Dimitar Angelov / Ali Hamiche / Jan Bendar / Seyit Kale / Bruno P Klaholz / Stefan Dimitrov /
Abstract: Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome ...Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure, and therefore also to chromatin, is unclear. Efforts to investigate potential asymmetry due to H1s have been hampered by the DNA sequence, which naturally differs in each gyre. To overcome this issue, we designed and analyzed by cryo-EM a nucleosome reconstituted with a palindromic (601L) 197-bp DNA. As in the non-palindromic 601 sequence, H1 restricts linker DNA flexibility but reveals partial asymmetrical unwrapping. However, in contrast to the non-palindromic nucleosome, in the palindromic nucleosome H1 CTD collapses to the proximal linker. Molecular dynamics simulations show that this could be dictated by a slightly tilted orientation of the globular domain (GD) of H1, which could be linked to the DNA sequence of the nucleosome dyad.
History
DepositionJul 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA/RNA (185-MER)
J: DNA/RNA (185-MER)
Z: Histone H1.0-B
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B type 1-C/E/F/G/I


Theoretical massNumber of molelcules
Total (without water)252,69211
Polymers252,69211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA/RNA (185- ... , 2 types, 2 molecules IJ

#1: DNA/RNA hybrid DNA/RNA (185-MER)


Mass: 61553.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: DNA/RNA hybrid DNA/RNA (185-MER)


Mass: 61343.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Protein , 5 types, 9 molecules ZAEBFCGDH

#3: Protein Histone H1.0-B / H1-SA / H1D / Histone H1(0)-2 / Histone H5A / XlH5A


Mass: 21129.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h1f0-b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22844
#4: Protein Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62805
#6: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The model and sample sequence do not match the experimental sequence / taxonomy because a previously published model (pdb 5nl0) from different organism was utilized. Experimental sequence - ...Details: The model and sample sequence do not match the experimental sequence / taxonomy because a previously published model (pdb 5nl0) from different organism was utilized. Experimental sequence - MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK TESHHKAKGK
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#7: Protein Histone H2B type 1-C/E/F/G/I


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The model and sample sequence do not match the experimental sequence / taxonomy because a previously published model (pdb 5nl0) from different organism was utilized. Experimental sequence - ...Details: The model and sample sequence do not match the experimental sequence / taxonomy because a previously published model (pdb 5nl0) from different organism was utilized. Experimental sequence - MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT KYTSSK
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1H1-bound palindromic nucleosome, state 1COMPLEXall0MULTIPLE SOURCES
2Human core histone octamerCOMPLEX#4-#71RECOMBINANT
3Linker histoneCOMPLEX#31RECOMBINANT
4Palindromic DNACOMPLEX#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.27 MDaNO
220.15 MDaNO
330.021 MDaNO
410.12 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Xenopus laevis (African clawed frog)8355
54synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
54synthetic construct (others)32630
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMTris-HClTrisNH2C(CH2OH)3HCl1
210 mMSodium chlorideNaClSodium chloride1
30.25 mMEDTAEthylenediaminetetraacetic acidC10H16N2O81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording

Imaging-ID: 1 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

IDAverage exposure time (sec.)Electron dose (e/Å2)Num. of real images
110493999
25.540.74891
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4Gctf1.06CTF correction
5RELION3CTF correction
8UCSF Chimera1.13model fittingRigid body
9Graphite Life Explorermodel fittingDe novo DNA modelling
13RELION3classification
14RELION33D reconstruction
15PHENIX1.18model refinementEach chain as a rigid body and secondary structure constraints
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6284 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5NL0

5nl0

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00715185
ELECTRON MICROSCOPYf_angle_d0.84922093
ELECTRON MICROSCOPYf_dihedral_angle_d32.6666288
ELECTRON MICROSCOPYf_chiral_restr0.0462511
ELECTRON MICROSCOPYf_plane_restr0.0051512

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