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- PDB-8xjv: Structural basis for the linker histone H5-nucleosome binding and... -

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Basic information

Entry
Database: PDB / ID: 8xjv
TitleStructural basis for the linker histone H5-nucleosome binding and chromatin compaction
Components
  • (DNA) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone H5
KeywordsGENE REGULATION / Chromatin Fiber / Histone / DNA / Linker Histone / Nucleosome / Epigenetics / Genome Folding / Interaction
Function / homology
Function and homology information


negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / double-stranded DNA binding / protein heterodimerization activity / DNA binding / 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 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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
DNA / DNA (> 10) / DNA (> 100) / DNA (> 1000) / Histone H3 / Histone H5 / Histone H2B 1.1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi, W.Y. / Song, F. / Zhu, P.
Funding support China, United States, 10items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300100 China
National Natural Science Foundation of China (NSFC)31991161 China
National Natural Science Foundation of China (NSFC)32230020 China
National Natural Science Foundation of China (NSFC)32241029 China
National Natural Science Foundation of China (NSFC)31730023 China
National Natural Science Foundation of China (NSFC)31500606 China
National Natural Science Foundation of China (NSFC)62131004 China
Chinese Academy of SciencesXDB37010100 China
Howard Hughes Medical Institute (HHMI)55008737 United States
Chinese Academy of Sciences153311KYSB20170020 China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction.
Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai ...Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai / Zongjun Mou / Min Zhou / Haonan Zhang / Zheng Zhou / Huidong Zhang / Yawen Bai / Jin-Qiu Zhou / Wei Li / Guohong Li / Ping Zhu /
Abstract: The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order ...The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.
History
DepositionDec 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Data collection / Source and taxonomy
Category: em_admin / em_entity_assembly_naturalsource / em_entity_assembly_recombinant
Item: _em_admin.last_update / _em_entity_assembly_recombinant.id
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Au: DNA
Av: DNA
A: Histone H2A
B: Histone H2A
C: Histone H2A
D: Histone H2A
E: Histone H2A
F: Histone H2A
G: Histone H2A
H: Histone H2A
I: Histone H2A
J: Histone H2B 1.1
K: Histone H2A
L: Histone H2A
M: Histone H2B 1.1
N: Histone H2B 1.1
O: Histone H2B 1.1
P: Histone H2B 1.1
Q: Histone H2B 1.1
R: Histone H2B 1.1
S: Histone H2B 1.1
T: Histone H2B 1.1
U: Histone H2B 1.1
V: Histone H2B 1.1
W: Histone H2B 1.1
X: Histone H3
Y: Histone H3
Z: Histone H3
a: Histone H3
b: Histone H3
c: Histone H3
d: Histone H3
e: Histone H3
f: Histone H3
g: Histone H3
h: Histone H3
i: Histone H3
j: Histone H3
k: Histone H3
l: Histone H3
m: Histone H3
n: Histone H3
o: Histone H3
p: Histone H3
q: Histone H3
r: Histone H3
s: Histone H3
t: Histone H3
u: Histone H3
v: Histone H4
w: Histone H4
x: Histone H4
y: Histone H4
z: Histone H4
0: Histone H4
1: Histone H4
2: Histone H4
3: Histone H4
4: Histone H4
5: Histone H4
6: Histone H4
7: Histone H4
8: Histone H4
9: Histone H4
CD: Histone H4
a2: Histone H4
a3: Histone H4
a4: Histone H4
a5: Histone H4
a6: Histone H4
a7: Histone H4
a8: Histone H4
a9: Histone H4
aj: Histone H2A
ak: Histone H2A
al: Histone H2A
am: Histone H2A
an: Histone H2A
ao: Histone H2A
ap: Histone H2A
aq: Histone H2A
ar: Histone H2A
as: Histone H2A
at: Histone H2A
au: Histone H2A
av: Histone H2B 1.1
aw: Histone H2B 1.1
ax: Histone H2B 1.1
ay: Histone H2B 1.1
az: Histone H2B 1.1
Aa: Histone H2B 1.1
Ab: Histone H2B 1.1
Ac: Histone H2B 1.1
Ad: Histone H2B 1.1
Ae: Histone H2A
Af: Histone H2B 1.1
Ag: Histone H2B 1.1
Ah: Histone H5
Ai: Histone H5
Aj: Histone H5
Ak: Histone H5
Al: Histone H5
Am: Histone H5
An: Histone H5
Ao: Histone H5
Ap: Histone H5
Aq: Histone H5
Ar: Histone H5
As: Histone H5
At: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)2,882,028110
Polymers2,882,028110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules AuAv

#1: DNA chain DNA


Mass: 651873.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA


Mass: 660629.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein , 5 types, 108 molecules ABCDEFGHIKLajakalamanaoapaqarasatauAeJMNOPQ...

#3: Protein ...
Histone H2A


Mass: 14109.436 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Details: H2A / Source: (gene. exp.) Xenopus laevis (African clawed frog)
Gene: h2ac14.L, h2ac14, hist1h2aj, LOC494591, XELAEV_18003602mg
Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein ...
Histone H2B 1.1 / H2B1.1


Mass: 13641.922 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#5: Protein ...
Histone H3


Mass: 15435.126 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#6: Protein ...
Histone H4


Mass: 11394.426 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#7: Protein
Histone H5


Mass: 21631.875 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P02259

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Details

Has protein modificationN

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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
112x177bp-H5 chromatinCOMPLEXall0MULTIPLE SOURCES
2Widom 601 DNACOMPLEX#1-#21RECOMBINANT
3Histone H2ACOMPLEX#31RECOMBINANT
4Histone H2BCOMPLEX#41RECOMBINANT
5Histone H3.1COMPLEX#51RECOMBINANT
6Histone H4COMPLEX#61RECOMBINANT
7Linker histone H5COMPLEX#71RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
44
55
66
77
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Xenopus laevis (African clawed frog)8355
44Xenopus laevis (African clawed frog)8355
55Xenopus laevis (African clawed frog)8355
66Xenopus laevis (African clawed frog)8355
77Gallus gallus (chicken)9031
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
44Escherichia coli (E. coli)562
55Escherichia coli (E. coli)562
66Escherichia coli (E. coli)562
77Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: NITROGEN

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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 FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7UCSF Chimeramodel fitting
8Rosettamodel fitting
13RELION33D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13670 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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