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- PDB-8z50: Crystal structure of the ASF1-H3T-H4 complex -

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Basic information

Entry
Database: PDB / ID: 8z50
TitleCrystal structure of the ASF1-H3T-H4 complex
Components
  • Histone H3.1t
  • Histone H4
  • Histone chaperone ASF1A
KeywordsNUCLEAR PROTEIN / ASF1 / histone / H3-H4 / H3T / H2A-H2B / Nucleosome
Function / homology
Function and homology information


spermatogonial cell division / histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / regulation of cell differentiation / heterochromatin / negative regulation of megakaryocyte differentiation ...spermatogonial cell division / histone chaperone activity / DNA replication-dependent chromatin assembly / muscle cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / replication fork processing / regulation of cell differentiation / heterochromatin / 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 / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / DNA repair / chromatin binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 ...Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Histone H3 signature 1. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H3.1t / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural insights into instability of the nucleosome driven by histone variant H3T.
Authors: Hu, S. / Liu, Y. / Yang, Y. / Xu, L.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone ASF1A
B: Histone H3.1t
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)47,5523
Polymers47,5523
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-51 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.940, 103.873, 85.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone chaperone ASF1A / Anti-silencing function protein 1 homolog A / hAsf1 / hAsf1a / CCG1-interacting factor A / CIA / hCIA


Mass: 20615.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A, CGI-98, HSPC146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y294
#2: Protein Histone H3.1t / H3/t / H3t / H3/g / Histone H3.4


Mass: 15541.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-4, H3FT, HIST3H3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16695
#3: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium chloride, 0.1 M MES pH 6.0, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11137 / % possible obs: 100 % / Redundancy: 8.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.043 / Rrim(I) all: 0.125 / Χ2: 0.974 / Net I/σ(I): 5.6 / Num. measured all: 92323
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.857.60.5995530.9030.9740.2280.6420.918100
2.85-2.98.20.5595390.9210.9790.2040.5960.862100
2.9-2.968.70.4965620.9420.9850.1750.5270.913100
2.96-3.028.70.3845240.9550.9890.1360.4080.908100
3.02-3.088.70.3745720.9640.9910.1320.3980.907100
3.08-3.158.60.3235320.9710.9930.1150.3430.915100
3.15-3.238.50.2615510.9770.9940.0940.2780.914100
3.23-3.328.40.2275430.9860.9960.0820.2420.937100
3.32-3.427.90.2045510.9870.9970.0770.2190.973100
3.42-3.537.80.155470.990.9980.0570.1610.979100
3.53-3.658.80.1515470.9930.9980.0530.161.059100
3.65-3.88.70.1235580.9940.9990.0440.1311.017100
3.8-3.978.60.1135690.9960.9990.040.121.003100
3.97-4.188.50.0975470.9960.9990.0350.1031.052100
4.18-4.448.10.0835620.9970.9990.0310.0891.127100
4.44-4.7980.0755610.9960.9990.0280.081.061100
4.79-5.278.70.0715560.9970.9990.0250.0750.96699.8
5.27-6.038.50.0735610.9960.9990.0260.0770.936100
6.03-7.597.60.0655820.9960.9990.0250.070.902100
7.59-507.50.0576200.9960.9990.0220.0611.11899.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.96 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 573 5.28 %
Rwork0.2065 --
obs0.2092 10852 99.34 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 0 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042499
X-RAY DIFFRACTIONf_angle_d0.6213384
X-RAY DIFFRACTIONf_dihedral_angle_d4.472338
X-RAY DIFFRACTIONf_chiral_restr0.047383
X-RAY DIFFRACTIONf_plane_restr0.006439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.33551370.26692504X-RAY DIFFRACTION98
3.08-3.530.27941280.23692559X-RAY DIFFRACTION100
3.53-4.440.23411450.18442579X-RAY DIFFRACTION100
4.44-32.960.23361630.18842637X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1299-0.6250.32254.31830.41113.0179-0.1335-0.06230.1549-0.07240.12670.1017-0.2301-0.1102-0.00970.081-0.0233-0.0140.2137-0.03920.1125-13.2715-32.909710.9067
24.68851.2795-0.49314.5720.25533.50650.15350.23160.5363-0.17170.06560.1605-0.5886-0.0378-0.1320.24120.00110.06890.1765-0.03730.269710.076-25.28342.5385
32.73131.5466-1.1851.9530.14083.97940.19980.50880.902-0.1624-0.19510.3235-0.7362-0.45910.04360.3425-0.00260.05040.33890.08510.44938.8592-21.93471.2445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 153)
2X-RAY DIFFRACTION2(chain 'B' and resid 60 through 133)
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 100)

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