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- PDB-2iij: Structure of human Asf1a in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 2iij
TitleStructure of human Asf1a in complex with histone H3
Components
  • ASF1A protein
  • Histone H3
KeywordsCHAPERONE / protein-protein complex
Function / homology
Function and homology information


muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...muscle cell differentiation / histone chaperone activity / DNA replication-dependent chromatin assembly / DNA repair-dependent chromatin remodeling / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / replication fork processing / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / osteoblast differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / DNA repair / chromatin binding / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone ASF1A / Histone H3.2 / Histone chaperone ASF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsAgez, M. / Guerois, R. / van Heijenoort, C. / Mann, C. / Ochsenbein, F.
CitationJournal: Structure / Year: 2007
Title: Structure of the histone chaperone asf1 bound to the histone h3 C-terminal helix and functional insights.
Authors: Agez, M. / Chen, J. / Guerois, R. / van Heijenoort, C. / Thuret, J.Y. / Mann, C. / Ochsenbein, F.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASF1A protein
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)19,9312
Polymers19,9312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ASF1A protein


Mass: 17927.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1A / Plasmid: petM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q6IA08, UniProt: Q9Y294*PLUS
#2: Protein/peptide Histone H3 /


Mass: 2003.359 Da / Num. of mol.: 1 / Fragment: residues 122-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: petM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q71DI3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D 12C14N filtered 13Cseparated NOESY
141HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM Asf1 (1-156) U-15N/13C/ 2.5 mM Histone H3 (122-135) Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.4, 90% H2O, 10% D2O90% H2O/10% D2O
22 mM Asf1 (1-156) U-15N/13C/ 2.5 mM Histone H3 (122-135) Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.4, 100% D2O100% D2O
32 mM Asf1 (1-156) U-15N/ 2.5 mM Histone H3 (122-135) Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.4, 90% H2O, 10% D2O90% H2O/10% D2O
42.5 mM Asf1 (1-156) / 2 mM Histone H3 (122-135)U-15N/13C Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.4, 90% H2O, 10% D2O90% H2O/10% D2O
52.5 mM Asf1 (1-156) / 2 mM Histone H3 (122-135)U-15N/13C Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.4, 100% D2O100% D2O
62.5 mM Asf1 (1-156) / 2 mM Histone H3 (122-135)U-15N Tris D11 20 mM, NaN3 0.1%, EDTA 1 mM, DSS 0.1 mM pH 7.490% H2O/10% D2O
Sample conditionspH: 7.4 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5brukercollection
Sparky3.111T. D. Goddard and D. G. Kneller, University of California, San Franciscodata analysis
ARIA2M. Nilges, Institut Pasteur, Francestructure solution
ARIA2M. Nilges, Institut Pasteur, Francerefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: the structures are based on a total of 5185 restraints, 4945 are NOE-derived distance constraints, 170 dihedral angle restraints, 70 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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