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- PDB-2jss: NMR structure of chaperone Chz1 complexed with histone H2A.Z-H2B -

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Basic information

Entry
Database: PDB / ID: 2jss
TitleNMR structure of chaperone Chz1 complexed with histone H2A.Z-H2B
Components
  • Chimera of Histone H2B.1 and Histone H2A.Z
  • Uncharacterized protein YER030W
KeywordsChaperone/Nuclear Protein / Histone-chaperone complex / intrinsically unfolded protein / Chaperone-Structural Protein COMPLEX / Chaperone-Nuclear Protein COMPLEX
Function / homology
Function and homology information


HATs acetylate histones / nuclear-transcribed mRNA catabolic process, non-stop decay / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / postreplication repair ...HATs acetylate histones / nuclear-transcribed mRNA catabolic process, non-stop decay / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / postreplication repair / silent mating-type cassette heterochromatin formation / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / Ub-specific processing proteases / transcription elongation by RNA polymerase II / chromatin DNA binding / euchromatin / structural constituent of chromatin / nucleosome / heterochromatin formation / chromatin organization / histone binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
Histone chaperone domain CHZ / Histone chaperone domain CHZ / Histone chaperone domain CHZ / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B ...Histone chaperone domain CHZ / Histone chaperone domain CHZ / Histone chaperone domain CHZ / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B.1 / Histone H2A.Z-specific chaperone CHZ1 / Histone H2A.Z
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
AuthorsZhou, Z. / Feng, H. / Hansen, D.F. / Kato, H. / Luk, E. / Freedberg, D.I. / Kay, L.E. / Wu, C. / Bai, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B.
Authors: Zhou, Z. / Feng, H. / Hansen, D.F. / Kato, H. / Luk, E. / Freedberg, D.I. / Kay, L.E. / Wu, C. / Bai, Y.
History
DepositionJul 11, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_exptl.solution_id / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera of Histone H2B.1 and Histone H2A.Z
B: Uncharacterized protein YER030W


Theoretical massNumber of molelcules
Total (without water)28,0342
Polymers28,0342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy and no violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Chimera of Histone H2B.1 and Histone H2A.Z / Chimera of suppressor of Ty protein 12 and H2AZ / HTA3


Mass: 21074.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTB1, H2B1, SPT12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codonplus(DE3)-RIL / References: UniProt: P02293, UniProt: Q12692
#2: Protein Uncharacterized protein YER030W


Mass: 6959.446 Da / Num. of mol.: 1 / Fragment: sequence database residues 71-132 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-1H NOESY
1333D CBCA(CO)NH
1443D HN(CA)CB
1553D HNCO
1663D HNCA
1773D HN(CO)CA
1883D H(CCO)NH
1993D (H)CCH-TOCSY
110103D HBHA(CO)NH
111113D HNHA
112123D HNCANNH
113133D TOCSY-HSQC
11413D 1H-15N NOESY
11513D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0~1.2 mM [U-35%2H]/[U-100% 2H] H2A.Z-H2B/Chz1sample_190% H2O/10% D2O/100%D2O
solution21.0~1.2 mM [U-100% 15N;U-100%2H]/[U-30%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_290% H2O/10% D2O/100%D2O
solution31.0~1.2 mM [U-100% 13C;U-30%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_390% H2O/10% D2O/100%D2O
solution41.0~1.2 mM [U-13C; U-15N; U-2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_490% H2O/10% D2O/100%D2O
solution51.0~1.2 mM [U-100% 15N;U-30%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_590% H2O/10% D2O/100%D2O
solution61.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_690% H2O/10% D2O/100%D2O
solution71.0~1.2 mM [U-100% 15N;U-100%2H]/[U-30%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_790% H2O/10% D2O/100%D2O
solution81.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTAsample_890% H2O/10% D2O/100%D2O
solution91.0~1.2 mM [U-100% 15N;U-30%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTAsample_990% H2O/10% D2O/100%D2O
solution101.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTAsample_1090% H2O/10% D2O/100%D2O
solution111.0~1.2 mM [U-100%15N;U-100% 2H] Chz1/H2a.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTAsample_1190% H2O/10% D2O/100%D2O
solution121.0~1.2 mM [U-100% 13C; U-100% 15N;U-100%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTAsample_1290% H2O/10% D2O/100%D2O
solution131.0~1.2 mM [U-10% 13C; U-100% 15N]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTAsample_1390% H2O/10% D2O/100%D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMH2A.Z-H2B/Chz1[U-35%2H]/[U-100% 2H]1
1.0 mMH2A.Z-H2B/Chz1[U-100% 15N;U-100%2H]/[U-30%2H]2
1.0 mMH2A.Z-H2B/Chz1[U-100% 13C;U-30%2H]/[U-100% 2H]3
1.0 mMH2A.Z-H2B/Chz1[U-13C; U-15N; U-2H]/[U-100% 2H]4
1.0 mMH2A.Z-H2B/Chz1[U-100% 15N;U-30%2H]/[U-100% 2H]5
1.0 mMH2A.Z-H2B/Chz1[U-100% 13C;U-35%2H]/[U-100% 2H]6
1.0 mMH2A.Z-H2B/Chz1[U-100% 15N;U-100%2H]/[U-30%2H]7
1.0 mMChz1/H2A.Z-H2B[U-100% 13C;U-35%2H]/[U-100% 2H]8
1.0 mMChz1/H2A.Z-H2B[U-100% 15N;U-30%2H]/[U-100% 2H]9
1.0 mMChz1/H2A.Z-H2B[U-100% 13C;U-35%2H]/[U-100% 2H]10
1.0 mMChz1/H2a.Z-H2B[U-100%15N;U-100% 2H]11
1.0 mMH2A.Z-H2B/Chz1[U-100% 13C; U-100% 15N;U-100%2H]12
1.0 mMChz1/H2A.Z-H2B[U-10% 13C; U-100% 15N]/[U-100% 2H]13
25 mMMESnatural abundance1
200 mMKClnatural abundance1
1 mMEDTAnatural abundance1
25 mMMESnatural abundance2
200 mMKClnatural abundance2
1 mMEDTAnatural abundance2
25 mMMESnatural abundance3
200 mMKClnatural abundance3
1 mMEDTAnatural abundance3
25 mMMESnatural abundance4
200 mMKClnatural abundance4
1 mMEDTAnatural abundance4
25 mMMESnatural abundance5
200 mMKClnatural abundance5
1 mMEDTAnatural abundance5
25 mMMESnatural abundance6
200 mMKClnatural abundance6
1 mMEDTAnatural abundance6
25 mMMESnatural abundance7
200 mMKClnatural abundance7
1 mMEDTAnatural abundance7
25 mMMESnatural abundance8
200 mMKClnatural abundance8
1 mMEDTAnatural abundance8
25 mMMESnatural abundance9
200 mMKClnatural abundance9
1 mMEDTAnatural abundance9
25 mMMESnatural abundance10
200 mMKClnatural abundance10
1 mMEDTAnatural abundance10
25 mMMESnatural abundance11
200 mMKClnatural abundance11
1 mMEDTAnatural abundance11
25 mMMESnatural abundance12
200 mMKClnatural abundance12
1 mMEDTAnatural abundance12
25 mMMESnatural abundance13
200 mMKClnatural abundance13
1 mMEDTAnatural abundance13
Sample conditionsIonic strength: 200 mM KCl / pH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnson, One Moon Scientificnmr data process and analysis
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificpeak picking
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipe2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipe2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipe2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPP4.3.3Garrettchemical shift assignment
PIPP4.3.3Garrettpeak picking
TALOS2004Cornilescu, Delaglio and Baxdata analysis
ProcheckNMR3.5.4Laskowski and MacArthurstructure analysis
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 5
NMR constraintsNOE constraints total: 4180 / NOE intraresidue total count: 765 / NOE long range total count: 1008 / NOE medium range total count: 1173 / NOE sequential total count: 1234 / Hydrogen bond constraints total count: 198 / Protein chi angle constraints total count: 110 / Protein other angle constraints total count: 110 / Protein phi angle constraints total count: 120 / Protein psi angle constraints total count: 120
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy and no violations
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0.046 Å / Distance rms dev error: 0.005 Å

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