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- PDB-5zbb: Crystal structure of Rtt109-Asf1-H3-H4 complex -

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Basic information

Entry
Database: PDB / ID: 5zbb
TitleCrystal structure of Rtt109-Asf1-H3-H4 complex
Components
  • DNA damage response protein Rtt109, putative
  • Histone H3
  • Histone H4
  • Histone chaperone asf1
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / Histone / acetylation / chaperone / DNA replication / nucleosome assembly / DNA damage / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / 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 ...H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / 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 / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / nucleosome disassembly / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / cellular response to stress / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / subtelomeric heterochromatin formation / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / CENP-A containing nucleosome / histone acetyltransferase / aerobic respiration / positive regulation of transcription elongation by RNA polymerase II / protein modification process / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / DNA damage response / regulation of DNA-templated transcription / chromatin / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein ...Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone, subunit A / Histone, subunit A / 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 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / Histone H4 / Histone H3 / histone acetyltransferase / Histone chaperone asf1
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsZhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M.
Funding support China, United States, 7items
OrganizationGrant numberCountry
NSFC31210103914 China
NSFC31521002 China
NSFC31430018 China
Ministry of Science and Technology of China2015CB856200 China
Chinese Academy of SciencesXDB08010100 China
Beijing Municipal Science and Technology ProjectZ171100000417001 China
NIHGM118015 United States
CitationJournal: Cell / Year: 2018
Title: Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.
Authors: Zhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M.
History
DepositionFeb 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage response protein Rtt109, putative
B: Histone chaperone asf1
C: Histone H3
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68629
Polymers107,5694
Non-polymers3,11725
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16140 Å2
ΔGint-56 kcal/mol
Surface area29620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.251, 112.251, 333.057
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-204-

IOD

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein DNA damage response protein Rtt109, putative


Mass: 59684.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G09540 / Plasmid: pET28a-smt3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4WUS9
#2: Protein Histone chaperone asf1 / Anti-silencing function protein 1


Mass: 21097.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: asf1, AFUA_3G11030 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4WXX5
#3: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Plasmid: pETDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61830
#4: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Plasmid: pETDuet / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02309

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Non-polymers , 3 types, 25 molecules

#5: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 15314 / % possible obs: 99.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 58.44 Å2 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.058 / Rrim(I) all: 0.256 / Χ2: 0.922 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.7319.10.83114750.9380.1950.8531.22999.9
3.73-3.8819.20.6614910.960.1530.6780.84100
3.88-4.0518.80.53814850.9680.1280.5531.232100
4.05-4.2719.30.34714780.9860.0810.3570.83100
4.27-4.5419.10.25715020.9920.060.2640.88100
4.54-4.89190.2115260.9930.0490.2160.847100
4.89-5.3819.10.2215150.9940.0510.2260.857100
5.38-6.15190.24115330.990.0560.2480.897100
6.15-7.7518.80.16115810.9960.0380.1650.937100
7.75-5018.10.05517280.9990.0130.0570.70599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZB9, 2HUE

5zb9

2hue


Resolution: 3.6→42.921 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.21
RfactorNum. reflection% reflection
Rfree0.2643 785 5.18 %
Rwork0.2154 --
obs0.2179 15148 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.1 Å2 / Biso mean: 56.639 Å2 / Biso min: 18.62 Å2
Refinement stepCycle: final / Resolution: 3.6→42.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 36 0 5501
Biso mean--56.83 --
Num. residues----689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035603
X-RAY DIFFRACTIONf_angle_d0.6127599
X-RAY DIFFRACTIONf_chiral_restr0.023859
X-RAY DIFFRACTIONf_plane_restr0.003976
X-RAY DIFFRACTIONf_dihedral_angle_d11.1732076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6001-3.82560.30931250.293423152440100
3.8256-4.12070.36381520.27752270242298
4.1207-4.5350.22541150.192723642479100
4.535-5.19020.21021460.174323682514100
5.1902-6.53550.25011150.210724392554100
6.5355-42.9240.24881320.191626072739100

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