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- PDB-8i3f: Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal -

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Basic information

Entry
Database: PDB / ID: 8i3f
TitleCrystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
Components
  • Chromatin modification-related protein EAF3
  • Histone H3
  • RCO1 isoform 1
KeywordsSTRUCTURAL PROTEIN / MRG domain / complex / PHD domain
Function / homology
Function and homology information


Rpd3S complex / NuA4 histone acetyltransferase complex / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / metal ion binding
Similarity search - Function
MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily ...MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RCO1 isoform 1 / Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsChen, Z. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Molecular basis for Eaf3-mediated assembly of Rpd3S and NuA4.
Authors: Chen, Z. / Lundy, T. / Zhu, Z. / Hoskins, V.E. / Zhang, J. / Yao, X. / Strahl, B.D. / Xu, C.
History
DepositionJan 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2May 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: Chromatin modification-related protein EAF3
B: RCO1 isoform 1
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4965
Polymers35,3663
Non-polymers1312
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-37 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.513, 75.546, 73.421
Angle α, β, γ (deg.)90.00, 114.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromatin modification-related protein EAF3


Mass: 21127.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4F719
#2: Protein RCO1 isoform 1


Mass: 13532.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RCO1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BXB0
#3: Protein/peptide Histone H3


Mass: 705.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.2 M NDSB-201

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→33.49 Å / Num. obs: 53957 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2480 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→28.237 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 2594 4.98 %
Rwork0.1674 --
obs0.1684 52126 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→28.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 2 295 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122495
X-RAY DIFFRACTIONf_angle_d1.1873388
X-RAY DIFFRACTIONf_dihedral_angle_d4.632098
X-RAY DIFFRACTIONf_chiral_restr0.069383
X-RAY DIFFRACTIONf_plane_restr0.008437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.64950.2381290.20112601X-RAY DIFFRACTION99
1.6495-1.68120.24921170.19022591X-RAY DIFFRACTION100
1.6812-1.71550.21911530.19372567X-RAY DIFFRACTION100
1.7155-1.75280.23851420.1772623X-RAY DIFFRACTION100
1.7528-1.79360.19571320.17422615X-RAY DIFFRACTION100
1.7936-1.83840.24271400.18882557X-RAY DIFFRACTION100
1.8384-1.88810.21651250.18332636X-RAY DIFFRACTION100
1.8881-1.94360.19721250.18382616X-RAY DIFFRACTION100
1.9436-2.00640.18861430.17542579X-RAY DIFFRACTION100
2.0064-2.07810.17921370.17312600X-RAY DIFFRACTION100
2.0781-2.16120.20541340.17132627X-RAY DIFFRACTION100
2.1612-2.25960.19851390.17922569X-RAY DIFFRACTION100
2.2596-2.37860.20821280.17762634X-RAY DIFFRACTION100
2.3786-2.52760.20411290.17882646X-RAY DIFFRACTION100
2.5276-2.72260.22041360.18412583X-RAY DIFFRACTION100
2.7226-2.99630.18141350.18612632X-RAY DIFFRACTION100
2.9963-3.42920.1891420.16822610X-RAY DIFFRACTION100
3.4292-4.31790.16091590.14122625X-RAY DIFFRACTION100
4.3179-28.2370.16981490.15052621X-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)
11.6003-0.2049-0.15492.11530.51111.560.0080.094-0.0382-0.0325-0.0054-0.04730.08760.07050.00240.1533-0.0008-0.02320.17080.01610.14411.568822.712124.5249
20.6290.35470.0851.57890.50421.4473-0.03880.34790.3128-0.36730.1904-0.3437-0.3330.32960.00280.3276-0.04880.05970.36040.04490.3279.846536.533515.7821
30.03840.0193-0.00670.02110.00340.01520.05150.0291-0.00680.05940.18740.0511-0.0518-0.0263-0.00010.8286-0.15950.12020.7361-0.05390.948913.382453.610620.9113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 218 through 400)
2X-RAY DIFFRACTION2(chain 'B' and resid 258 through 375)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 6)

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