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- PDB-8i3g: Crystal structure of Eaf3-Eaf7 complex -

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Basic information

Entry
Database: PDB / ID: 8i3g
TitleCrystal structure of Eaf3-Eaf7 complex
Components
  • Chromatin modification-related protein EAF3
  • Chromatin modification-related protein EAF7
KeywordsSTRUCTURAL PROTEIN / Complex / MRG domain
Function / homology
Function and homology information


H4/H2A histone acetyltransferase complex / Rpd3S complex / NuA4 histone acetyltransferase complex / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Chromatin modification-related protein Eaf7/MRGBP / Chromatin modification-related protein EAF7 / 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 modification-related protein Eaf7/MRGBP / Chromatin modification-related protein EAF7 / 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
Similarity search - Domain/homology
Chromatin modification-related protein EAF7 / Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

Downloads & links

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Assembly

Deposited unit
A: Chromatin modification-related protein EAF3
B: Chromatin modification-related protein EAF3
C: Chromatin modification-related protein EAF7
D: Chromatin modification-related protein EAF7


Theoretical massNumber of molelcules
Total (without water)51,3374
Polymers51,3374
Non-polymers00
Water1,54986
1
A: Chromatin modification-related protein EAF3
D: Chromatin modification-related protein EAF7


Theoretical massNumber of molelcules
Total (without water)25,6692
Polymers25,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area10680 Å2
MethodPISA
2
B: Chromatin modification-related protein EAF3
C: Chromatin modification-related protein EAF7


Theoretical massNumber of molelcules
Total (without water)25,6692
Polymers25,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-20 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.032, 42.088, 80.789
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromatin modification-related protein EAF3


Mass: 21258.576 Da / Num. of mol.: 2
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/peptide Chromatin modification-related protein EAF7


Mass: 4409.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF7, GI527_G0004968 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BXU7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.025% v/v Dichloromethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→40.24 Å / Num. obs: 18423 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1907 / CC1/2: 0.947 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F5J

2f5j


Resolution: 2.4→36.39 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1839 10.01 %
Rwork0.2081 --
obs0.2128 18365 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 86 3271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053237
X-RAY DIFFRACTIONf_angle_d0.7414396
X-RAY DIFFRACTIONf_dihedral_angle_d4.999433
X-RAY DIFFRACTIONf_chiral_restr0.044524
X-RAY DIFFRACTIONf_plane_restr0.007548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.341420.30421274X-RAY DIFFRACTION99
2.47-2.540.32231360.281218X-RAY DIFFRACTION99
2.54-2.620.29551390.27251254X-RAY DIFFRACTION99
2.62-2.710.30821400.25231254X-RAY DIFFRACTION100
2.71-2.820.31881420.24671267X-RAY DIFFRACTION100
2.82-2.950.28811390.25831256X-RAY DIFFRACTION100
2.95-3.110.29481430.23721273X-RAY DIFFRACTION100
3.11-3.30.2471410.22531270X-RAY DIFFRACTION100
3.3-3.550.25351410.19211274X-RAY DIFFRACTION100
3.55-3.910.25131410.18971275X-RAY DIFFRACTION100
3.91-4.480.20071440.17311292X-RAY DIFFRACTION100
4.48-5.640.24331430.19111288X-RAY DIFFRACTION100
5.64-36.390.24621480.19571331X-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)
11.9374-0.0407-0.50061.4155-0.37071.60230.0130.07820.0780.0147-0.0471-0.08630.0196-0.187-0.00010.3688-0.03340.00980.4027-0.01580.4416-11.3395-10.138617.024
22.43850.0427-0.27180.89720.15941.38530.06060.09550.1966-0.0258-0.08310.1512-0.02640.3016-00.3951-0.0416-0.00480.4712-0.04030.4732-41.2489-18.473519.6549
30.2677-0.07080.06640.05250.1540.4022-0.0339-0.6069-0.14620.194-0.07540.46870.3282-0.28540.0010.4849-0.0246-0.02320.50110.04560.6215-53.6383-20.456722.4847
40.28590.1376-0.0270.306-0.46140.79830.04180.15290.0124-0.22650.0025-0.0602-0.0120.1845-0.00010.45060.00050.0410.39320.01860.5776-2.2391-8.075514.6105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 218 through 401)
2X-RAY DIFFRACTION2(chain 'B' and resid 220 through 401)
3X-RAY DIFFRACTION3(chain 'C' and resid 111 through 142)
4X-RAY DIFFRACTION4(chain 'D' and resid 108 through 142)

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