+Open data
-Basic information
Entry | Database: PDB / ID: 5y81 | ||||||||||||
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Title | NuA4 TEEAA sub-complex | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / NuA4 complex / Histone acetyltransferases / Tra1/TRRAP / PIKK family | ||||||||||||
Function / homology | Function and homology information RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / mitotic actomyosin contractile ring contraction / vacuole inheritance / actin cortical patch / SLIK (SAGA-like) complex / Swr1 complex / kinetochore assembly ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / mitotic actomyosin contractile ring contraction / vacuole inheritance / actin cortical patch / SLIK (SAGA-like) complex / Swr1 complex / kinetochore assembly / Ino80 complex / SWI/SNF complex / SAGA complex / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / protein secretion / Ub-specific processing proteases / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / chromatin organization / histone binding / protein-containing complex assembly / chromatin remodeling / DNA repair / chromatin binding / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 4.7 Å | ||||||||||||
Authors | Wang, X. / Cai, G. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex. Authors: Xuejuan Wang / Salar Ahmad / Zhihui Zhang / Jacques Côté / Gang Cai / Abstract: The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and ...The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and regulatory mechanism. Here, we report the 4.7 Å cryo-electron microscopy (cryo-EM) structure of a NuA4/TIP60 TEEAA assembly (Tra1, Eaf1, Eaf5, actin and Arp4) and the 7.6 Å cryo-EM structure of a TEEAA-piccolo assembly (Esa1, Epl1, Yng2 and Eaf6). The Tra1 and Eaf1 constitute the assembly scaffold. The Eaf1 SANT domain tightly binds to the LBE and FATC domains of Tra1 by ionic interactions. The actin/Arp4 peripherally associates with Eaf1 HSA domain. The Eaf5/7/3 (TINTIN) and piccolo modules largely pack against the FAT and HEAT repeats of Tra1 and their association depends on Eaf1 N-terminal and HSA regions, respectively. These structures elucidate the detailed architecture and molecular interactions between NuA4 subunits and offer exciting insights into the scaffolding and regulatory mechanisms of Tra1 pseudokinase. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5y81.cif.gz | 864.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y81.ent.gz | 639.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y81_validation.pdf.gz | 945.8 KB | Display | wwPDB validaton report |
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Full document | 5y81_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5y81_validation.xml.gz | 112.9 KB | Display | |
Data in CIF | 5y81_validation.cif.gz | 178.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/5y81 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/5y81 | HTTPS FTP |
-Related structure data
Related structure data | 6816MC 6815C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Transcription-associated protein ... , 2 types, 2 molecules BA
#1: Protein | Mass: 130470.539 Da / Num. of mol.: 1 / Fragment: UNP residues 2630-3744 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38811 |
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#5: Protein | Mass: 303020.531 Da / Num. of mol.: 1 / Fragment: UNP residues 1-2627 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38811 |
-Chromatin modification-related protein ... , 3 types, 3 molecules CHE
#2: Protein | Mass: 39431.434 Da / Num. of mol.: 1 / Fragment: UNP residues 647-982 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06337 |
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#4: Protein | Mass: 31689.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P39995 |
#8: Protein/peptide | Mass: 4882.613 Da / Num. of mol.: 1 / Fragment: UNP residues 357-397 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06337 |
-Protein , 3 types, 3 molecules DFG
#3: Protein | Mass: 42570.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#6: Protein | Mass: 54991.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P80428 |
#7: Protein | Mass: 41735.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P60010 |
-Details
Sequence details | The authors know the sequence of the chain D but do not know how the coordinates align with the ...The authors know the sequence of the chain D but do not know how the coordinates align with the sequence. Therefore there are currently UNK (unknown residues) in this chain and the residue numbers in the coordinates are meaningless. The authors provide the sequence of the chain D as follows: MSSRPSSAVP |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NuA4 TEEAA sub-complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NONE / Material: Uranyl Formate |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2247: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63197 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 4.7 Å | ||||||||||||||||||||||||
Refine LS restraints |
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