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- PDB-5y81: NuA4 TEEAA sub-complex -

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Basic information

Entry
Database: PDB / ID: 5y81
TitleNuA4 TEEAA sub-complex
Components
  • (Chromatin modification-related protein ...) x 3
  • (Transcription-associated protein ...) x 2
  • Actin
  • Actin-related protein 4
  • Eaf1-disorder domain
KeywordsTRANSCRIPTION / 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 / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / SLIK (SAGA-like) complex / kinetochore assembly ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / SLIK (SAGA-like) complex / kinetochore assembly / Ino80 complex / SAGA complex / SWI/SNF 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 / hydrolase activity / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Chromatin modification-related protein EAF5 / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain ...Chromatin modification-related protein EAF5 / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Homeobox-like domain superfamily / ATPase, nucleotide binding domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transcription-associated protein 1 / Chromatin modification-related protein EAF5 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 4.7 Å
AuthorsWang, X. / Cai, G.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program2014CB910700 China
the National Natural Science Foundation of China31570726 China
the National Natural Science Foundation of China31170694 China
CitationJournal: 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
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
B: Transcription-associated protein 1
C: Chromatin modification-related protein EAF1
D: Eaf1-disorder domain
H: Chromatin modification-related protein EAF5
A: Transcription-associated protein 1
F: Actin-related protein 4
G: Actin
E: Chromatin modification-related protein EAF1


Theoretical massNumber of molelcules
Total (without water)648,7928
Polymers648,7928
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription-associated protein ... , 2 types, 2 molecules BA

#1: Protein Transcription-associated protein 1 / p400 kDa component of SAGA


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
#5: Protein Transcription-associated protein 1 / p400 kDa component of SAGA


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

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Chromatin modification-related protein ... , 3 types, 3 molecules CHE

#2: Protein Chromatin modification-related protein EAF1 / ESA1-associated factor 1 / Vacuolar import and degradation protein 21


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
#4: Protein Chromatin modification-related protein EAF5 / ESA1-associated factor 5


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 Chromatin modification-related protein EAF1 / ESA1-associated factor 1 / Vacuolar import and degradation protein 21


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

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Protein , 3 types, 3 molecules DFG

#3: Protein Eaf1-disorder domain


Mass: 42570.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#6: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


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 Actin


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

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Details

Sequence detailsThe 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: MSSRPSSAVPNSASLSEDQSSDRSKFPKADDLIDERDRKLTELYCVSRLNQLLELTDENK LRKEIDAFLKKNDIRRGIRFDEASLPKLLHTAATPITKKKLKDVNLINVPNQRLSDSKMS RELPENSENVSVKSESHFVPSHDNSIRENMMDSLRPAEKTGGMWNKRPLESTMGGEEERH EKRQKMQSQSLESSNNSEMASLPISPRPPVPNALAHYTYYENIEYPPADPTEVQPAVKFK DPLIKNIMAKEIDTSDHYNENNVDALETVFLLMNDYIPSKIPQALPLAELKYMSQTLPLI NLIPRAHKALTTNIINNALNEARITVVGSRIEELRRLGLWSLRQPKRFIDPWKQHNTHQN ILLEEAKWMQADFKEGHKYKVAICTAMAQAIKDYWTYGEICCVKRKTLLPGKENKLSDDG RISEKSGRPSDTSRNDSDISIAGKDDIGIIANVDDITEKESAAANDNDENGKNEAGAKSD FDFADGLLSQEGAHDQIISSIDTKLLLKKPSSSSEVVLIQHEVAASSALIETEESKKELA PPFKLSIFVDELNTFEKTLIQDLPLYNGINEERPKKDDSLPFIPISKSVVSLDDNGFYKL LERQLIDEEPSISQLSKRRGMFYGNRRNHYLRPPAVPSLRYLQNRTPTIWLSEDDQELVK NINTYGYNWELISAHMTHRLTYSYLSNIERRTPWQCFERFVQLNERFNFSDLKGPRAHSA QQWLIEAHKFQQRQNRRISPLGVNTESIQRGHRRLRWASMFEAIRKCMKKRENTPRPNPT QPRKPLDCKNMKVPTPAEMSLLKAQRDEALRRDIQLRRTVKNRLQQRQQQSQQAHSSRAQ SPIPSNGKSSSNLARNGQASAPRPNQKQYTEQDIIESYSRKLLEQKPDIGPEMALKAAKN YYRTLREQQQQLKQHQIQQQRQQLQEESSHVQQLQQLQPGSQAPPPKSSPSQSSLSNISN INSAPRIKSPTPQEILQRFQKQ

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NuA4 TEEAA sub-complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NONE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2247: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63197 / Symmetry type: POINT
RefinementHighest resolution: 4.7 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00726223
ELECTRON MICROSCOPYf_angle_d0.94836003
ELECTRON MICROSCOPYf_dihedral_angle_d8.45119092
ELECTRON MICROSCOPYf_chiral_restr0.0414746
ELECTRON MICROSCOPYf_plane_restr0.0064853

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