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- PDB-9caf: Cryo-EM structure of the reconstituted TRRAP lobe of the human TI... -

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Basic information

Entry
Database: PDB / ID: 9caf
TitleCryo-EM structure of the reconstituted TRRAP lobe of the human TIP60 complex (composite structure)
Components
  • E1A-binding protein p400,Haloalkane dehalogenase chimera
  • Isoform 2 of Transformation/transcription domain-associated protein
KeywordsGENE REGULATION / histone acetyltransferase / chromatin regulator / transcription regulation
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex ...haloalkane dehalogenase / haloalkane dehalogenase activity / transcription factor TFTC complex / Swr1 complex / protein antigen binding / regulation of double-strand break repair / SAGA complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA repair-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / regulation of RNA splicing / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / helicase activity / DNA Damage/Telomere Stress Induced Senescence / response to toxic substance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosome / HATs acetylate histones / chromatin organization / regulation of apoptotic process / regulation of cell cycle / hydrolase activity / Ub-specific processing proteases / nuclear speck / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Haloalkane dehalogenase, subfamily 2 / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain ...E1A-binding protein p400, N-terminal / E1A-binding protein p400, N-terminal / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Haloalkane dehalogenase, subfamily 2 / Myb-like domain profile. / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / : / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Epoxide hydrolase-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / alpha/beta hydrolase fold / SANT/Myb domain / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Alpha/beta hydrolase fold-1 / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / Alpha/Beta hydrolase fold / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Haloalkane dehalogenase / E1A-binding protein p400 / Transformation/transcription domain-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLouder, R.K. / Park, G. / Patel, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60
Authors: Park, G. / Patel, A.B. / Wu, C. / Louder, R.K.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E1A-binding protein p400,Haloalkane dehalogenase chimera
D: Isoform 2 of Transformation/transcription domain-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)559,6753
Polymers559,0152
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein E1A-binding protein p400,Haloalkane dehalogenase chimera


Mass: 125783.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP400, CAGH32, KIAA1498, KIAA1818, TNRC12, dhaA / Plasmid: pHOE / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: Q96L91, UniProt: P0A3G4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, haloalkane dehalogenase
#2: Protein Isoform 2 of Transformation/transcription domain-associated protein / 350/400 kDa PCAF-associated factor / PAF350/400 / STAF40 / Tra1 homolog


Mass: 433231.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRRAP, PAF400 / Plasmid: pHOE / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y4A5
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
Has ligand of interestN
Has protein modificationN

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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: Reconstituted TRRAP lobe of the TIP60 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.56 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: expi293 / Plasmid: pHOE
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
5CTFFINDCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141352 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 38.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003630558
ELECTRON MICROSCOPYf_angle_d0.593341397
ELECTRON MICROSCOPYf_chiral_restr0.0784741
ELECTRON MICROSCOPYf_plane_restr0.00655238
ELECTRON MICROSCOPYf_dihedral_angle_d13.903711525

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