9C57

Reconstituted P400 Subcomplex of the human TIP60 complex

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-06-05 Released: 2024-08-21 
  • Deposition Author(s): Yang, Z., Mameri, A., Florez Ariza, A.J., Cote, J., Nogales, E.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), Canada Research Chairs, Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex.

Yang, Z.Mameri, A.Cattoglio, C.Lachance, C.Florez Ariza, A.J.Luo, J.Humbert, J.Sudarshan, D.Banerjea, A.Galloy, M.Fradet-Turcotte, A.Lambert, J.P.Ranish, J.A.Cote, J.Nogales, E.

(2024) Science 385: eadl5816-eadl5816

  • DOI: https://doi.org/10.1126/science.adl5816
  • Primary Citation of Related Structures:  
    9C47, 9C4B, 9C57, 9C62, 9C6N

  • PubMed Abstract: 

    The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the EP400 subunit serves as a scaffold holding the different functional modules in specific positions, creating a unique arrangement of the ARP module. EP400 interacts with the TRRAP subunit using a footprint that overlaps with that of the SAGA acetyltransferase complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.


  • Organizational Affiliation

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1A [auth E],
E [auth C],
M [auth A]
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1INO80HNMP238TIP49TIP49A
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens)
Explore Q9Y265 
Go to UniProtKB:  Q9Y265
PHAROS:  Q9Y265
GTEx:  ENSG00000175792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y265
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Enhancer of polycomb homolog 1B [auth H]836Homo sapiensMutation(s): 0 
Gene Names: EPC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2F5 (Homo sapiens)
Explore Q9H2F5 
Go to UniProtKB:  Q9H2F5
PHAROS:  Q9H2F5
GTEx:  ENSG00000120616 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2F5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6AC [auth M],
L
429Homo sapiensMutation(s): 0 
Gene Names: ACTL6ABAF53BAF53AINO80K
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens)
Explore O96019 
Go to UniProtKB:  O96019
PHAROS:  O96019
GTEx:  ENSG00000136518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96019
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2D [auth B],
F [auth D],
G [auth F]
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2INO80JTIP48TIP49BCGI-46
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens)
Explore Q9Y230 
Go to UniProtKB:  Q9Y230
PHAROS:  Q9Y230
GTEx:  ENSG00000183207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y230
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
E1A-binding protein p400H [auth G]3,159Homo sapiensMutation(s): 0 
Gene Names: EP400CAGH32KIAA1498KIAA1818TNRC12
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L91 (Homo sapiens)
Explore Q96L91 
Go to UniProtKB:  Q96L91
PHAROS:  Q96L91
GTEx:  ENSG00000183495 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96L91
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA methyltransferase 1-associated protein 1467Homo sapiensMutation(s): 0 
Gene Names: DMAP1KIAA1425
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF5 (Homo sapiens)
Explore Q9NPF5 
Go to UniProtKB:  Q9NPF5
PHAROS:  Q9NPF5
GTEx:  ENSG00000178028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPF5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Homo sapiensMutation(s): 0 
Gene Names: ACTB
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72 homolog364Homo sapiensMutation(s): 0 
Gene Names: VPS72TCFL1YL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15906 (Homo sapiens)
Explore Q15906 
Go to UniProtKB:  Q15906
PHAROS:  Q15906
GTEx:  ENSG00000163159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15906
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
N [auth E]
O [auth B]
P [auth C]
Q [auth D]
R [auth F]
N [auth E],
O [auth B],
P [auth C],
Q [auth D],
R [auth F],
S [auth G],
U [auth A]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
T [auth L]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
Canada Research ChairsCanada--
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--
Canadian Institutes of Health Research (CIHR)Canada--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-11
    Changes: Data collection