8XVG

Structure of human NuA4/TIP60 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the human TIP60 complex.

Chen, K.Wang, L.Yu, Z.Yu, J.Ren, Y.Wang, Q.Xu, Y.

(2024) Nat Commun 15: 7092-7092

  • DOI: https://doi.org/10.1038/s41467-024-51259-z
  • Primary Citation of Related Structures:  
    8XVG, 8XVT, 8XVV

  • PubMed Abstract: 

    Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell cycle control, and embryonic development. Here we report the cryo-electron microscopy structures of the human TIP60 complex with the core subcomplex and TRRAP module refined to 3.2-Å resolution. The structures show that EP400 acts as a backbone integrating the motor module, the ARP module, and the TRRAP module. The RUVBL1-RUVBL2 hexamer serves as a rigid core for the assembly of EP400 ATPase and YL1 in the motor module. In the ARP module, an ACTL6A-ACTB heterodimer and an extra ACTL6A make hydrophobic contacts with EP400 HSA helix, buttressed by network interactions among DMAP1, EPC1, and EP400. The ARP module stably associates with the motor module but is flexibly tethered to the TRRAP module, exhibiting a unique feature of human TIP60. The architecture of the nucleosome-bound human TIP60 reveals an unengaged nucleosome that is located between the core subcomplex and the TRRAP module. Our work illustrates the molecular architecture of human TIP60 and provides architectural insights into how this complex is bound by the nucleosome.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transformation/transcription domain-associated proteinA [auth L]3,830Homo sapiensMutation(s): 0 
Gene Names: TRRAPPAF400
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Find proteins for Q9Y4A5 (Homo sapiens)
Explore Q9Y4A5 
Go to UniProtKB:  Q9Y4A5
PHAROS:  Q9Y4A5
GTEx:  ENSG00000196367 
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UniProt GroupQ9Y4A5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1B [auth A],
D [auth C],
F [auth E]
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1INO80HNMP238TIP49TIP49A
EC: 3.6.4.12
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Find proteins for Q9Y265 (Homo sapiens)
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PHAROS:  Q9Y265
GTEx:  ENSG00000175792 
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UniProt GroupQ9Y265
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2C [auth B],
E [auth D],
G [auth F]
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2INO80JTIP48TIP49BCGI-46
EC: 3.6.4.12
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Find proteins for Q9Y230 (Homo sapiens)
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PHAROS:  Q9Y230
GTEx:  ENSG00000183207 
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UniProt GroupQ9Y230
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA methyltransferase 1-associated protein 1H [auth G]467Homo sapiensMutation(s): 0 
Gene Names: DMAP1KIAA1425
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PHAROS:  Q9NPF5
GTEx:  ENSG00000178028 
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UniProt GroupQ9NPF5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of E1A-binding protein p400I [auth H]3,123Homo sapiensMutation(s): 0 
Gene Names: EP400CAGH32KIAA1498KIAA1818TNRC12
EC: 3.6.4
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PHAROS:  Q96L91
GTEx:  ENSG00000183495 
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UniProt GroupQ96L91
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6AJ [auth I],
K [auth J]
429Homo sapiensMutation(s): 0 
Gene Names: ACTL6A
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GTEx:  ENSG00000136518 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACTB protein (Fragment)L [auth K]375Homo sapiensMutation(s): 0 
Gene Names: Actb
EC: 3.6.4
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Find proteins for P60709 (Homo sapiens)
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PHAROS:  P60709
GTEx:  ENSG00000075624 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Enhancer of polycomb homolog 1813Homo sapiensMutation(s): 0 
Gene Names: EPC1
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Find proteins for Q9H2F5 (Homo sapiens)
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PHAROS:  Q9H2F5
GTEx:  ENSG00000120616 
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UniProt GroupQ9H2F5
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72 homolog364Homo sapiensMutation(s): 0 
Gene Names: VPS72TCFL1YL1
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PHAROS:  Q15906
GTEx:  ENSG00000163159 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
O [auth L]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
P [auth A]
Q [auth B]
R [auth C]
S [auth D]
T [auth E]
P [auth A],
Q [auth B],
R [auth C],
S [auth D],
T [auth E],
U [auth F],
V [auth I],
W [auth J],
X [auth K]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-09-11
    Changes: Data collection