9CAC | pdb_00009cac

Cryo-EM structure of the RuvBL lobe of the native human TIP60 complex (composite structure)

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

  • Deposited: 2024-06-17 Released: 2025-06-18 
  • Deposition Author(s): Louder, R.K., Park, G., Patel, A.B.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60

Park, G.Patel, A.B.Wu, C.Louder, R.K.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E1A-binding protein p4003,159Homo sapiensMutation(s): 0 
EC: 3.6.4
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Find proteins for Q96L91 (Homo sapiens)
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PHAROS:  Q96L91
GTEx:  ENSG00000183495 
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UniProt GroupQ96L91
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 72 homolog364Homo sapiensMutation(s): 0 
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Find proteins for Q15906 (Homo sapiens)
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PHAROS:  Q15906
GTEx:  ENSG00000163159 
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UniProt GroupQ15906
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Enhancer of polycomb homolog 1836Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1D [auth E],
F [auth G],
H [auth I]
456Homo sapiensMutation(s): 0 
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2E [auth F],
G [auth H],
I [auth J]
463Homo sapiensMutation(s): 0 
EC: 3.6.4.12
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Find proteins for Q9Y230 (Homo sapiens)
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GTEx:  ENSG00000183207 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1J [auth K],
K [auth L]
375Homo sapiensMutation(s): 0 
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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6AL [auth M]429Homo sapiensMutation(s): 0 
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Find proteins for O96019 (Homo sapiens)
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PHAROS:  O96019
GTEx:  ENSG00000136518 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA methyltransferase 1-associated protein 1M [auth N]467Homo sapiensMutation(s): 0 
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Find proteins for Q9NPF5 (Homo sapiens)
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PHAROS:  Q9NPF5
GTEx:  ENSG00000178028 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BA [auth M]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
N [auth E]
P [auth F]
R [auth G]
T [auth H]
V [auth I]
N [auth E],
P [auth F],
R [auth G],
T [auth H],
V [auth I],
X [auth J],
Z [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth L]
CA [auth M]
O [auth E]
Q [auth F]
S [auth G]
AA [auth L],
CA [auth M],
O [auth E],
Q [auth F],
S [auth G],
U [auth H],
W [auth I],
Y [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release