9CAF | pdb_00009caf

Cryo-EM structure of the reconstituted TRRAP lobe of the human TIP60 complex (composite structure)

• PDB DOI: https://doi.org/10.2210/pdb9CAF/pdb
• EM Map EMD-45389: EMDB EMDataResource

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 559.68 kDa 
• Atom Count: 29,921 
• Modeled Residue Count: 3,724 
• Deposited Residue Count: 4,933 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1A-binding protein p400,Haloalkane dehalogenase chimera	A	1,122	Homo sapiens	Mutation(s): 0  Gene Names: EP400, CAGH32, KIAA1498, KIAA1818, TNRC12, dhaA EC: 3.6.4 (PDB Primary Data), 3.8.1.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P0A3G4 (Pseudomonas pavonaceae) Explore P0A3G4  Go to UniProtKB:  P0A3G4
Find proteins for Q96L91 (Homo sapiens) Explore Q96L91  Go to UniProtKB:  Q96L91
PHAROS:  Q96L91 GTEx:  ENSG00000183495
UniProt Groups	Q96L91P0A3G4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Transformation/transcription domain-associated protein	B [auth D]	3,811	Homo sapiens	Mutation(s): 0  Gene Names: TRRAP, PAF400
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4A5 (Homo sapiens) Explore Q9Y4A5  Go to UniProtKB:  Q9Y4A5
PHAROS:  Q9Y4A5 GTEx:  ENSG00000196367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	C [auth D]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Louder, R.K., Park, G., Patel, A.B.

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

Revision History  

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