9R04 | pdb_00009r04

p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample)

• PDB DOI: https://doi.org/10.2210/pdb9R04/pdb
• EM Map EMD-53478: EMDB EMDataResource
• NAKB: 9R04

• Classification: GENE REGULATION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-04-24 Released: 2025-07-02 
• Deposition Author(s): Chakraborty, D., Michael, A.K., Kempf, G., Cavadini, S., Kater, L., Thoma, N.H.
• Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample)

Chakraborty, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A7B4C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B2C2D2E2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 392.3 kDa 
• Atom Count: 15,855 
• Modeled Residue Count: 1,836 
• Deposited Residue Count: 2,986 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	139	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	128	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899 GTEx:  ENSG00000124635

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	K, L, M, N	417	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA-for	I	153	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA-rev	J	153	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Chakraborty, D., Michael, A.K., Kempf, G., Cavadini, S., Kater, L., Thoma, N.H.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--
Swiss National Science Foundation	Switzerland	--
Other private		--
Other private		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release