8XBW

The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8XBW/pdb
• EM Map EMD-38231: EMDB EMDataResource
• NAKB: 8XBW

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-07 Released: 2024-03-27 
• Deposition Author(s): Shioi, T., Hatazawa, S., Ogasawara, M., Takizawa, Y., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site

Shioi, T., Hatazawa, S., Oya, E., Hosoya, N., Kobayashi, W., Ogasawara, M., Kobayashi, T., Takizawa, Y., Kurumizaka, H.

(2024) Nature 628: 212-220

• DOI: https://doi.org/10.1038/s41586-024-07196-4

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 160.04 kDa 
• Atom Count: 2,671 
• Modelled Residue Count: 278 
• Deposited Residue Count: 896 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A [auth E]	139	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
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 [auth F]	106	Homo sapiens	Mutation(s): 0  Gene Names: H4C1
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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	E [auth L]	342	Homo sapiens	Mutation(s): 0  Gene Names: RAD51, RAD51A, RECA
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens) Explore Q06609  Go to UniProtKB:  Q06609
PHAROS:  Q06609 GTEx:  ENSG00000051180

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*CP*GP*CP*TP*TP*AP*AP*AP*CP*GP*CP*AP*CP*GP*TP*A)-3')	C [auth I]	156	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*CP*GP*TP*GP*CP*GP*TP*TP*TP*AP*AP*GP*CP*GP*GP*T)-3')	D [auth J]	153	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Shioi, T., Hatazawa, S., Ogasawara, M., Takizawa, Y., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K06098
Japan Society for the Promotion of Science (JSPS)	Japan	JP23H05475
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121009
Japan Science and Technology	Japan	JPMJER1901
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K14134

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Database references
• Version 1.2: 2024-04-17
  Changes: Database references
• Version 1.3: 2024-04-24
  Changes: Database references