5H1B | pdb_00005h1b

Human RAD51 presynaptic complex

• PDB DOI: https://doi.org/10.2210/pdb5H1B/pdb
• EM Map EMD-9566: EMDB EMDataResource
• NAKB: 5H1B

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-10-08 Released: 2016-12-21 
• Deposition Author(s): Xu, J., Zhao, L., Xu, Y., Zhao, W., Sung, P., Wang, H.W.
• Funding Organization(s): National Science Foundation of China, The Key Research and Development Program of MOST, The Beijing Municipal Science & Technology Commission, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange

Xu, J., Zhao, L., Xu, Y., Zhao, W., Sung, P., Wang, H.W.

(2017) Nat Struct Mol Biol 24: 40-46

• PubMed: 27941862 
• DOI: https://doi.org/10.1038/nsmb.3336
• Primary Citation Related Structures: 
  5H1B, 5H1C


• PubMed Abstract: 
  

  The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) and generates a helical filament that is able to search for and invade homologous double-stranded DNA (dsDNA), thus leading to strand separation and formation of new base pairs between the initiating ssDNA and the complementary strand within the duplex. Here, we used cryo-EM to solve the structures of human RAD51 in complex with DNA molecules, in presynaptic and postsynaptic states, at near-atomic resolution. Our structures reveal both conserved and distinct structural features of the human RAD51-DNA complexes compared with their prokaryotic counterpart. Notably, we also captured the structure of an arrested synaptic complex. Our results provide new insight into the molecular mechanisms of the DNA homology search and strand-exchange processes.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 115.31 kDa 
• Atom Count: 7,359 
• Modeled Residue Count: 933 
• Deposited Residue Count: 1,026 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	A, B, C	339	Homo sapiens	Mutation(s): 1  Gene Names: RAD51, RAD51A, RECA EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens) Explore Q06609  Go to UniProtKB:  Q06609
PHAROS:  Q06609 GTEx:  ENSG00000051180

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	D	9	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], G [auth B], I [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	F [auth A], H [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER	20.02
RECONSTRUCTION	RELION	1.2
MODEL REFINEMENT	Coot	0.7.2
MODEL REFINEMENT	PHENIX	1.9

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Xu, J., Zhao, L., Xu, Y., Zhao, W., Sung, P., Wang, H.W.

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Funding Organization	Location	Grant Number
National Science Foundation of China	China	31270765
The Key Research and Development Program of MOST	China	2016YFA0501101
The Beijing Municipal Science & Technology Commission	China	Z161100000116034
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA168635
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES007061
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES015252

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Database references
• Version 1.3: 2017-10-18
  Changes: Author supporting evidence, Data processing
• Version 1.4: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.5: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary