1PZN | pdb_00001pzn

Rad51 (RadA)

PDB DOI: https://doi.org/10.2210/pdb1PZN/pdb

Classification: RECOMBINATION
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-07-12 Released: 2003-09-09
Deposition Author(s): Shin, D.S., Tainer, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.307 (Depositor), 0.308 (DCC)
R-Value Work:
0.257 (Depositor), 0.263 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Full-length archaeal Rad51 structure and mutants: Mechanisms for RAD51 assembly and control by BRCA2

Shin, D.S., Pellegrini, L., Daniels, D.S., Yelent, B., Craig, L., Bates, D., Yu, D.S., Shivji, M.K., Hitomi, C., Arvai, A.S., Volkmann, N., Tsuruta, H., Blundell, T.L., Venkitaraman, A.R., Tainer, J.A.

(2003) EMBO J 22: 4566-4576

PubMed: 12941707 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/emboj/cdg429
Primary Citation Related Structures:
1PZN

PubMed Abstract:
To clarify RAD51 interactions controlling homologous recombination, we report here the crystal structure of the full-length RAD51 homolog from Pyrococcus furiosus. The structure reveals how RAD51 proteins assemble into inactive heptameric rings and active DNA-bound filaments matching three-dimensional electron microscopy reconstructions. A polymerization motif (RAD51-PM) tethers individual subunits together to form assemblies. Subunit interactions support an allosteric 'switch' promoting ATPase activity and DNA binding roles for the N-terminal domain helix-hairpin-helix (HhH) motif. Structural and mutational results characterize RAD51 interactions with the breast cancer susceptibility protein BRCA2 in higher eukaryotes. A designed P.furiosus RAD51 mutant binds BRC repeats and forms BRCA2-dependent nuclear foci in human cells in response to gamma-irradiation-induced DNA damage, similar to human RAD51. These results show that BRCA2 repeats mimic the RAD51-PM and imply analogous RAD51 interactions with RAD52 and RAD54. Both BRCA2 and RAD54 may act as antagonists and chaperones for RAD51 filament assembly by coupling RAD51 interface exchanges with DNA binding. Together, these structural and mutational results support an interface exchange hypothesis for coordinated protein interactions in homologous recombination.

Organizational Affiliation

Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 273.1 kDa
Atom Count: 13,820
Modeled Residue Count: 1,733
Deposited Residue Count: 2,443
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein rad51	A, B, C, D, E A, B, C, D, E, F, G	349	Pyrococcus furiosus	Mutation(s): 4
UniProt
Find proteins for O74036 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O74036 Go to UniProtKB: O74036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O74036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain JA [auth G] SDF format, chain IA [auth G] SDF format, chain BA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain BA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain BA [auth E]	BA [auth E], IA [auth G], JA [auth G], S [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain BA [auth E] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain S [auth B] Interactions & Density Focus chain BA [auth E] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain S [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain HA [auth G] SDF format, chain H [auth A] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain HA [auth G] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain HA [auth G] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth F]	CA [auth F] H [auth A] HA [auth G] N [auth B] T [auth C] CA [auth F], H [auth A], HA [auth G], N [auth B], T [auth C], X [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth F] Focus chain H [auth A] Focus chain HA [auth G] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain H [auth A] Focus chain HA [auth G] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] EA [auth F] FA [auth F] GA [auth F] M [auth A] AA [auth E], EA [auth F], FA [auth F], GA [auth F], M [auth A], R [auth B], V [auth C], W [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain M [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth F]	DA [auth F] I [auth A] J [auth A] K [auth A] L [auth A] DA [auth F], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], U [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.307 (Depositor), 0.308 (DCC)
R-Value Work: 0.257 (Depositor), 0.263 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.163	α = 90
b = 193.124	β = 90
c = 176.93	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-09-09

Deposition Author(s):

Shin, D.S.

Tainer, J.A.

Revision History (Full details and data files)

Version 1.0: 2003-09-09
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary