9B2D | pdb_00009b2d

Yeast Rad51-ssDNA filament

PDB DOI: https://doi.org/10.2210/pdb9B2D/pdb
EM Map EMD-44104: EMDB EMDataResource
NAKB: 9B2D

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2024-03-14 Released: 2025-01-29
Deposition Author(s): Liu, J., Gore, S., Heyer, W.-D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Yeast Rad51-ssDNA filament

Liu, J., Gore, S., Heyer, W.-D.

To be published.

Macromolecule Content

Total Structure Weight: 268.51 kDa
Atom Count: 14,766
Modeled Residue Count: 1,878
Deposited Residue Count: 2,424
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51	A [auth C] B [auth D] C [auth E] D [auth F] E [auth A] A [auth C], B [auth D], C [auth E], D [auth F], E [auth A], F [auth B]	400	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RAD51, YER095W
UniProt
Find proteins for P25454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25454 Go to UniProtKB: P25454
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25454
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	G [auth K]	24	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain T [auth A] SDF format, chain Q [auth F] SDF format, chain N [auth E] SDF format, chain K [auth D] SDF format, chain H [auth C] MOL2 format, chain W [auth B] MOL2 format, chain T [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth E] MOL2 format, chain K [auth D] MOL2 format, chain H [auth C] mmCIF format, chain W [auth B] mmCIF format, chain T [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth E] mmCIF format, chain K [auth D] mmCIF format, chain H [auth C]	H [auth C] K [auth D] N [auth E] Q [auth F] T [auth A] H [auth C], K [auth D], N [auth E], Q [auth F], T [auth A], W [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth C] Focus chain K [auth D] Focus chain N [auth E] Focus chain Q [auth F] Focus chain T [auth A] Focus chain W [auth B] Interactions & Density Focus chain H [auth C] Focus chain K [auth D] Focus chain N [auth E] Focus chain Q [auth F] Focus chain T [auth A] Focus chain W [auth B]
AF3 (Subject of Investigation/LOI) Query on AF3 Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain U [auth A] SDF format, chain R [auth F] SDF format, chain O [auth E] SDF format, chain L [auth D] SDF format, chain I [auth C] MOL2 format, chain X [auth B] MOL2 format, chain U [auth A] MOL2 format, chain R [auth F] MOL2 format, chain O [auth E] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] mmCIF format, chain X [auth B] mmCIF format, chain U [auth A] mmCIF format, chain R [auth F] mmCIF format, chain O [auth E] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C]	I [auth C] L [auth D] O [auth E] R [auth F] U [auth A] I [auth C], L [auth D], O [auth E], R [auth F], U [auth A], X [auth B]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain I [auth C] Focus chain L [auth D] Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth A] Focus chain X [auth B] Interactions & Density Focus chain I [auth C] Focus chain L [auth D] Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth A] Focus chain X [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain V [auth A] SDF format, chain S [auth F] SDF format, chain P [auth E] SDF format, chain M [auth D] SDF format, chain J [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth A] MOL2 format, chain S [auth F] MOL2 format, chain P [auth E] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth A] mmCIF format, chain S [auth F] mmCIF format, chain P [auth E] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C]	J [auth C] M [auth D] P [auth E] S [auth F] V [auth A] J [auth C], M [auth D], P [auth E], S [auth F], V [auth A], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain S [auth F] Focus chain V [auth A] Focus chain Y [auth B] Interactions & Density Focus chain J [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain S [auth F] Focus chain V [auth A] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Liu, J.

Gore, S.

Heyer, W.-D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM58015
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137751
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA093373
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM129541