9BYR | pdb_00009byr

Filamentous Epstein-Barr virus annealase BALF2 ssDNA-annealing complex

PDB DOI: https://doi.org/10.2210/pdb9BYR/pdb
EM Map EMD-45043: EMDB EMDataResource

Classification: RECOMBINATION/DNA
Organism(s): human gammaherpesvirus 4, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-05-24 Released: 2025-06-11
Deposition Author(s): Nicholls, J., Tolun, G., Brewster, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.75 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural determination of BALF2 annealing intermediate reveals the mechanism through which DNA annealing occurs

Nicholls, J., Brewster, J., Tolun, G.

To be published.

Macromolecule Content

Total Structure Weight: 3,039.41 kDa
Atom Count: 180,785
Modeled Residue Count: 22,880
Deposited Residue Count: 27,336
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major DNA-binding protein	A [auth N] B [auth M] BA [auth F] D [auth L] DA [auth U] A [auth N], B [auth M], BA [auth F], D [auth L], DA [auth U], F [auth O], FA [auth E], H [auth K], HA [auth V], J [auth P], JA [auth D], L [auth J], LA [auth W], N [auth Q], NA [auth C], P [auth I], PA [auth X], R, RA [auth B], SA [auth A], T [auth H], V [auth S], X [auth G], Z [auth T]	1,128	human gammaherpesvirus 4	Mutation(s): 0 Gene Names: DBP, BALF2
UniProt
Find proteins for P03227 (Epstein-Barr virus (strain B95-8)) Explore P03227 Go to UniProtKB: P03227
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03227
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA(5'-D(GPCPAPGPAPAPTPCPGPCPCPC)-3')	AA [auth t] C [auth n] EA [auth u] G [auth o] IA [auth v] AA [auth t], C [auth n], EA [auth u], G [auth o], IA [auth v], K [auth p], MA [auth w], O [auth q], QA [auth x], S [auth r], W [auth s]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA(5'-D(APGPCPTPCPGPAPTPTPTPTPT)-3')	CA [auth f] E [auth l] GA [auth e] I [auth k] KA [auth d] CA [auth f], E [auth l], GA [auth e], I [auth k], KA [auth d], M [auth j], OA [auth c], Q [auth i], TA [auth b], U [auth h], Y [auth g]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth Q] SDF format, chain BB [auth I] SDF format, chain CB [auth R] SDF format, chain DB [auth H] SDF format, chain FB [auth G] SDF format, chain GB [auth T] SDF format, chain HB [auth F] SDF format, chain LB [auth D] SDF format, chain OB [auth X] SDF format, chain VA [auth L] SDF format, chain XA [auth K] SDF format, chain YA [auth P] SDF format, chain ZA [auth J] SDF format, chain EB [auth S] SDF format, chain IB [auth U] SDF format, chain JB [auth E] SDF format, chain KB [auth V] SDF format, chain MB [auth W] SDF format, chain NB [auth C] SDF format, chain PB [auth B] SDF format, chain UA [auth N] SDF format, chain WA [auth O] MOL2 format, chain AB [auth Q] MOL2 format, chain BB [auth I] MOL2 format, chain CB [auth R] MOL2 format, chain DB [auth H] MOL2 format, chain FB [auth G] MOL2 format, chain GB [auth T] MOL2 format, chain HB [auth F] MOL2 format, chain LB [auth D] MOL2 format, chain OB [auth X] MOL2 format, chain VA [auth L] MOL2 format, chain XA [auth K] MOL2 format, chain YA [auth P] MOL2 format, chain ZA [auth J] MOL2 format, chain EB [auth S] MOL2 format, chain IB [auth U] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth V] MOL2 format, chain MB [auth W] MOL2 format, chain NB [auth C] MOL2 format, chain PB [auth B] MOL2 format, chain UA [auth N] MOL2 format, chain WA [auth O] mmCIF format, chain AB [auth Q] mmCIF format, chain BB [auth I] mmCIF format, chain CB [auth R] mmCIF format, chain DB [auth H] mmCIF format, chain FB [auth G] mmCIF format, chain GB [auth T] mmCIF format, chain HB [auth F] mmCIF format, chain LB [auth D] mmCIF format, chain OB [auth X] mmCIF format, chain VA [auth L] mmCIF format, chain XA [auth K] mmCIF format, chain YA [auth P] mmCIF format, chain ZA [auth J] mmCIF format, chain EB [auth S] mmCIF format, chain IB [auth U] mmCIF format, chain JB [auth E] mmCIF format, chain KB [auth V] mmCIF format, chain MB [auth W] mmCIF format, chain NB [auth C] mmCIF format, chain PB [auth B] mmCIF format, chain UA [auth N] mmCIF format, chain WA [auth O]	AB [auth Q] BB [auth I] CB [auth R] DB [auth H] EB [auth S] AB [auth Q], BB [auth I], CB [auth R], DB [auth H], EB [auth S], FB [auth G], GB [auth T], HB [auth F], IB [auth U], JB [auth E], KB [auth V], LB [auth D], MB [auth W], NB [auth C], OB [auth X], PB [auth B], UA [auth N], VA [auth L], WA [auth O], XA [auth K], YA [auth P], ZA [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth Q] Focus chain BB [auth I] Focus chain CB [auth R] Focus chain DB [auth H] Focus chain EB [auth S] Focus chain FB [auth G] Focus chain GB [auth T] Focus chain HB [auth F] Focus chain IB [auth U] Focus chain JB [auth E] Focus chain KB [auth V] Focus chain LB [auth D] Focus chain MB [auth W] Focus chain NB [auth C] Focus chain OB [auth X] Focus chain PB [auth B] Focus chain UA [auth N] Focus chain VA [auth L] Focus chain WA [auth O] Focus chain XA [auth K] Focus chain YA [auth P] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth Q] Focus chain BB [auth I] Focus chain CB [auth R] Focus chain DB [auth H] Focus chain EB [auth S] Focus chain FB [auth G] Focus chain GB [auth T] Focus chain HB [auth F] Focus chain IB [auth U] Focus chain JB [auth E] Focus chain KB [auth V] Focus chain LB [auth D] Focus chain MB [auth W] Focus chain NB [auth C] Focus chain OB [auth X] Focus chain PB [auth B] Focus chain UA [auth N] Focus chain VA [auth L] Focus chain WA [auth O] Focus chain XA [auth K] Focus chain YA [auth P] Focus chain ZA [auth J]