9RWG | pdb_00009rwg

Pentameric AAV2 Rep40 in complex with AAV8

PDB DOI: https://doi.org/10.2210/pdb9RWG/pdb
EM Map EMD-54328: EMDB EMDataResource

Classification: VIRUS
Organism(s): adeno-associated virus 8
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2025-07-09 Released: 2026-02-04
Deposition Author(s): Rouse, S.L., Bubeck, D., Barritt, J.D., Xu, V., Wake, M.
Funding Organization(s): Other government, Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.19 Å
Aggregation State: PARTICLE
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

Dynamic oligomerisation states of replicative helicase 40 coordinate during adeno-associated virus packaging

Xu, V., Barritt, J.D., Bubeck, D., Wake, M., Rouse, S.L.

To be published.

Macromolecule Content

Total Structure Weight: 1,453.61 kDa
Atom Count: 36,961
Modeled Residue Count: 4,581
Deposited Residue Count: 13,055
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A B C [auth E] D [auth F] E [auth G] A, B, C [auth E], D [auth F], E [auth G], F [auth H], G [auth I], H [auth Q], I [auth R], J [auth S], K [auth U], L [auth V], M [auth W], N [auth X], O [auth Y]	738	adeno-associated virus 8	Mutation(s): 0
UniProt
Find proteins for Q8JQF8 (Adeno-associated virus 8) Explore Q8JQF8 Go to UniProtKB: Q8JQF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8JQF8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Rep68	P [auth a], Q [auth b], R [auth c], S [auth d], T [auth e]	397	adeno-associated virus 8	Mutation(s): 0 Gene Names: Rep68 EC: 3.6.4.12
UniProt
Find proteins for P03132 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03132 Go to UniProtKB: P03132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03132
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 CA [auth Q] SDF format, chain EA [auth R] SDF format, chain GA [auth U] SDF format, chain KA [auth W] SDF format, chain OA [auth c] SDF format, chain PA [auth e] SDF format, chain W [auth F] SDF format, chain Y [auth G] SDF format, chain U [auth A] SDF format, chain MA [auth X] SDF format, chain IA [auth V] SDF format, chain AA [auth H] MOL2 format, chain CA [auth Q] MOL2 format, chain EA [auth R] MOL2 format, chain GA [auth U] MOL2 format, chain KA [auth W] MOL2 format, chain OA [auth c] MOL2 format, chain PA [auth e] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth A] MOL2 format, chain MA [auth X] MOL2 format, chain IA [auth V] MOL2 format, chain AA [auth H] mmCIF format, chain CA [auth Q] mmCIF format, chain EA [auth R] mmCIF format, chain GA [auth U] mmCIF format, chain KA [auth W] mmCIF format, chain OA [auth c] mmCIF format, chain PA [auth e] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth A] mmCIF format, chain MA [auth X] mmCIF format, chain IA [auth V] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth Q] EA [auth R] GA [auth U] IA [auth V] AA [auth H], CA [auth Q], EA [auth R], GA [auth U], IA [auth V], KA [auth W], MA [auth X], OA [auth c], PA [auth e], U [auth A], W [auth F], Y [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth Q] Focus chain EA [auth R] Focus chain GA [auth U] Focus chain IA [auth V] Focus chain KA [auth W] Focus chain MA [auth X] Focus chain OA [auth c] Focus chain PA [auth e] Focus chain U [auth A] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth Q] Focus chain EA [auth R] Focus chain GA [auth U] Focus chain IA [auth V] Focus chain KA [auth W] Focus chain MA [auth X] Focus chain OA [auth c] Focus chain PA [auth e] Focus chain U [auth A] Focus chain W [auth F] Focus chain Y [auth G]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain FA [auth R] SDF format, chain JA [auth V] SDF format, chain LA [auth W] SDF format, chain NA [auth X] SDF format, chain V [auth A] SDF format, chain X [auth F] SDF format, chain Z [auth G] SDF format, chain HA [auth U] SDF format, chain DA [auth Q] MOL2 format, chain BA [auth H] MOL2 format, chain FA [auth R] MOL2 format, chain JA [auth V] MOL2 format, chain LA [auth W] MOL2 format, chain NA [auth X] MOL2 format, chain V [auth A] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain HA [auth U] MOL2 format, chain DA [auth Q] mmCIF format, chain BA [auth H] mmCIF format, chain FA [auth R] mmCIF format, chain JA [auth V] mmCIF format, chain LA [auth W] mmCIF format, chain NA [auth X] mmCIF format, chain V [auth A] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain HA [auth U] mmCIF format, chain DA [auth Q]	BA [auth H] DA [auth Q] FA [auth R] HA [auth U] JA [auth V] BA [auth H], DA [auth Q], FA [auth R], HA [auth U], JA [auth V], LA [auth W], NA [auth X], V [auth A], X [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth Q] Focus chain FA [auth R] Focus chain HA [auth U] Focus chain JA [auth V] Focus chain LA [auth W] Focus chain NA [auth X] Focus chain V [auth A] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth Q] Focus chain FA [auth R] Focus chain HA [auth U] Focus chain JA [auth V] Focus chain LA [auth W] Focus chain NA [auth X] Focus chain V [auth A] Focus chain X [auth F] Focus chain Z [auth G]