9RM5 | pdb_00009rm5

Hexameric AAV2 Rep40-ssDNA (ITR) complex in presence of ATPyS

PDB DOI: https://doi.org/10.2210/pdb9RM5/pdb
EM Map EMD-54050: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): adeno-associated virus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-17 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: 2.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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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., Rouse, S.L.

To be published.

Macromolecule Content

Total Structure Weight: 270.81 kDa
Atom Count: 13,657
Modeled Residue Count: 1,678
Deposited Residue Count: 2,392
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
Protein Rep40	A [auth a] B [auth b] C [auth c] D [auth d] E [auth e] A [auth a], B [auth b], C [auth c], D [auth d], E [auth e], F [auth f]	397	adeno-associated virus 2	Mutation(s): 0 Gene Names: Rep40 EC: 3.6.4.12
UniProt
Find proteins for Q89269 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore Q89269 Go to UniProtKB: Q89269
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89269
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	G [auth s]	10	adeno-associated virus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain H [auth a] SDF format, chain J [auth b] SDF format, chain L [auth c] SDF format, chain N [auth d] MOL2 format, chain H [auth a] MOL2 format, chain J [auth b] MOL2 format, chain L [auth c] MOL2 format, chain N [auth d] mmCIF format, chain H [auth a] mmCIF format, chain J [auth b] mmCIF format, chain L [auth c] mmCIF format, chain N [auth d]	H [auth a], J [auth b], L [auth c], N [auth d]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain H [auth a] Focus chain J [auth b] Focus chain L [auth c] Focus chain N [auth d] Interactions & Density Focus chain H [auth a] Focus chain J [auth b] Focus chain L [auth c] Focus chain N [auth d]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain R [auth f] SDF format, chain P [auth e] MOL2 format, chain R [auth f] MOL2 format, chain P [auth e] mmCIF format, chain R [auth f] mmCIF format, chain P [auth e]	P [auth e], R [auth f]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth e] Focus chain R [auth f] Interactions & Density Focus chain P [auth e] Focus chain R [auth f]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth a] SDF format, chain K [auth b] SDF format, chain M [auth c] SDF format, chain O [auth d] SDF format, chain Q [auth e] MOL2 format, chain I [auth a] MOL2 format, chain K [auth b] MOL2 format, chain M [auth c] MOL2 format, chain O [auth d] MOL2 format, chain Q [auth e] mmCIF format, chain I [auth a] mmCIF format, chain K [auth b] mmCIF format, chain M [auth c] mmCIF format, chain O [auth d] mmCIF format, chain Q [auth e]	I [auth a], K [auth b], M [auth c], O [auth d], Q [auth e]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth a] Focus chain K [auth b] Focus chain M [auth c] Focus chain O [auth d] Focus chain Q [auth e] Interactions & Density Focus chain I [auth a] Focus chain K [auth b] Focus chain M [auth c] Focus chain O [auth d] Focus chain Q [auth e]