38OK | pdb_000038ok

AAV2 Rep68(delta1-209)/capsid/DNA complex

PDB DOI: https://doi.org/10.2210/pdb38OK/pdb
EM Map EMD-79003: EMDB EMDataResource

Classification: VIRUS
Organism(s): Adeno-associated virus 2 Srivastava/1982, synthetic construct
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2026-09-09 Released: 2026-09-23
Deposition Author(s): Kaelber, J.T., Barnakov, V., Shen, J., Escalante, C.R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.93 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

Insights into the AAV packaging mechanism: Cryo-EM Structure of the AAV2 Rep-Capsid Packaging Complex

Kaelber, J.T., Barnakov, V., Shen, J., Hernandez, K., Tarbox, H.J., Khan, A., Escalante, C.R.

To be published.

Macromolecule Content

Total Structure Weight: 484.66 kDa
Atom Count: 34,192
Modeled Residue Count: 4,225
Deposited Residue Count: 4,225
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Rep68	A, B, C, D, E A, B, C, D, E, F	278	Adeno-associated virus 2 Srivastava/1982	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03132
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	H [auth V], I [auth W], J [auth X], K [auth Y], L [auth Z]	510	Adeno-associated virus 2 Srivastava/1982	Mutation(s): 0 Gene Names: VP1
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03135 Go to UniProtKB: P03135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03135
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
ssDNA	G	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 R [auth D] SDF format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C]	P [auth C], R [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain P [auth C] Focus chain R [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Z [auth W] SDF format, chain X [auth V] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain M [auth A] SDF format, chain FA [auth Z] SDF format, chain DA [auth Y] SDF format, chain BA [auth X] MOL2 format, chain Z [auth W] MOL2 format, chain X [auth V] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth Z] MOL2 format, chain DA [auth Y] MOL2 format, chain BA [auth X] mmCIF format, chain Z [auth W] mmCIF format, chain X [auth V] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth Z] mmCIF format, chain DA [auth Y] mmCIF format, chain BA [auth X]	BA [auth X] DA [auth Y] FA [auth Z] M [auth A] T [auth E] BA [auth X], DA [auth Y], FA [auth Z], M [auth A], T [auth E], V [auth F], X [auth V], Z [auth W]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth X] Focus chain DA [auth Y] Focus chain FA [auth Z] Focus chain M [auth A] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth V] Focus chain Z [auth W] Interactions & Density Focus chain BA [auth X] Focus chain DA [auth Y] Focus chain FA [auth Z] Focus chain M [auth A] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth V] Focus chain Z [auth W]
POP (Subject of Investigation/LOI) Query on POP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth V] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain GA [auth Z] SDF format, chain EA [auth Y] SDF format, chain CA [auth X] SDF format, chain AA [auth W] MOL2 format, chain Y [auth V] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain GA [auth Z] MOL2 format, chain EA [auth Y] MOL2 format, chain CA [auth X] MOL2 format, chain AA [auth W] mmCIF format, chain Y [auth V] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain GA [auth Z] mmCIF format, chain EA [auth Y] mmCIF format, chain CA [auth X] mmCIF format, chain AA [auth W]	AA [auth W] CA [auth X] EA [auth Y] GA [auth Z] O [auth B] AA [auth W], CA [auth X], EA [auth Y], GA [auth Z], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth V]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth W] Focus chain CA [auth X] Focus chain EA [auth Y] Focus chain GA [auth Z] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth V] Interactions & Density Focus chain AA [auth W] Focus chain CA [auth X] Focus chain EA [auth Y] Focus chain GA [auth Z] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth V]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_6010
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI190168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM124204