7L6H | pdb_00007l6h

The genome-containing AAV13 capsid

PDB DOI: https://doi.org/10.2210/pdb7L6H/pdb
EM Map EMD-23204: EMDB EMDataResource

Classification: VIRUS
Organism(s): Adeno-associated virus 13
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-12-23 Released: 2021-02-03
Deposition Author(s): Mietzsch, M., Agbandje-McKenna, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Completion of the AAV Structural Atlas: Serotype Capsid Structures Reveals Clade-Specific Features.

Mietzsch, M., Jose, A., Chipman, P., Bhattacharya, N., Daneshparvar, N., McKenna, R., Agbandje-McKenna, M.

(2021) Viruses 13

PubMed: 33450892 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/v13010101
Primary Citation Related Structures:
7L5Q, 7L5U, 7L6A, 7L6B, 7L6E, 7L6F, 7L6H, 7L6I

PubMed Abstract:
The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of AAV7, AAV11, AAV12, and AAV13 determined by cryo-electron microscopy and three-dimensional image reconstruction to 2.96, 2.86, 2.54, and 2.76 Å resolution, respectively. These structures complete the structural atlas of the AAV serotype capsids. AAV7 represents the first clade D capsid structure; AAV11 and AAV12 are of a currently unassigned clade that would include AAV4; and AAV13 represents the first AAV2-AAV3 hybrid clade C capsid structure. These newly determined capsid structures all exhibit the AAV capsid features including 5-fold channels, 3-fold protrusions, 2-fold depressions, and a nucleotide binding pocket with an ordered nucleotide in genome-containing capsids. However, these structures have viral proteins that display clade-specific loop conformations. This structural characterization completes our three-dimensional library of the current AAV serotypes to provide an atlas of surface loop configurations compatible with capsid assembly and amenable for future vector engineering efforts. Derived vectors could improve gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Macromolecule Content

Total Structure Weight: 3,533.2 kDa
Atom Count: 251,400
Modeled Residue Count: 31,020
Deposited Residue Count: 31,020
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A AA [auth a] AB [auth 1] B BA [auth b] A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	517	Adeno-associated virus 13	Mutation(s): 0
UniProt
Find proteins for B5SUY7 (Adeno-associated virus 13) Explore B5SUY7 Go to UniProtKB: B5SUY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5SUY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D5M Query on D5M Download:Ideal Coordinates CCD File SDF format, chain AC [auth S] SDF format, chain BD [auth t] SDF format, chain GD [auth y] SDF format, chain HC [auth Z] SDF format, chain ID [auth 1] SDF format, chain KC [auth c] SDF format, chain KD [auth 3] SDF format, chain MB [auth E] SDF format, chain MD [auth 5] SDF format, chain NB [auth F] SDF format, chain NC [auth f] SDF format, chain PB [auth H] SDF format, chain RB [auth J] SDF format, chain UC [auth m] SDF format, chain ZC [auth r] SDF format, chain ZB [auth R] SDF format, chain YC [auth q] SDF format, chain YB [auth Q] SDF format, chain XC [auth p] SDF format, chain XB [auth P] SDF format, chain WC [auth o] SDF format, chain WB [auth O] SDF format, chain VC [auth n] SDF format, chain VB [auth N] SDF format, chain UB [auth M] SDF format, chain TC [auth l] SDF format, chain TB [auth L] SDF format, chain SC [auth k] SDF format, chain SB [auth K] SDF format, chain RC [auth j] SDF format, chain QC [auth i] SDF format, chain QB [auth I] SDF format, chain PD [auth 8] SDF format, chain PC [auth h] SDF format, chain OD [auth 7] SDF format, chain OC [auth g] SDF format, chain OB [auth G] SDF format, chain ND [auth 6] SDF format, chain MC [auth e] SDF format, chain LD [auth 4] SDF format, chain LC [auth d] SDF format, chain LB [auth D] SDF format, chain KB [auth C] SDF format, chain JD [auth 2] SDF format, chain JC [auth b] SDF format, chain JB [auth B] SDF format, chain IC [auth a] SDF format, chain IB [auth A] SDF format, chain HD [auth z] SDF format, chain GC [auth Y] SDF format, chain FD [auth x] SDF format, chain FC [auth X] SDF format, chain ED [auth w] SDF format, chain EC [auth W] SDF format, chain DD [auth v] SDF format, chain DC [auth V] SDF format, chain CD [auth u] SDF format, chain CC [auth U] SDF format, chain BC [auth T] SDF format, chain AD [auth s] MOL2 format, chain AC [auth S] MOL2 format, chain BD [auth t] MOL2 format, chain GD [auth y] MOL2 format, chain HC [auth Z] MOL2 format, chain ID [auth 1] MOL2 format, chain KC [auth c] MOL2 format, chain KD [auth 3] MOL2 format, chain MB [auth E] MOL2 format, chain MD [auth 5] MOL2 format, chain NB [auth F] MOL2 format, chain NC [auth f] MOL2 format, chain PB [auth H] MOL2 format, chain RB [auth J] MOL2 format, chain UC [auth m] MOL2 format, chain ZC [auth r] MOL2 format, chain ZB [auth R] MOL2 format, chain YC [auth q] MOL2 format, chain YB [auth Q] MOL2 format, chain XC [auth p] MOL2 format, chain XB [auth P] MOL2 format, chain WC [auth o] MOL2 format, chain WB [auth O] MOL2 format, chain VC [auth n] MOL2 format, chain VB [auth N] MOL2 format, chain UB [auth M] MOL2 format, chain TC [auth l] MOL2 format, chain TB [auth L] MOL2 format, chain SC [auth k] MOL2 format, chain SB [auth K] MOL2 format, chain RC [auth j] MOL2 format, chain QC [auth i] MOL2 format, chain QB [auth I] MOL2 format, chain PD [auth 8] MOL2 format, chain PC [auth h] MOL2 format, chain OD [auth 7] MOL2 format, chain OC [auth g] MOL2 format, chain OB [auth G] MOL2 format, chain ND [auth 6] MOL2 format, chain MC [auth e] MOL2 format, chain LD [auth 4] MOL2 format, chain LC [auth d] MOL2 format, chain LB [auth D] MOL2 format, chain KB [auth C] MOL2 format, chain JD [auth 2] MOL2 format, chain JC [auth b] MOL2 format, chain JB [auth B] MOL2 format, chain IC [auth a] MOL2 format, chain IB [auth A] MOL2 format, chain HD [auth z] MOL2 format, chain GC [auth Y] MOL2 format, chain FD [auth x] MOL2 format, chain FC [auth X] MOL2 format, chain ED [auth w] MOL2 format, chain EC [auth W] MOL2 format, chain DD [auth v] MOL2 format, chain DC [auth V] MOL2 format, chain CD [auth u] MOL2 format, chain CC [auth U] MOL2 format, chain BC [auth T] MOL2 format, chain AD [auth s] mmCIF format, chain AC [auth S] mmCIF format, chain BD [auth t] mmCIF format, chain GD [auth y] mmCIF format, chain HC [auth Z] mmCIF format, chain ID [auth 1] mmCIF format, chain KC [auth c] mmCIF format, chain KD [auth 3] mmCIF format, chain MB [auth E] mmCIF format, chain MD [auth 5] mmCIF format, chain NB [auth F] mmCIF format, chain NC [auth f] mmCIF format, chain PB [auth H] mmCIF format, chain RB [auth J] mmCIF format, chain UC [auth m] mmCIF format, chain ZC [auth r] mmCIF format, chain ZB [auth R] mmCIF format, chain YC [auth q] mmCIF format, chain YB [auth Q] mmCIF format, chain XC [auth p] mmCIF format, chain XB [auth P] mmCIF format, chain WC [auth o] mmCIF format, chain WB [auth O] mmCIF format, chain VC [auth n] mmCIF format, chain VB [auth N] mmCIF format, chain UB [auth M] mmCIF format, chain TC [auth l] mmCIF format, chain TB [auth L] mmCIF format, chain SC [auth k] mmCIF format, chain SB [auth K] mmCIF format, chain RC [auth j] mmCIF format, chain QC [auth i] mmCIF format, chain QB [auth I] mmCIF format, chain PD [auth 8] mmCIF format, chain PC [auth h] mmCIF format, chain OD [auth 7] mmCIF format, chain OC [auth g] mmCIF format, chain OB [auth G] mmCIF format, chain ND [auth 6] mmCIF format, chain MC [auth e] mmCIF format, chain LD [auth 4] mmCIF format, chain LC [auth d] mmCIF format, chain LB [auth D] mmCIF format, chain KB [auth C] mmCIF format, chain JD [auth 2] mmCIF format, chain JC [auth b] mmCIF format, chain JB [auth B] mmCIF format, chain IC [auth a] mmCIF format, chain IB [auth A] mmCIF format, chain HD [auth z] mmCIF format, chain GC [auth Y] mmCIF format, chain FD [auth x] mmCIF format, chain FC [auth X] mmCIF format, chain ED [auth w] mmCIF format, chain EC [auth W] mmCIF format, chain DD [auth v] mmCIF format, chain DC [auth V] mmCIF format, chain CD [auth u] mmCIF format, chain CC [auth U] mmCIF format, chain BC [auth T] mmCIF format, chain AD [auth s]	AC [auth S] AD [auth s] BC [auth T] BD [auth t] CC [auth U] AC [auth S], AD [auth s], BC [auth T], BD [auth t], CC [auth U], CD [auth u], DC [auth V], DD [auth v], EC [auth W], ED [auth w], FC [auth X], FD [auth x], GC [auth Y], GD [auth y], HC [auth Z], HD [auth z], IB [auth A], IC [auth a], ID [auth 1], JB [auth B], JC [auth b], JD [auth 2], KB [auth C], KC [auth c], KD [auth 3], LB [auth D], LC [auth d], LD [auth 4], MB [auth E], MC [auth e], MD [auth 5], NB [auth F], NC [auth f], ND [auth 6], OB [auth G], OC [auth g], OD [auth 7], PB [auth H], PC [auth h], PD [auth 8], QB [auth I], QC [auth i], RB [auth J], RC [auth j], SB [auth K], SC [auth k], TB [auth L], TC [auth l], UB [auth M], UC [auth m], VB [auth N], VC [auth n], WB [auth O], WC [auth o], XB [auth P], XC [auth p], YB [auth Q], YC [auth q], ZB [auth R], ZC [auth r]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₆ P KHWCHTKSEGGWEX-RRKCRQDMSA-N		Interactions Focus chain AC [auth S] Focus chain AD [auth s] Focus chain BC [auth T] Focus chain BD [auth t] Focus chain CC [auth U] Focus chain CD [auth u] Focus chain DC [auth V] Focus chain DD [auth v] Focus chain EC [auth W] Focus chain ED [auth w] Focus chain FC [auth X] Focus chain FD [auth x] Focus chain GC [auth Y] Focus chain GD [auth y] Focus chain HC [auth Z] Focus chain HD [auth z] Focus chain IB [auth A] Focus chain IC [auth a] Focus chain ID [auth 1] Focus chain JB [auth B] Focus chain JC [auth b] Focus chain JD [auth 2] Focus chain KB [auth C] Focus chain KC [auth c] Focus chain KD [auth 3] Focus chain LB [auth D] Focus chain LC [auth d] Focus chain LD [auth 4] Focus chain MB [auth E] Focus chain MC [auth e] Focus chain MD [auth 5] Focus chain NB [auth F] Focus chain NC [auth f] Focus chain ND [auth 6] Focus chain OB [auth G] Focus chain OC [auth g] Focus chain OD [auth 7] Focus chain PB [auth H] Focus chain PC [auth h] Focus chain PD [auth 8] Focus chain QB [auth I] Focus chain QC [auth i] Focus chain RB [auth J] Focus chain RC [auth j] Focus chain SB [auth K] Focus chain SC [auth k] Focus chain TB [auth L] Focus chain TC [auth l] Focus chain UB [auth M] Focus chain UC [auth m] Focus chain VB [auth N] Focus chain VC [auth n] Focus chain WB [auth O] Focus chain WC [auth o] Focus chain XB [auth P] Focus chain XC [auth p] Focus chain YB [auth Q] Focus chain YC [auth q] Focus chain ZB [auth R] Focus chain ZC [auth r] Interactions & Density Focus chain AC [auth S] Focus chain AD [auth s] Focus chain BC [auth T] Focus chain BD [auth t] Focus chain CC [auth U] Focus chain CD [auth u] Focus chain DC [auth V] Focus chain DD [auth v] Focus chain EC [auth W] Focus chain ED [auth w] Focus chain FC [auth X] Focus chain FD [auth x] Focus chain GC [auth Y] Focus chain GD [auth y] Focus chain HC [auth Z] Focus chain HD [auth z] Focus chain IB [auth A] Focus chain IC [auth a] Focus chain ID [auth 1] Focus chain JB [auth B] Focus chain JC [auth b] Focus chain JD [auth 2] Focus chain KB [auth C] Focus chain KC [auth c] Focus chain KD [auth 3] Focus chain LB [auth D] Focus chain LC [auth d] Focus chain LD [auth 4] Focus chain MB [auth E] Focus chain MC [auth e] Focus chain MD [auth 5] Focus chain NB [auth F] Focus chain NC [auth f] Focus chain ND [auth 6] Focus chain OB [auth G] Focus chain OC [auth g] Focus chain OD [auth 7] Focus chain PB [auth H] Focus chain PC [auth h] Focus chain PD [auth 8] Focus chain QB [auth I] Focus chain QC [auth i] Focus chain RB [auth J] Focus chain RC [auth j] Focus chain SB [auth K] Focus chain SC [auth k] Focus chain TB [auth L] Focus chain TC [auth l] Focus chain UB [auth M] Focus chain UC [auth m] Focus chain VB [auth N] Focus chain VC [auth n] Focus chain WB [auth O] Focus chain WC [auth o] Focus chain XB [auth P] Focus chain XC [auth p] Focus chain YB [auth Q] Focus chain YC [auth q] Focus chain ZB [auth R] Focus chain ZC [auth r]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cisTEM

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Mietzsch, M.

Agbandje-McKenna, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 2.0: 2024-05-29
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description
Version 2.1: 2025-05-28
Changes: Data collection, Structure summary