7L5U

The full AAV7 capsid

PDB DOI: https://doi.org/10.2210/pdb7L5U/pdb
EM Map EMD-23190: EMDB EMDataResource

Classification: VIRUS
Organism(s): Adeno-associated virus - 7
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-12-22 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: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/v13010101
Primary Citation of 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: 3,533.87 kDa
Atom Count: 250,020
Modelled Residue Count: 31,200
Deposited Residue Count: 31,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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]	520	Adeno-associated virus - 7	Mutation(s): 0
UniProt
Find proteins for Q8JQG0 (Adeno-associated virus - 7) Explore Q8JQG0 Go to UniProtKB: Q8JQG0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8JQG0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DA Query on DA Download Ideal Coordinates CCD File SDF format, chain AC [auth S] SDF format, chain AD [auth s] SDF format, chain BC [auth T] SDF format, chain BD [auth t] SDF format, chain CD [auth u] SDF format, chain DC [auth V] SDF format, chain DD [auth v] SDF format, chain EC [auth W] SDF format, chain ED [auth w] SDF format, chain FC [auth X] SDF format, chain GC [auth Y] SDF format, chain GD [auth y] SDF format, chain HC [auth Z] SDF format, chain HD [auth z] SDF format, chain IB [auth A] SDF format, chain ID [auth 1] SDF format, chain JB [auth B] SDF format, chain JD [auth 2] SDF format, chain KB [auth C] SDF format, chain KC [auth c] SDF format, chain LB [auth D] SDF format, chain LC [auth d] SDF format, chain LD [auth 4] SDF format, chain MC [auth e] SDF format, chain MD [auth 5] SDF format, chain NB [auth F] SDF format, chain NC [auth f] SDF format, chain OB [auth G] SDF format, chain OC [auth g] SDF format, chain OD [auth 7] SDF format, chain PB [auth H] SDF format, chain PC [auth h] SDF format, chain PD [auth 8] SDF format, chain QB [auth I] SDF format, chain QC [auth i] SDF format, chain SB [auth K] SDF format, chain SC [auth k] SDF format, chain TB [auth L] SDF format, chain TC [auth l] SDF format, chain UB [auth M] SDF format, chain UC [auth m] SDF format, chain VB [auth N] SDF format, chain VC [auth n] SDF format, chain WB [auth O] SDF format, chain WC [auth o] SDF format, chain XB [auth P] SDF format, chain YB [auth Q] SDF format, chain YC [auth q] SDF format, chain ZC [auth r] SDF format, chain CC [auth U] SDF format, chain FD [auth x] SDF format, chain IC [auth a] SDF format, chain JC [auth b] SDF format, chain KD [auth 3] SDF format, chain MB [auth E] SDF format, chain ND [auth 6] SDF format, chain RB [auth J] SDF format, chain RC [auth j] SDF format, chain XC [auth p] SDF format, chain ZB [auth R] MOL2 format, chain AC [auth S] MOL2 format, chain AD [auth s] MOL2 format, chain BC [auth T] MOL2 format, chain BD [auth t] MOL2 format, chain CD [auth u] MOL2 format, chain DC [auth V] MOL2 format, chain DD [auth v] MOL2 format, chain EC [auth W] MOL2 format, chain ED [auth w] MOL2 format, chain FC [auth X] MOL2 format, chain GC [auth Y] MOL2 format, chain GD [auth y] MOL2 format, chain HC [auth Z] MOL2 format, chain HD [auth z] MOL2 format, chain IB [auth A] MOL2 format, chain ID [auth 1] MOL2 format, chain JB [auth B] MOL2 format, chain JD [auth 2] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth c] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth d] MOL2 format, chain LD [auth 4] MOL2 format, chain MC [auth e] MOL2 format, chain MD [auth 5] MOL2 format, chain NB [auth F] MOL2 format, chain NC [auth f] MOL2 format, chain OB [auth G] MOL2 format, chain OC [auth g] MOL2 format, chain OD [auth 7] MOL2 format, chain PB [auth H] MOL2 format, chain PC [auth h] MOL2 format, chain PD [auth 8] MOL2 format, chain QB [auth I] MOL2 format, chain QC [auth i] MOL2 format, chain SB [auth K] MOL2 format, chain SC [auth k] MOL2 format, chain TB [auth L] MOL2 format, chain TC [auth l] MOL2 format, chain UB [auth M] MOL2 format, chain UC [auth m] MOL2 format, chain VB [auth N] MOL2 format, chain VC [auth n] MOL2 format, chain WB [auth O] MOL2 format, chain WC [auth o] MOL2 format, chain XB [auth P] MOL2 format, chain YB [auth Q] MOL2 format, chain YC [auth q] MOL2 format, chain ZC [auth r] MOL2 format, chain CC [auth U] MOL2 format, chain FD [auth x] MOL2 format, chain IC [auth a] MOL2 format, chain JC [auth b] MOL2 format, chain KD [auth 3] MOL2 format, chain MB [auth E] MOL2 format, chain ND [auth 6] MOL2 format, chain RB [auth J] MOL2 format, chain RC [auth j] MOL2 format, chain XC [auth p] MOL2 format, chain ZB [auth R]	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]