7MUA

Structure of the adeno-associated virus 9 capsid at pH pH 5.5 in complex with terminal galactose

PDB DOI: https://doi.org/10.2210/pdb7MUA/pdb
EM Map EMD-24003: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Adeno-associated virus 9
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-05-14 Released: 2021-06-09
Deposition Author(s): Penzes, J.J., Chipman, P., Bhattacharya, N., Zeher, A., Huang, R., McKenna, R., 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: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 3,519.27 kDa
Atom Count: 248,580
Modelled Residue Count: 31,080
Deposited Residue Count: 31,080
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 VP1	A AA [auth 1] AB [auth u] B BA [auth 2] A, AA [auth 1], AB [auth u], B, BA [auth 2], BB [auth v], C, CA [auth 3], CB [auth w], D, DA [auth 4], DB [auth x], E, EA [auth 5], EB [auth y], F, FA [auth 6], FB [auth z], G, GA [auth a], GB [auth 7], H, HA [auth b], HB [auth 8], I, IA [auth c], J, JA [auth d], K, KA [auth e], L, LA [auth f], M, MA [auth g], N, NA [auth h], O, OA [auth i], P, PA [auth j], Q, QA [auth k], R, RA [auth l], S, SA [auth m], T, TA [auth n], U, UA [auth o], V, VA [auth p], W, WA [auth q], X, XA [auth r], Y, YA [auth s], Z, ZA [auth t]	518	Adeno-associated virus 9	Mutation(s): 0 Gene Names: cap
UniProt
Find proteins for Q6JC40 (Adeno-associated virus 9) Explore Q6JC40 Go to UniProtKB: Q6JC40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6JC40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL (Subject of Investigation/LOI) Query on GAL Download Ideal Coordinates CCD File SDF format, chain AC [auth S] SDF format, chain AD [auth m] SDF format, chain BC [auth T] SDF format, chain BD [auth n] SDF format, chain CC [auth U] SDF format, chain CD [auth o] SDF format, chain DC [auth V] SDF format, chain DD [auth p] SDF format, chain EC [auth W] SDF format, chain ED [auth q] SDF format, chain FC [auth X] SDF format, chain FD [auth r] SDF format, chain GC [auth Y] SDF format, chain GD [auth s] SDF format, chain HC [auth Z] SDF format, chain HD [auth t] SDF format, chain IB [auth A] SDF format, chain IC [auth 1] SDF format, chain ID [auth u] SDF format, chain JB [auth B] SDF format, chain JC [auth 2] SDF format, chain JD [auth v] SDF format, chain KB [auth C] SDF format, chain KC [auth 3] SDF format, chain KD [auth w] SDF format, chain LB [auth D] SDF format, chain LC [auth 4] SDF format, chain LD [auth x] SDF format, chain MB [auth E] SDF format, chain MC [auth 5] SDF format, chain MD [auth y] SDF format, chain NB [auth F] SDF format, chain NC [auth 6] SDF format, chain ND [auth z] SDF format, chain OB [auth G] SDF format, chain OC [auth a] SDF format, chain OD [auth 7] SDF format, chain PB [auth H] SDF format, chain PC [auth b] SDF format, chain PD [auth 8] SDF format, chain QB [auth I] SDF format, chain QC [auth c] SDF format, chain RB [auth J] SDF format, chain RC [auth d] SDF format, chain SB [auth K] SDF format, chain SC [auth e] SDF format, chain TB [auth L] SDF format, chain TC [auth f] SDF format, chain UB [auth M] SDF format, chain UC [auth g] SDF format, chain VB [auth N] SDF format, chain VC [auth h] SDF format, chain WB [auth O] SDF format, chain WC [auth i] SDF format, chain XB [auth P] SDF format, chain XC [auth j] SDF format, chain YB [auth Q] SDF format, chain YC [auth k] SDF format, chain ZB [auth R] SDF format, chain ZC [auth l] MOL2 format, chain AC [auth S] MOL2 format, chain AD [auth m] MOL2 format, chain BC [auth T] MOL2 format, chain BD [auth n] MOL2 format, chain CC [auth U] MOL2 format, chain CD [auth o] MOL2 format, chain DC [auth V] MOL2 format, chain DD [auth p] MOL2 format, chain EC [auth W] MOL2 format, chain ED [auth q] MOL2 format, chain FC [auth X] MOL2 format, chain FD [auth r] MOL2 format, chain GC [auth Y] MOL2 format, chain GD [auth s] MOL2 format, chain HC [auth Z] MOL2 format, chain HD [auth t] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth 1] MOL2 format, chain ID [auth u] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth 2] MOL2 format, chain JD [auth v] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth 3] MOL2 format, chain KD [auth w] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth 4] MOL2 format, chain LD [auth x] MOL2 format, chain MB [auth E] MOL2 format, chain MC [auth 5] MOL2 format, chain MD [auth y] MOL2 format, chain NB [auth F] MOL2 format, chain NC [auth 6] MOL2 format, chain ND [auth z] MOL2 format, chain OB [auth G] MOL2 format, chain OC [auth a] MOL2 format, chain OD [auth 7] MOL2 format, chain PB [auth H] MOL2 format, chain PC [auth b] MOL2 format, chain PD [auth 8] MOL2 format, chain QB [auth I] MOL2 format, chain QC [auth c] MOL2 format, chain RB [auth J] MOL2 format, chain RC [auth d] MOL2 format, chain SB [auth K] MOL2 format, chain SC [auth e] MOL2 format, chain TB [auth L] MOL2 format, chain TC [auth f] MOL2 format, chain UB [auth M] MOL2 format, chain UC [auth g] MOL2 format, chain VB [auth N] MOL2 format, chain VC [auth h] MOL2 format, chain WB [auth O] MOL2 format, chain WC [auth i] MOL2 format, chain XB [auth P] MOL2 format, chain XC [auth j] MOL2 format, chain YB [auth Q] MOL2 format, chain YC [auth k] MOL2 format, chain ZB [auth R] MOL2 format, chain ZC [auth l]	AC [auth S] AD [auth m] BC [auth T] BD [auth n] CC [auth U] AC [auth S], AD [auth m], BC [auth T], BD [auth n], CC [auth U], CD [auth o], DC [auth V], DD [auth p], EC [auth W], ED [auth q], FC [auth X], FD [auth r], GC [auth Y], GD [auth s], HC [auth Z], HD [auth t], IB [auth A], IC [auth 1], ID [auth u], JB [auth B], JC [auth 2], JD [auth v], KB [auth C], KC [auth 3], KD [auth w], LB [auth D], LC [auth 4], LD [auth x], MB [auth E], MC [auth 5], MD [auth y], NB [auth F], NC [auth 6], ND [auth z], OB [auth G], OC [auth a], OD [auth 7], PB [auth H], PC [auth b], PD [auth 8], QB [auth I], QC [auth c], RB [auth J], RC [auth d], SB [auth K], SC [auth e], TB [auth L], TC [auth f], UB [auth M], UC [auth g], VB [auth N], VC [auth h], WB [auth O], WC [auth i], XB [auth P], XC [auth j], YB [auth Q], YC [auth k], ZB [auth R], ZC [auth l]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain AC [auth S] Focus chain AD [auth m] Focus chain BC [auth T] Focus chain BD [auth n] Focus chain CC [auth U] Focus chain CD [auth o] Focus chain DC [auth V] Focus chain DD [auth p] Focus chain EC [auth W] Focus chain ED [auth q] Focus chain FC [auth X] Focus chain FD [auth r] Focus chain GC [auth Y] Focus chain GD [auth s] Focus chain HC [auth Z] Focus chain HD [auth t] Focus chain IB [auth A] Focus chain IC [auth 1] Focus chain ID [auth u] Focus chain JB [auth B] Focus chain JC [auth 2] Focus chain JD [auth v] Focus chain KB [auth C] Focus chain KC [auth 3] Focus chain KD [auth w] Focus chain LB [auth D] Focus chain LC [auth 4] Focus chain LD [auth x] Focus chain MB [auth E] Focus chain MC [auth 5] Focus chain MD [auth y] Focus chain NB [auth F] Focus chain NC [auth 6] Focus chain ND [auth z] Focus chain OB [auth G] Focus chain OC [auth a] Focus chain OD [auth 7] Focus chain PB [auth H] Focus chain PC [auth b] Focus chain PD [auth 8] Focus chain QB [auth I] Focus chain QC [auth c] Focus chain RB [auth J] Focus chain RC [auth d] Focus chain SB [auth K] Focus chain SC [auth e] Focus chain TB [auth L] Focus chain TC [auth f] Focus chain UB [auth M] Focus chain UC [auth g] Focus chain VB [auth N] Focus chain VC [auth h] Focus chain WB [auth O] Focus chain WC [auth i] Focus chain XB [auth P] Focus chain XC [auth j] Focus chain YB [auth Q] Focus chain YC [auth k] Focus chain ZB [auth R] Focus chain ZC [auth l] Interactions & Density Focus chain AC [auth S] Focus chain AD [auth m] Focus chain BC [auth T] Focus chain BD [auth n] Focus chain CC [auth U] Focus chain CD [auth o] Focus chain DC [auth V] Focus chain DD [auth p] Focus chain EC [auth W] Focus chain ED [auth q] Focus chain FC [auth X] Focus chain FD [auth r] Focus chain GC [auth Y] Focus chain GD [auth s] Focus chain HC [auth Z] Focus chain HD [auth t] Focus chain IB [auth A] Focus chain IC [auth 1] Focus chain ID [auth u] Focus chain JB [auth B] Focus chain JC [auth 2] Focus chain JD [auth v] Focus chain KB [auth C] Focus chain KC [auth 3] Focus chain KD [auth w] Focus chain LB [auth D] Focus chain LC [auth 4] Focus chain LD [auth x] Focus chain MB [auth E] Focus chain MC [auth 5] Focus chain MD [auth y] Focus chain NB [auth F] Focus chain NC [auth 6] Focus chain ND [auth z] Focus chain OB [auth G] Focus chain OC [auth a] Focus chain OD [auth 7] Focus chain PB [auth H] Focus chain PC [auth b] Focus chain PD [auth 8] Focus chain QB [auth I] Focus chain QC [auth c] Focus chain RB [auth J] Focus chain RC [auth d] Focus chain SB [auth K] Focus chain SC [auth e] Focus chain TB [auth L] Focus chain TC [auth f] Focus chain UB [auth M] Focus chain UC [auth g] Focus chain VB [auth N] Focus chain VC [auth h] Focus chain WB [auth O] Focus chain WC [auth i] Focus chain XB [auth P] Focus chain XC [auth j] Focus chain YB [auth Q] Focus chain YC [auth k] Focus chain ZB [auth R] Focus chain ZC [auth l]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.8.9.3
RECONSTRUCTION	cisTEM	1.0.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM109524
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM082946
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10 OD018142
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10 RR025080
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM116788