8FYW

Cryo-EM Structure of genome containing AAV2

PDB DOI: https://doi.org/10.2210/pdb8FYW/pdb
EM Map EMD-29598: EMDB EMDataResource

Classification: VIRUS
Organism(s): adeno-associated virus 2
Expression System: Baculoviridae
Mutation(s): No

Deposited: 2023-01-26 Released: 2023-06-07
Deposition Author(s): Bennett, A.D., Mckenna, R.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cryo-EM Structure of genome containing AAV2

Bennett, A.D., Mckenna, R.

To be published.

Macromolecule Content

Total Structure Weight: 4,941.75 kDa
Atom Count: 251,220
Modelled Residue Count: 31,140
Deposited Residue Count: 44,100
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 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]	735	adeno-associated virus 2	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D5M (Subject of Investigation/LOI) Query on D5M 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 CC [auth U] 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 FD [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 IC [auth a] SDF format, chain ID [auth 1] SDF format, chain JB [auth B] SDF format, chain JC [auth b] SDF format, chain JD [auth 2] SDF format, chain KB [auth C] SDF format, chain KC [auth c] SDF format, chain KD [auth 3] SDF format, chain LB [auth D] SDF format, chain LC [auth d] SDF format, chain LD [auth 4] SDF format, chain MB [auth E] 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 ND [auth 6] 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 RB [auth J] SDF format, chain RC [auth j] 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 XC [auth p] SDF format, chain YB [auth Q] SDF format, chain YC [auth q] SDF format, chain ZB [auth R] SDF format, chain ZC [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 CC [auth U] 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 FD [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 IC [auth a] MOL2 format, chain ID [auth 1] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth b] MOL2 format, chain JD [auth 2] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth c] MOL2 format, chain KD [auth 3] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth d] MOL2 format, chain LD [auth 4] MOL2 format, chain MB [auth E] 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 ND [auth 6] 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 RB [auth J] MOL2 format, chain RC [auth j] 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 XC [auth p] MOL2 format, chain YB [auth Q] MOL2 format, chain YC [auth q] MOL2 format, chain ZB [auth R] MOL2 format, chain ZC [auth r] mmCIF format, chain AC [auth S] mmCIF format, chain AD [auth s] mmCIF format, chain BC [auth T] mmCIF format, chain BD [auth t] mmCIF format, chain CC [auth U] mmCIF format, chain CD [auth u] mmCIF format, chain DC [auth V] mmCIF format, chain DD [auth v] mmCIF format, chain EC [auth W] mmCIF format, chain ED [auth w] mmCIF format, chain FC [auth X] mmCIF format, chain FD [auth x] mmCIF format, chain GC [auth Y] mmCIF format, chain GD [auth y] mmCIF format, chain HC [auth Z] mmCIF format, chain HD [auth z] mmCIF format, chain IB [auth A] mmCIF format, chain IC [auth a] mmCIF format, chain ID [auth 1] mmCIF format, chain JB [auth B] mmCIF format, chain JC [auth b] mmCIF format, chain JD [auth 2] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth c] mmCIF format, chain KD [auth 3] mmCIF format, chain LB [auth D] mmCIF format, chain LC [auth d] mmCIF format, chain LD [auth 4] mmCIF format, chain MB [auth E] mmCIF format, chain MC [auth e] mmCIF format, chain MD [auth 5] mmCIF format, chain NB [auth F] mmCIF format, chain NC [auth f] mmCIF format, chain ND [auth 6] mmCIF format, chain OB [auth G] mmCIF format, chain OC [auth g] mmCIF format, chain OD [auth 7] mmCIF format, chain PB [auth H] mmCIF format, chain PC [auth h] mmCIF format, chain PD [auth 8] mmCIF format, chain QB [auth I] mmCIF format, chain QC [auth i] mmCIF format, chain RB [auth J] mmCIF format, chain RC [auth j] mmCIF format, chain SB [auth K] mmCIF format, chain SC [auth k] mmCIF format, chain TB [auth L] mmCIF format, chain TC [auth l] mmCIF format, chain UB [auth M] mmCIF format, chain UC [auth m] mmCIF format, chain VB [auth N] mmCIF format, chain VC [auth n] mmCIF format, chain WB [auth O] mmCIF format, chain WC [auth o] mmCIF format, chain XB [auth P] mmCIF format, chain XC [auth p] mmCIF format, chain YB [auth Q] mmCIF format, chain YC [auth q] mmCIF format, chain ZB [auth R] mmCIF format, chain ZC [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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Bennett, A.D.

Mckenna, R.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMS 1563234
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	GM082946

Revision History (Full details and data files)

Version 1.0: 2023-06-07
Type: Initial release
Version 2.0: 2024-05-29
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description