9ZD8 | pdb_00009zd8

The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status

• PDB DOI: https://doi.org/10.2210/pdb9ZD8/pdb
• EM Map EMD-74057: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Pakpunavirus
• Mutation(s): No 


• Deposited: 2025-11-25 Released: 2026-04-15 
• Deposition Author(s): Li, F., Cingolani, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status

Li, F., Cingolani, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 63-mer - A12B6C6D6E6F6G6H6I3J3K3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 63-mer - A12B12C6D6E6F6G3H3I3J3K3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,301.76 kDa 
• Atom Count: 107,757 
• Modeled Residue Count: 13,914 
• Deposited Residue Count: 20,961 
• Unique protein chains: 10

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp88	A [auth 0], EA [auth f], FA [auth g], GA [auth h], M [auth L], N [auth M], NA [auth o], O [auth N], TA [auth u], V, W, X	487	Pakpunavirus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
gp89	B [auth 1], HA [auth i], OA [auth p], P [auth O], UA [auth v], Y	243	Pakpunavirus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gp83	C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F]	253	Pakpunavirus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
gp79	AA [auth a], I [auth G], JA [auth k], PA [auth q], R [auth Q], VA [auth w]	159	Pakpunavirus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
gp78	BA [auth b], J [auth H], KA [auth l], QA [auth r], S [auth R], WA [auth x]	166	Pakpunavirus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
gp84	CA [auth c], K [auth I], LA [auth m], RA [auth s], T [auth S], XA [auth y]	118	Pakpunavirus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
gp87	DA [auth e], L [auth K], MA [auth n], SA [auth t], U, YA [auth z]	123	Pakpunavirus	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
gp86	IA [auth j], Q [auth P], Z	246	Pakpunavirus	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
gp85	AB [auth T], BB [auth d], ZA [auth J]	305	Pakpunavirus	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
gp88	CB [auth 4], DB [auth 2], EB [auth 3], FB [auth 5], GB [auth 6], HB [auth 7], IB [auth 8], JB [auth 9], KB [auth AA]	788	Pakpunavirus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Li, F., Cingolani, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM140733

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release