9T9V | pdb_00009t9v

Structure of bacteriophage NO16

• PDB DOI: https://doi.org/10.2210/pdb9T9V/pdb
• EM Map EMD-55739: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Vibrio phage fNo16
• Mutation(s): No 


• Deposited: 2025-11-17 Released: 2026-08-19 
• Deposition Author(s): Otaegi-Ugartemendia, S., Condezo, G.N., Martinez, M., Kalatzis, P.G., Middelboe, M., San Martin, C.
• Funding Organization(s): Agencia Estatal de Investigacion (AEI), European Regional Development Fund, Other government, Ministerio de Ciencia e Innovacion (MCIN), European Union (EU), Danish National Research Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of NO16, a marine non-tailed vibriophage with an unusual symmetry-mismatched vertex arrangement

Otaegi-Ugartemendia, S., Condezo, G.N., Martinez, M., Kalatzis, P.G., Middelboe, M., San Martin, C.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 900-mer - A600B120C60D60E60 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 900-mer - AA600AB180AC60AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1BK1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 337.57 kDa 
• Atom Count: 22,072 
• Modeled Residue Count: 2,865 
• Deposited Residue Count: 3,088 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double jelly roll capsid protein	A, B, C, D, E, F, G, H, I, J	265	Vibrio phage fNo16	Mutation(s): 0
UniProt
Find proteins for A0A3G1SVL0 (Vibrio phage fNo16) Explore A0A3G1SVL0  Go to UniProtKB:  A0A3G1SVL0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Penton base (GP14)	K	180	Vibrio phage fNo16	Mutation(s): 0
UniProt
Find proteins for A0A3G1SVM6 (Vibrio phage fNo16) Explore A0A3G1SVM6  Go to UniProtKB:  A0A3G1SVM6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LPXTG cell wall anchor domain-containing protein	L, M, N	82	Vibrio phage fNo16	Mutation(s): 0
UniProt
Find proteins for A0A3G1SVN4 (Vibrio phage fNo16) Explore A0A3G1SVN4  Go to UniProtKB:  A0A3G1SVN4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown1	O	12	Vibrio phage fNo16	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	P [auth A], Q [auth E], R [auth I], S [auth J]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-19 
Deposition Author(s): Otaegi-Ugartemendia, S., Condezo, G.N., Martinez, M., Kalatzis, P.G., Middelboe, M., San Martin, C.

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Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	AEI/10.13039/501100011033
European Regional Development Fund	European Union	PID2019-104098GB-I00
European Regional Development Fund	European Union	PID2022-136456NB-I00
Agencia Estatal de Investigacion (AEI)	Spain	SEV-2017-0712
Agencia Estatal de Investigacion (AEI)	Spain	CEX2023-001386-S
Other government		JAE-SOMdM20-20
Ministerio de Ciencia e Innovacion (MCIN)	Spain	FPU2020-05148
European Union (EU)	European Union	101084204
Other government		2105-00014B
Danish National Research Foundation	Denmark	DNRF145

Revision History  

• Version 1.0: 2026-08-19
  Type: Initial release