9D9W

Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model

• PDB DOI: https://doi.org/10.2210/pdb9D9W/pdb
• EM Map EMD-46681: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Mycobacterium phage Bxb1
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2024-10-09 
• Deposition Author(s): Freeman, K.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), National Institutes of Health/Office of the Director, Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and infection dynamics of mycobacteriophage Bxb1

Freeman, K.G., Mondal, S., Macale, L.S., Podgorski, J., White, S.J., Silva, B., Ortiz, V., Huet, A., Narsico, J.T., Ho, M.C., Jacobs-Sera, D., Lowary, T.L., Conway, J.F., Park, D., Hatfull, G.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 42-mer - A30B12 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 30-mer - A30 Local Symmetry: Cyclic - C12  (Explore in 3D)
Local Stoichiometry: Homo 12-mer - B12 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,902.13 kDa 
• Atom Count: 130,467 
• Modelled Residue Count: 17,270 
• Deposited Residue Count: 17,766 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A [auth Aa], AA [auth Ec], B [auth Ab], BA [auth Ed], C [auth Ac], CA [auth Ee], D [auth Ad], DA [auth Ef], E [auth Ae], F [auth Af], G [auth Ba], H [auth Bb], I [auth Bc], J [auth Bd], K [auth Be], L [auth Bf], M [auth Ca], N [auth Cb], O [auth Cc], P [auth Cd], Q [auth Ce], R [auth Cf], S [auth Da], T [auth Db], U [auth Dc], V [auth Dd], W [auth De], X [auth Df], Y [auth Ea], Z [auth Eb]	397	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0A7 (Mycobacterium phage Bxb1) Explore Q9B0A7  Go to UniProtKB:  Q9B0A7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	EA [auth Fa], FA [auth Fb], GA [auth Fc], HA [auth Fd], IA [auth Fe], JA [auth Ff], KA [auth Fg], LA [auth Fh], MA [auth Fi], NA [auth Fj], OA [auth Fk], PA [auth Fl]	488	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0B0 (Mycobacterium phage Bxb1) Explore Q9B0B0  Go to UniProtKB:  Q9B0B0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Freeman, K.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	K99AI173544
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116884
Howard Hughes Medical Institute (HHMI)	United States	GT12053
National Institutes of Health/Office of the Director	United States	S10 OD025009
National Institutes of Health/Office of the Director	United States	S10 OD019995
National Institutes of Health/Office of the Director	United States	S10OD032467
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM129547
Academia Sinica (Taiwan)	Taiwan	AS-IDR-110-06

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release