9D94

Mycobacteriophage Bxb1 portal and connector assembly - Composite map and model

• PDB DOI: https://doi.org/10.2210/pdb9D94/pdb
• EM Map EMD-46669: EMDB EMDataResource

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


• Deposited: 2024-08-20 Released: 2024-09-25 
• 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)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 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: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A12B12C12D6E6 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,359.87 kDa 
• Atom Count: 91,614 
• Modelled Residue Count: 11,816 
• Deposited Residue Count: 12,396 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A [auth Fa], B [auth Fb], C [auth Fc], D [auth Fd], E [auth Fe], F [auth Ff], G [auth Fg], H [auth Fh], I [auth Fi], J [auth Fj], K [auth Fk], L [auth Fl]	488	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0B0 (Mycobacterium phage Bxb1) Explore Q9B0B0  Go to UniProtKB:  Q9B0B0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Head-to-tail adaptor	M [auth Ga], N [auth Gb], O [auth Gc], P [auth Gd], Q [auth Ge], R [auth Gf], S [auth Gg], T [auth Gh], U [auth Gi], V [auth Gj], W [auth Gk], X [auth Gl]	125	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0A6 (Mycobacterium phage Bxb1) Explore Q9B0A6  Go to UniProtKB:  Q9B0A6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Head-to-tail stopper	AA [auth Hc], BA [auth Hd], CA [auth He], DA [auth Hf], Y [auth Ha], Z [auth Hb]	126	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0A5 (Mycobacterium phage Bxb1) Explore Q9B0A5  Go to UniProtKB:  Q9B0A5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail terminator	EA [auth Ia], FA [auth Ib], GA [auth Ic], HA [auth Id], IA [auth Ie], JA [auth If]	148	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for A0A345MFM5 (Mycobacterium phage NEHalo) Explore A0A345MFM5  Go to UniProtKB:  A0A345MFM5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail protein	KA [auth Ja], LA [auth Jb], MA [auth Jc], NA [auth Jd], OA [auth Je], PA [auth Jf], QA [auth Jg], RA [auth Jh], SA [auth Ji], TA [auth Jj], UA [auth Jk], VA [auth Jl]	283	Mycobacterium phage Bxb1	Mutation(s): 0
UniProt
Find proteins for Q9B0A2 (Mycobacterium phage Bxb1) Explore Q9B0A2  Go to UniProtKB:  Q9B0A2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 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: 2024-09-25 
Deposition Author(s): Freeman, K.G.

---

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: 2024-09-25
  Type: Initial release