9KMH | pdb_00009kmh

The Composite Cryo-EM Structure of the Portal Vertex of Bacteriophage FCWL1

• PDB DOI: https://doi.org/10.2210/pdb9KMH/pdb
• EM Map EMD-62433: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage FCWL1
• Mutation(s): No 


• Deposited: 2024-11-16 Released: 2025-01-22 
• Deposition Author(s): Cai, C., Wang, Y., Liu, Y., Shao, Q., Wang, A., Fang, Q.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Literature

Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage

Cai, C., Wang, Y., Liu, Y., Shao, Q., Wang, A., Li, L., Zheng, Y., Zhang, T., Luo, Z., Yang, C., Fang, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 107-mer - A30B30C12D12E6F6G6H5 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 107-mer - A35B30C12D12E6F6G6 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - H5 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Hetero 60-mer - A30B30 Local Symmetry: Cyclic - C12  (Explore in 3D)
Local Stoichiometry: Hetero 24-mer - C12D12 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Hetero 42-mer - C12D12E6F6G6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,810.48 kDa 
• Atom Count: 179,175 
• Modelled Residue Count: 23,085 
• Deposited Residue Count: 25,455 
• Unique protein chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A [auth aa], BB [auth cf], CB [auth cg], DA [auth bf], DB [auth ch], EA [auth bg], EB [auth ci], F [auth af], FA [auth bh], FB [auth cj], G [auth ag], GA [auth bi], H [auth ah], HA [auth bj], I [auth ai], J [auth aj], KA [auth bn], M [auth an], PA [auth bs], QA [auth bt], R [auth as], RA [auth bu], S [auth at], SA [auth bv], T [auth au], TA [auth bw], U [auth av], V [auth aw], WA [auth ca], Y [auth ba]	319	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MTV7 (Escherichia phage FCWL1) Explore A0AAX4MTV7  Go to UniProtKB:  A0AAX4MTV7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Decoration protein	AA [auth bc], AB [auth ce], B [auth ab], BA [auth bd], C [auth ac], CA [auth be], D [auth ad], E [auth ae], GB [auth cl], HB [auth cm], IA [auth bl], JA [auth bm], K [auth al], L [auth am], LA [auth bo], MA [auth bp], N [auth ao], NA [auth bq], O [auth ap], OA [auth br], P [auth aq], Q [auth ar], UA [auth by], VA [auth bz], W [auth ay], X [auth az], XA [auth cb], YA [auth cc], Z [auth bb], ZA [auth cd]	158	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MUC4 (Escherichia phage FCWL1) Explore A0AAX4MUC4  Go to UniProtKB:  A0AAX4MUC4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	EC [auth dj], IB [auth cn], JB [auth co], KB [auth cp], LB [auth cq], PC [auth du], TB [auth cy], TC [auth dy], UC [auth dz], VC [auth ea], WC [auth eb], XC [auth ec]	444	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MU40 (Escherichia phage FCWL1) Explore A0AAX4MU40  Go to UniProtKB:  A0AAX4MU40

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminator protein	MB [auth cr], NB [auth cs], OB [auth ct], PB [auth cu], QB [auth cv], RB [auth cw]	132	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MU51 (Escherichia phage FCWL1) Explore A0AAX4MU51  Go to UniProtKB:  A0AAX4MU51

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Adaptor protein	AC [auth df], BC [auth dg], CC [auth dh], DC [auth di], FC [auth dk], SB [auth cx], UB [auth cz], VB [auth da], WB [auth db], XB [auth dc], YB [auth dd], ZB [auth de]	140	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MUE8 (Escherichia phage FCWL1) Explore A0AAX4MUE8  Go to UniProtKB:  A0AAX4MUE8

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein	GC [auth dl], HC [auth dm], IC [auth dn], JC [auth do], KC [auth dp], LC [auth dq]	222	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MUP2 (Escherichia phage FCWL1) Explore A0AAX4MUP2  Go to UniProtKB:  A0AAX4MUP2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Connector protein	MC [auth dr], NC [auth ds], OC [auth dt], QC [auth dv], RC [auth dw], SC [auth dx]	123	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MUS4 (Escherichia phage FCWL1) Explore A0AAX4MUS4  Go to UniProtKB:  A0AAX4MUS4

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Decoration protein gp29	AD [auth bx], BD [auth ck], CD [auth ax], YC [auth ak], ZC [auth bk]	255	Escherichia phage FCWL1	Mutation(s): 0
UniProt
Find proteins for A0AAX4MTZ1 (Escherichia phage FCWL1) Explore A0AAX4MTZ1  Go to UniProtKB:  A0AAX4MTZ1

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	1.19.2-4158-000

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Cai, C., Wang, Y., Liu, Y., Shao, Q., Wang, A., Fang, Q.

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Funding Organization	Location	Grant Number
Other government		D2301008
National Natural Science Foundation of China (NSFC)	China	32371285

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release