7SPB | pdb_00007spb

Models for C13 reconstruction of Outer Membrane Core Complex (OMCC) of Type IV Secretion System (T4SS) encoded by F-plasmid (pED208).

• PDB DOI: https://doi.org/10.2210/pdb7SPB/pdb
• EM Map EMD-24769: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2021-11-02 Released: 2022-02-02 
• Deposition Author(s): Liu, X., Khara, P., Baker, M.L., Christie, P.J., Hu, B.
• 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: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids

Liu, X., Khara, P., Baker, M.L., Christie, P.J., Hu, B.

(2022) Nat Commun 13: 379

• DOI: https://doi.org/10.1038/s41467-022-28058-5

Biological Assembly 1  

Global Symmetry: Cyclic - C13  (Explore in 3D)
Global Stoichiometry: Hetero 78-mer - A26B26C26 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 78-mer - A26B13C13D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,478.76 kDa 
• Atom Count: 57,408 
• Modelled Residue Count: 7,488 
• Deposited Residue Count: 23,478 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TraV	A [auth A1], B [auth A2], C [auth A3], D [auth A4], E [auth A5], F [auth A6], G [auth A7], H [auth A8], I [auth A9], J [auth A10], K [auth A11], L [auth A12], M [auth A13], N [auth B1], O [auth B2], P [auth B3], Q [auth B4], R [auth B5], S [auth B6], T [auth B7], U [auth B8], V [auth B9], W [auth B10], X [auth B11], Y [auth B12], Z [auth B13]	204	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8KNL2 (Salmonella typhi) Explore Q8KNL2  Go to UniProtKB:  Q8KNL2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TraK	AA [auth C1], BA [auth C2], CA [auth C3], DA [auth C4], EA [auth C5], FA [auth C6], GA [auth C7], HA [auth C8], IA [auth C9], JA [auth C10], KA [auth C11], LA [auth C12], MA [auth C13], NA [auth D1], OA [auth D2], PA [auth D3], QA [auth D4], RA [auth D5], SA [auth D6], TA [auth D7], UA [auth D8], VA [auth D9], WA [auth D10], XA [auth D11], YA [auth D12], ZA [auth D13]	246	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8KNL8 (Salmonella typhi) Explore Q8KNL8  Go to UniProtKB:  Q8KNL8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TraB	AB [auth E1], BB [auth E2], CB [auth E3], DB [auth E4], EB [auth E5], FB [auth E6], GB [auth E7], HB [auth E8], IB [auth E9], JB [auth E10], KB [auth E11], LB [auth E12], MB [auth E13], NB [auth F1], OB [auth F2], PB [auth F3], QB [auth F4], RB [auth F5], SB [auth F6], TB [auth F7], UB [auth F8], VB [auth F9], WB [auth F10], XB [auth F11], YB [auth F12], ZB [auth F13]	453	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0
UniProt
Find proteins for Q8KNL7 (Salmonella typhi) Explore Q8KNL7  Go to UniProtKB:  Q8KNL7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Liu, X., Khara, P., Baker, M.L., Christie, P.J., Hu, B.

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

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection