8RTD

Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.

• PDB DOI: https://doi.org/10.2210/pdb8RTD/pdb
• EM Map EMD-19488: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-25 Released: 2024-06-19 
• Deposition Author(s): Mace, K., Waksman, G.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a conjugative type 4 secretion system identifies a molecular switch regulating conjugative pilus biogenesis

Mace, K., Waksman, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 34-mer - A5B5C5D5E3F3G2H2I1J1K1L1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 34-mer - A5B5C5D4E3F3G2H1I1J1K1L1M1N1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - C5 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - G2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - H2 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Hetero 10-mer - A5B5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,339 kDa 
• Atom Count: 40,078 
• Modelled Residue Count: 8,254 
• Deposited Residue Count: 12,062 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwJ protein	A, C [auth B], E [auth C], G [auth K], I [auth E]	229	Escherichia coli	Mutation(s): 0  Gene Names: trwJ
UniProt
Find proteins for A8R752 (Salmonella dublin) Explore A8R752  Go to UniProtKB:  A8R752

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwG protein	AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	231	Escherichia coli	Mutation(s): 0  Gene Names: trwG
UniProt
Find proteins for A8R756 (Salmonella dublin) Explore A8R756  Go to UniProtKB:  A8R756

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwE protein	DA [auth e], H [auth a], Z	395	Escherichia coli	Mutation(s): 0  Gene Names: trwE
UniProt
Find proteins for A8R758 (Salmonella dublin) Explore A8R758  Go to UniProtKB:  A8R758

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwI protein	J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	342	Escherichia coli	Mutation(s): 0  Gene Names: trwI
UniProt
Find proteins for A8R754 (Salmonella dublin) Explore A8R754  Go to UniProtKB:  A8R754

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TrwM protein	EA [auth f], L [auth j], S [auth R]	104	Escherichia coli	Mutation(s): 0  Gene Names: trwM
UniProt
Find proteins for A8R750 (Salmonella dublin) Explore A8R750  Go to UniProtKB:  A8R750

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Type IV secretion system protein virB4	FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	823	Escherichia coli	Mutation(s): 0  Gene Names: trwK
UniProt
Find proteins for A8R751 (Salmonella dublin) Explore A8R751  Go to UniProtKB:  A8R751

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Mace, K., Waksman, G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098302
Wellcome Trust	United Kingdom	217089
Wellcome Trust	United Kingdom	202679/Z/16/Z
Wellcome Trust	United Kingdom	206166/Z/17/Z

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release