8EXH | pdb_00008exh

Agrobacterium tumefaciens Tpilus

PDB DOI: https://doi.org/10.2210/pdb8EXH/pdb
EM Map EMD-28657: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Agrobacterium fabrum str. C58
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2022-10-25 Released: 2023-03-22
Deposition Author(s): Beltran, L.C., Egelman, E.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Beltran, L.C., Cvirkaite-Krupovic, V., Miller, J., Wang, F., Kreutzberger, M.A.B., Patkowski, J.B., Costa, T.R.D., Schouten, S., Levental, I., Conticello, V.P., Egelman, E.H., Krupovic, M.

(2023) Nat Commun 14: 666-666

PubMed: 36750723 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-36349-8
Primary Citation Related Structures:
8DFT, 8DFU, 8EXH

PubMed Abstract:
Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

Organizational Affiliation

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.

Macromolecule Content

Total Structure Weight: 295.87 kDa
Atom Count: 20,640
Modeled Residue Count: 2,760
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein virB2	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, P, Q, R, S, T, U, V, W, X, Y, Z	69	Agrobacterium fabrum str. C58	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P17792 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore P17792 Go to UniProtKB: P17792
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X3D (Subject of Investigation/LOI) Query on X3D Download:Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain DB [auth P] SDF format, chain FB [auth R] SDF format, chain HB [auth T] SDF format, chain IB [auth U] SDF format, chain LB [auth X] SDF format, chain MB [auth Y] SDF format, chain NB [auth Z] SDF format, chain PB [auth b] SDF format, chain QA [auth C] SDF format, chain QB [auth c] SDF format, chain RA [auth D] SDF format, chain SA [auth E] SDF format, chain SB [auth e] SDF format, chain TB [auth f] SDF format, chain UA [auth G] SDF format, chain VB [auth h] SDF format, chain WA [auth I] SDF format, chain ZA [auth L] SDF format, chain ZB [auth l] SDF format, chain YB [auth k] SDF format, chain YA [auth K] SDF format, chain XB [auth j] SDF format, chain XA [auth J] SDF format, chain WB [auth i] SDF format, chain VA [auth H] SDF format, chain UB [auth g] SDF format, chain TA [auth F] SDF format, chain RB [auth d] SDF format, chain PA [auth B] SDF format, chain OB [auth a] SDF format, chain OA [auth A] SDF format, chain KB [auth W] SDF format, chain JB [auth V] SDF format, chain GB [auth S] SDF format, chain EB [auth Q] SDF format, chain CB [auth O] SDF format, chain BC [auth n] SDF format, chain BB [auth N] SDF format, chain AC [auth m] MOL2 format, chain AB [auth M] MOL2 format, chain DB [auth P] MOL2 format, chain FB [auth R] MOL2 format, chain HB [auth T] MOL2 format, chain IB [auth U] MOL2 format, chain LB [auth X] MOL2 format, chain MB [auth Y] MOL2 format, chain NB [auth Z] MOL2 format, chain PB [auth b] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth c] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth e] MOL2 format, chain TB [auth f] MOL2 format, chain UA [auth G] MOL2 format, chain VB [auth h] MOL2 format, chain WA [auth I] MOL2 format, chain ZA [auth L] MOL2 format, chain ZB [auth l] MOL2 format, chain YB [auth k] MOL2 format, chain YA [auth K] MOL2 format, chain XB [auth j] MOL2 format, chain XA [auth J] MOL2 format, chain WB [auth i] MOL2 format, chain VA [auth H] MOL2 format, chain UB [auth g] MOL2 format, chain TA [auth F] MOL2 format, chain RB [auth d] MOL2 format, chain PA [auth B] MOL2 format, chain OB [auth a] MOL2 format, chain OA [auth A] MOL2 format, chain KB [auth W] MOL2 format, chain JB [auth V] MOL2 format, chain GB [auth S] MOL2 format, chain EB [auth Q] MOL2 format, chain CB [auth O] MOL2 format, chain BC [auth n] MOL2 format, chain BB [auth N] MOL2 format, chain AC [auth m] mmCIF format, chain AB [auth M] mmCIF format, chain DB [auth P] mmCIF format, chain FB [auth R] mmCIF format, chain HB [auth T] mmCIF format, chain IB [auth U] mmCIF format, chain LB [auth X] mmCIF format, chain MB [auth Y] mmCIF format, chain NB [auth Z] mmCIF format, chain PB [auth b] mmCIF format, chain QA [auth C] mmCIF format, chain QB [auth c] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth e] mmCIF format, chain TB [auth f] mmCIF format, chain UA [auth G] mmCIF format, chain VB [auth h] mmCIF format, chain WA [auth I] mmCIF format, chain ZA [auth L] mmCIF format, chain ZB [auth l] mmCIF format, chain YB [auth k] mmCIF format, chain YA [auth K] mmCIF format, chain XB [auth j] mmCIF format, chain XA [auth J] mmCIF format, chain WB [auth i] mmCIF format, chain VA [auth H] mmCIF format, chain UB [auth g] mmCIF format, chain TA [auth F] mmCIF format, chain RB [auth d] mmCIF format, chain PA [auth B] mmCIF format, chain OB [auth a] mmCIF format, chain OA [auth A] mmCIF format, chain KB [auth W] mmCIF format, chain JB [auth V] mmCIF format, chain GB [auth S] mmCIF format, chain EB [auth Q] mmCIF format, chain CB [auth O] mmCIF format, chain BC [auth n] mmCIF format, chain BB [auth N] mmCIF format, chain AC [auth m]	AB [auth M] AC [auth m] BB [auth N] BC [auth n] CB [auth O] AB [auth M], AC [auth m], BB [auth N], BC [auth n], CB [auth O], DB [auth P], EB [auth Q], FB [auth R], GB [auth S], HB [auth T], IB [auth U], JB [auth V], KB [auth W], LB [auth X], MB [auth Y], NB [auth Z], OA [auth A], OB [auth a], PA [auth B], PB [auth b], QA [auth C], QB [auth c], RA [auth D], RB [auth d], SA [auth E], SB [auth e], TA [auth F], TB [auth f], UA [auth G], UB [auth g], VA [auth H], VB [auth h], WA [auth I], WB [auth i], XA [auth J], XB [auth j], YA [auth K], YB [auth k], ZA [auth L], ZB [auth l]	(14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate C₃₀ H₆₀ N O₈ P BMOFTHAXXFOIRF-NDEPHWFRSA-N		Interactions Focus chain AB [auth M] Focus chain AC [auth m] Focus chain BB [auth N] Focus chain BC [auth n] Focus chain CB [auth O] Focus chain DB [auth P] Focus chain EB [auth Q] Focus chain FB [auth R] Focus chain GB [auth S] Focus chain HB [auth T] Focus chain IB [auth U] Focus chain JB [auth V] Focus chain KB [auth W] Focus chain LB [auth X] Focus chain MB [auth Y] Focus chain NB [auth Z] Focus chain OA [auth A] Focus chain OB [auth a] Focus chain PA [auth B] Focus chain PB [auth b] Focus chain QA [auth C] Focus chain QB [auth c] Focus chain RA [auth D] Focus chain RB [auth d] Focus chain SA [auth E] Focus chain SB [auth e] Focus chain TA [auth F] Focus chain TB [auth f] Focus chain UA [auth G] Focus chain UB [auth g] Focus chain VA [auth H] Focus chain VB [auth h] Focus chain WA [auth I] Focus chain WB [auth i] Focus chain XA [auth J] Focus chain XB [auth j] Focus chain YA [auth K] Focus chain YB [auth k] Focus chain ZA [auth L] Focus chain ZB [auth l] Interactions & Density Focus chain AB [auth M] Focus chain AC [auth m] Focus chain BB [auth N] Focus chain BC [auth n] Focus chain CB [auth O] Focus chain DB [auth P] Focus chain EB [auth Q] Focus chain FB [auth R] Focus chain GB [auth S] Focus chain HB [auth T] Focus chain IB [auth U] Focus chain JB [auth V] Focus chain KB [auth W] Focus chain LB [auth X] Focus chain MB [auth Y] Focus chain NB [auth Z] Focus chain OA [auth A] Focus chain OB [auth a] Focus chain PA [auth B] Focus chain PB [auth b] Focus chain QA [auth C] Focus chain QB [auth c] Focus chain RA [auth D] Focus chain RB [auth d] Focus chain SA [auth E] Focus chain SB [auth e] Focus chain TA [auth F] Focus chain TB [auth f] Focus chain UA [auth G] Focus chain UB [auth g] Focus chain VA [auth H] Focus chain VB [auth h] Focus chain WA [auth I] Focus chain WB [auth i] Focus chain XA [auth J] Focus chain XB [auth j] Focus chain YA [auth K] Focus chain YB [auth k] Focus chain ZA [auth L] Focus chain ZB [auth l]