6TBA image
Deposition Date 2019-11-01
Release Date 2020-07-22
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6TBA
Keywords:
VIRUS
Title:
Virion of native gene transfer agent (GTA) particle
Biological Source:
Source Organism(s):
Rhodobacter capsulatus SB 1003 (Taxon ID: 272942)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6TBA validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Portal protein Rcc01684
Gene (Uniprot):RCAP_rcc01684
Chain IDs:DH (auth: 1A), EH (auth: 1B), NH (auth: 1K), OH (auth: 1L), XH (auth: 1I), YH (auth: 1J), HI (auth: 1G), II (auth: 1H), RI (auth: 1E), SI (auth: 1F), BJ (auth: 1C), CJ (auth: 1D)
Chain Length:396
Number of Molecules:12
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ0 Pfam ID:PF04860
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01688
Chain IDs:CH (auth: 2A), FH (auth: 2B), MH (auth: 2K), PH (auth: 2L), WH (auth: 2I), ZH (auth: 2J), GI (auth: 2G), JI (auth: 2H), QI (auth: 2E), TI (auth: 2F), AJ (auth: 2C), DJ (auth: 2D)
Chain Length:197
Number of Molecules:12
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ4
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01689
Chain IDs:HH (auth: 3A), RH (auth: 3F), BI (auth: 3E), LI (auth: 3D), VI (auth: 3C), FJ (auth: 3B)
Chain Length:112
Number of Molecules:6
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ5 Pfam ID:PF05521
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01690
Chain IDs:GH (auth: 4A), QH (auth: 4F), AI (auth: 4E), KI (auth: 4D), UI (auth: 4C), EJ (auth: 4B)
Chain Length:135
Number of Molecules:6
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ6 Pfam ID:PF11367
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Phage major tail protein, TP901-1 family
Gene (Uniprot):RCAP_rcc01691
Chain IDs:IH (auth: 5A), JH (auth: 5S), KH (auth: 5G), LH (auth: 5M), SH (auth: 5F), TH (auth: 5X), UH (auth: 5L), VH (auth: 5R), CI (auth: 5E), DI (auth: 5W), EI (auth: 5K), FI (auth: 5Q), MI (auth: 5D), NI (auth: 5V), OI (auth: 5J), PI (auth: 5P), WI (auth: 5C), XI (auth: 5U), YI (auth: 5I), ZI (auth: 5O), GJ (auth: 5B), HJ (auth: 5T), IJ (auth: 5H), JJ (auth: 5N), OJ (auth: 5Y), PJ (auth: 5Z), UJ (auth: 52), VJ (auth: 53), AK (auth: 50), BK (auth: 51)
Chain Length:137
Number of Molecules:30
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ7 Pfam ID:PF06199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01695
Chain IDs:MJ (auth: 6B), NJ (auth: 6A), SJ (auth: 6F), TJ (auth: 6E), YJ (auth: 6D), ZJ (auth: 6C)
Chain Length:210
Number of Molecules:6
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5AU01 Pfam ID:PF09343
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01696
Chain IDs:KJ (auth: 7A), QJ (auth: 7C), WJ (auth: 7B)
Chain Length:296
Number of Molecules:3
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5AU02 Pfam ID:PF09931, PF09356
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01698
Chain IDs:LJ (auth: 8A), RJ (auth: 8C), XJ (auth: 8B)
Chain Length:1304
Number of Molecules:3
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5AU04 Pfam ID:PF13547, PF13550, PF23666
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Phage major capsid protein, HK97 family
Gene (Uniprot):RCAP_rcc01687
Chain IDs:A (auth: C5), B (auth: X4), C (auth: Y4), D (auth: Z4), E (auth: A5), F (auth: B5), G (auth: N4), H (auth: R4), I (auth: M4), J (auth: Q4), K (auth: O4), L (auth: P4), M (auth: W4), N (auth: U4), O (auth: T4), P (auth: S4), Q (auth: K4), R (auth: J4), S (auth: V4), T (auth: L4), U (auth: H4), V (auth: I4), W (auth: A4), X (auth: D4), Y (auth: E4), Z (auth: F4), AA (auth: G4), BA (auth: B4), CA (auth: C4), QA (auth: CP), RA (auth: XO), SA (auth: YO), TA (auth: ZO), UA (auth: AP), VA (auth: BP), WA (auth: NO), XA (auth: RO), YA (auth: MO), ZA (auth: QO), AB (auth: OO), BB (auth: PO), CB (auth: WO), DB (auth: UO), EB (auth: TO), FB (auth: SO), GB (auth: KO), HB (auth: JO), IB (auth: VO), JB (auth: LO), KB (auth: HO), LB (auth: IO), MB (auth: AO), NB (auth: DO), OB (auth: EO), PB (auth: FO), QB (auth: GO), RB (auth: BO), SB (auth: CO), GC (auth: CK), HC (auth: XJ), IC (auth: YJ), JC (auth: ZJ), KC (auth: AK), LC (auth: BK), MC (auth: NJ), NC (auth: RJ), OC (auth: MJ), PC (auth: QJ), QC (auth: OJ), RC (auth: PJ), SC (auth: WJ), TC (auth: UJ), UC (auth: TJ), VC (auth: SJ), WC (auth: KJ), XC (auth: JJ), YC (auth: VJ), ZC (auth: LJ), AD (auth: HJ), BD (auth: IJ), CD (auth: AJ), DD (auth: DJ), ED (auth: EJ), FD (auth: FJ), GD (auth: GJ), HD (auth: BJ), ID (auth: CJ), WD (auth: CF), XD (auth: XE), YD (auth: YE), ZD (auth: ZE), AE (auth: AF), BE (auth: BF), CE (auth: NE), DE (auth: RE), EE (auth: ME), FE (auth: QE), GE (auth: OE), HE (auth: PE), IE (auth: WE), JE (auth: UE), KE (auth: TE), LE (auth: SE), ME (auth: KE), NE (auth: JE), OE (auth: VE), PE (auth: LE), QE (auth: HE), RE (auth: IE), SE (auth: AE), TE (auth: DE), UE (auth: EE), VE (auth: FE), WE (auth: GE), XE (auth: BE), YE (auth: CE), MF (auth: CA), NF (auth: X9), OF (auth: Y9), PF (auth: Z9), QF (auth: AA), RF (auth: BA), SF (auth: N9), TF (auth: R9), UF (auth: M9), VF (auth: Q9), WF (auth: O9), XF (auth: P9), YF (auth: W9), ZF (auth: U9), AG (auth: T9), BG (auth: S9), CG (auth: K9), DG (auth: J9), EG (auth: V9), FG (auth: L9), GG (auth: H9), HG (auth: I9), IG (auth: A9), JG (auth: D9), KG (auth: E9), LG (auth: F9), MG (auth: G9), NG (auth: B9), OG (auth: C9)
Chain Length:385
Number of Molecules:145
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5ATZ3 Pfam ID:PF05065
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01079
Chain IDs:DA (auth: E3), EA (auth: D3), FA (auth: A3), GA (auth: C3), HA (auth: B3), JA (auth: A1), KA (auth: E2), LA (auth: D2), MA (auth: A2), NA (auth: C2), OA (auth: B2), TB (auth: EN), UB (auth: DN), VB (auth: AN), WB (auth: CN), XB (auth: BN), ZB (auth: AL), AC (auth: EM), BC (auth: DM), CC (auth: AM), DC (auth: CM), EC (auth: BM), JD (auth: EI), KD (auth: DI), LD (auth: AI), MD (auth: CI), ND (auth: BI), PD (auth: AG), QD (auth: EH), RD (auth: DH), SD (auth: AH), TD (auth: CH), UD (auth: BH), ZE (auth: ED), AF (auth: DD), BF (auth: AD), CF (auth: CD), DF (auth: BD), FF (auth: AB), GF (auth: EC), HF (auth: DC), IF (auth: AC), JF (auth: CC), KF (auth: BC), PG (auth: E8), QG (auth: D8), RG (auth: A8), SG (auth: C8), TG (auth: B8), VG (auth: A6), WG (auth: E7), XG (auth: D7), YG (auth: A7), ZG (auth: C7), AH (auth: B7)
Chain Length:84
Number of Molecules:55
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5AR33
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):RCAP_rcc01080
Chain IDs:IA (auth: F3), PA (auth: F2), YB (auth: FN), FC (auth: FM), OD (auth: FI), VD (auth: FH), EF (auth: FD), LF (auth: FC), UG (auth: F8), BH (auth: F7)
Chain Length:325
Number of Molecules:10
Biological Source:Rhodobacter capsulatus SB 1003
UniProt ID:D5AR34
Ligand Molecules
SF4
Primary Citation
Structure and mechanism of DNA delivery of a gene transfer agent.
Nat Commun 11 3034 3034 (2020)
PMID: 32541663 DOI: 10.1038/s41467-020-16669-9

Abstact

Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.

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Primary Citation of related structures
6TUI
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