6TBA

Virion of native gene transfer agent (GTA) particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of DNA delivery of a gene transfer agent.

Bardy, P.Fuzik, T.Hrebik, D.Pantucek, R.Thomas Beatty, J.Plevka, P.

(2020) Nat Commun 11: 3034-3034

  • DOI: https://doi.org/10.1038/s41467-020-16669-9
  • Primary Citation of Related Structures:  
    6TB9, 6TBA, 6TE8, 6TE9, 6TEA, 6TEB, 6TEH, 6TO8, 6TOA, 6TSU, 6TSV, 6TSW, 6TUI

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage major capsid protein, HK97 family
A [auth C5],
AA [auth G4],
AB [auth OO],
AD [auth HJ],
AE [auth AF],
AG [auth T9],
B [auth X4],
BA [auth B4],
BB [auth PO],
BD [auth IJ],
BE [auth BF],
BG [auth S9],
C [auth Y4],
CA [auth C4],
CB [auth WO],
CD [auth AJ],
CE [auth NE],
CG [auth K9],
D [auth Z4],
DB [auth UO],
DD [auth DJ],
DE [auth RE],
DG [auth J9],
E [auth A5],
EB [auth TO],
ED [auth EJ],
EE [auth ME],
EG [auth V9],
F [auth B5],
FB [auth SO],
FD [auth FJ],
FE [auth QE],
FG [auth L9],
G [auth N4],
GB [auth KO],
GC [auth CK],
GD [auth GJ],
GE [auth OE],
GG [auth H9],
H [auth R4],
HB [auth JO],
HC [auth XJ],
HD [auth BJ],
HE [auth PE],
HG [auth I9],
I [auth M4],
IB [auth VO],
IC [auth YJ],
ID [auth CJ],
IE [auth WE],
IG [auth A9],
J [auth Q4],
JB [auth LO],
JC [auth ZJ],
JE [auth UE],
JG [auth D9],
K [auth O4],
KB [auth HO],
KC [auth AK],
KE [auth TE],
KG [auth E9],
L [auth P4],
LB [auth IO],
LC [auth BK],
LE [auth SE],
LG [auth F9],
M [auth W4],
MB [auth AO],
MC [auth NJ],
ME [auth KE],
MF [auth CA],
MG [auth G9],
N [auth U4],
NB [auth DO],
NC [auth RJ],
NE [auth JE],
NF [auth X9],
NG [auth B9],
O [auth T4],
OB [auth EO],
OC [auth MJ],
OE [auth VE],
OF [auth Y9],
OG [auth C9],
P [auth S4],
PB [auth FO],
PC [auth QJ],
PE [auth LE],
PF [auth Z9],
Q [auth K4],
QA [auth CP],
QB [auth GO],
QC [auth OJ],
QE [auth HE],
QF [auth AA],
R [auth J4],
RA [auth XO],
RB [auth BO],
RC [auth PJ],
RE [auth IE],
RF [auth BA],
S [auth V4],
SA [auth YO],
SB [auth CO],
SC [auth WJ],
SE [auth AE],
SF [auth N9],
T [auth L4],
TA [auth ZO],
TC [auth UJ],
TE [auth DE],
TF [auth R9],
U [auth H4],
UA [auth AP],
UC [auth TJ],
UE [auth EE],
UF [auth M9],
V [auth I4],
VA [auth BP],
VC [auth SJ],
VE [auth FE],
VF [auth Q9],
W [auth A4],
WA [auth NO],
WC [auth KJ],
WD [auth CF],
WE [auth GE],
WF [auth O9],
X [auth D4],
XA [auth RO],
XC [auth JJ],
XD [auth XE],
XE [auth BE],
XF [auth P9],
Y [auth E4],
YA [auth MO],
YC [auth VJ],
YD [auth YE],
YE [auth CE],
YF [auth W9],
Z [auth F4],
ZA [auth QO],
ZC [auth LJ],
ZD [auth ZE],
ZF [auth U9]
385Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ3 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein84Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AR33 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5AR33
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein325Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AR34 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein197Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ4 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein Rcc01684396Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ0 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein135Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ6 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein112Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ5 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ5
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Phage major tail protein, TP901-1 family137Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinKJ [auth 7A],
QJ [auth 7C],
WJ [auth 7B]
296Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AU02 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinLJ [auth 8A],
RJ [auth 8C],
XJ [auth 8B]
1,304Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AU04 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5AU04
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein210Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AU01 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5AU01
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Czech Republic)Czech RepublicLQ1601
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0070
Ministry of Education (MoE, Czech Republic)Czech RepublicLM2011033
Czech Science FoundationCzech Republic15-21631Y
Czech Science FoundationCzech Republic18-17810S
European Molecular Biology Organization (EMBO)Czech Republic3041
Grant Agency of the Czech RepublicCzech Republic18-13064S

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Other
  • Version 1.2: 2021-07-14
    Changes: Derived calculations