8CUE

CryoEM structure of the T-pilus from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the Agrobacterium tumefaciens T-pilus reveals the importance of positive charges in the lumen.

Amro, J.Black, C.Jemouai, Z.Rooney, N.Daneault, C.Zeytuni, N.Ruiz, M.Bui, K.H.Baron, C.

(2023) Structure 31: 375-384.e4

  • DOI: https://doi.org/10.1016/j.str.2022.11.007
  • Primary Citation of Related Structures:  
    8CUE, 8CW4

  • PubMed Abstract: 

    Agrobacterium tumefaciens is a natural genetic engineer that transfers DNA into plants, which is the most applied process for generation of genetically modified plants. DNA transfer is mediated by a type IV secretion system in the cell envelope and extracellular T-pili. We here report the cryo-electron microscopic structures of the T-pilus at 3.2-Å resolution and of the plasmid pKM101-determined N-pilus at 3-Å resolution. Both pili contain a main pilus protein (VirB2 in A. tumefaciens, TraM in pKM101) and phospholipids arranged in a five-start helical assembly. They contain positively charged amino acids in the lumen, and the lipids are positively charged in the T-pilus (phosphatidylcholine) conferring overall positive charge. Mutagenesis of the lumen-exposed Arg91 in VirB2 results in protein destabilization and loss of pilus formation. Our results reveal that different phospholipids can be incorporated into type IV secretion pili and that the charge of the lumen may be of functional importance.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec, QC, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein virB2121Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for P17792 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P17792 
Go to UniProtKB:  P17792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17792
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL (Subject of Investigation/LOI)
Query on CPL

Download Ideal Coordinates CCD File 
AC [auth 1I]
AD [auth 3G]
AE [auth 5E]
BC [auth 1J]
BD [auth 3H]
AC [auth 1I],
AD [auth 3G],
AE [auth 5E],
BC [auth 1J],
BD [auth 3H],
BE [auth 5F],
CC [auth 1K],
CD [auth 3I],
CE [auth 5G],
DC [auth 1L],
DD [auth 3J],
DE [auth 5H],
EC [auth 1M],
ED [auth 3K],
EE [auth 5I],
FC [auth 1N],
FD [auth 3L],
FE [auth 5J],
GC [auth 2A],
GD [auth 3M],
GE [auth 5K],
HC [auth 2B],
HD [auth 3N],
HE [auth 5L],
IC [auth 2C],
ID [auth 4A],
IE [auth 5M],
JC [auth 2D],
JD [auth 4B],
JE [auth 5N],
KC [auth 2E],
KD [auth 4C],
LC [auth 2F],
LD [auth 4D],
MC [auth 2G],
MD [auth 4E],
NC [auth 2H],
ND [auth 4F],
OC [auth 2I],
OD [auth 4G],
PC [auth 2J],
PD [auth 4H],
QC [auth 2K],
QD [auth 4I],
RC [auth 2L],
RD [auth 4J],
SB [auth 1A],
SC [auth 2M],
SD [auth 4K],
TB [auth 1B],
TC [auth 2N],
TD [auth 4L],
UB [auth 1C],
UC [auth 3A],
UD [auth 4M],
VB [auth 1D],
VC [auth 3B],
VD [auth 4N],
WB [auth 1E],
WC [auth 3C],
WD [auth 5A],
XB [auth 1F],
XC [auth 3D],
XD [auth 5B],
YB [auth 1G],
YC [auth 3E],
YD [auth 5C],
ZB [auth 1H],
ZC [auth 3F],
ZD [auth 5D]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1
MODEL REFINEMENTPHENIX1.19.2
MODEL REFINEMENTCoot0.9.5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references