3JC9

Architectural model of the type IVa pilus machine in a non-piliated state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of the type IVa pilus machine.

Chang, Y.W.Rettberg, L.A.Treuner-Lange, A.Iwasa, J.Sgaard-Andersen, L.Jensen, G.J.

(2016) Science 351: aad2001-aad2001

  • DOI: https://doi.org/10.1126/science.aad2001
  • Primary Citation of Related Structures:  
    3JC8, 3JC9

  • PubMed Abstract: 

    Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.


  • Organizational Affiliation

    University of Utah, Salt Lake City, UT 84112, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PilAA [auth Aa],
B [auth Ab],
C [auth Ac],
D [auth Ad],
E [auth Ae]
158Myxococcus xanthus DK 1622Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PilCF [auth Ca],
G [auth Cb]
417Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
Find proteins for Q1D0A0 (Myxococcus xanthus (strain DK1622))
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Go to UniProtKB:  Q1D0A0
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UniProt GroupQ1D0A0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PilN225Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
Find proteins for Q306N5 (Myxococcus xanthus (strain DK1622))
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UniProt GroupQ306N5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PilO205Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
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UniProt GroupQ306N4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PilM395Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
Find proteins for Q1D0B0 (Myxococcus xanthus (strain DK1622))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PilQ901Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
Find proteins for Q9ZFG1 (Myxococcus xanthus (strain DK1622))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PilP172Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
TsaP411Myxococcus xanthus DK 1622Mutation(s): 0 
UniProt
Find proteins for Q1D813 (Myxococcus xanthus (strain DK1622))
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
CC [auth Ma]
EC [auth Mb]
GC [auth Mc]
IC [auth Md]
KC [auth Me]
CC [auth Ma],
EC [auth Mb],
GC [auth Mc],
IC [auth Md],
KC [auth Me],
MC [auth Mf],
OC [auth Mg],
QC [auth Mh],
SC [auth Mi],
UC [auth Mj],
WC [auth Mk],
YC [auth Ml]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

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BC [auth Ma]
DC [auth Mb]
FC [auth Mc]
HC [auth Md]
JC [auth Me]
BC [auth Ma],
DC [auth Mb],
FC [auth Mc],
HC [auth Md],
JC [auth Me],
LC [auth Mf],
NC [auth Mg],
PC [auth Mh],
RC [auth Mi],
TC [auth Mj],
VC [auth Mk],
XC [auth Ml]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
A [auth Aa],
B [auth Ab],
C [auth Ac],
D [auth Ad],
E [auth Ae]
L-PEPTIDE LINKINGC10 H13 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMOD
RECONSTRUCTIONPEET
RECONSTRUCTIONTOMO3D

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection