5IT5 | pdb_00005it5

Thermus thermophilus PilB core ATPase region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.274 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of a Type IV Pilus Assembly ATPase: Insights into the Molecular Mechanism of PilB from Thermus thermophilus.

Mancl, J.M.Black, W.P.Robinson, H.Yang, Z.Schubot, F.D.

(2016) Structure 24: 1886-1897

  • DOI: https://doi.org/10.1016/j.str.2016.08.010
  • Primary Citation Related Structures: 
    5IT5

  • PubMed Abstract: 

    Type IV pili (T4P) mediate bacterial motility and virulence. The PilB/GspE family ATPases power the assembly of T4P and type 2 secretion systems. We determined the structure of the ATPase region of PilB (PilB ATP ) in complex with ATPγS to provide a model of a T4P assembly ATPase and a view of a PilB/GspE family hexamer at better than 3-Å resolution. Spatial positioning and conformations of the protomers suggest a mechanism of force generation. All six PilB ATP protomers contain bound ATPγS. Two protomers form a closed conformation poised for ATP hydrolysis. The other four molecules assume an open conformation but separate into two pairs with distinct active-site accessibilities. We propose that one pair represents the post-hydrolysis phase while the other pair appears poised for ADP/ATP exchange. Collectively, the data suggest that T4P assembly is powered by coordinating concurrent substrate binding with ATP hydrolysis across the PilB hexamer.


  • Organizational Affiliation
    • Department of Biological Sciences, Virginia Polytechnic Institute and State University, 125 Life Sciences 1 (MC 0910), 970 Washington Street Southwest, Blacksburg, VA 24061, USA.

Macromolecule Content 

  • Total Structure Weight: 258.73 kDa 
  • Atom Count: 18,466 
  • Modeled Residue Count: 2,310 
  • Deposited Residue Count: 2,310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP binding motif-containing protein PilF385Thermus thermophilusMutation(s): 0 
Gene Names: pilF
UniProt
Find proteins for Q5SLC9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLC9 
Go to UniProtKB:  Q5SLC9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLC9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS

Query on AGS



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
N [auth E],
Q [auth C],
S [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ATP

Query on ATP



Download:Ideal Coordinates CCD File
H [auth F]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth F]
J [auth A]
L [auth B]
O [auth E]
R [auth C]
G [auth F],
J [auth A],
L [auth B],
O [auth E],
R [auth C],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth B],
P [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.55α = 90
b = 133.56β = 90
c = 208.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1417726

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2016-11-09
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description