6PBK | pdb_00006pbk

Archaellum periplasmic stator protein complex FlaF and FlaG from Sulfolobus acidocaldarius

• PDB DOI: https://doi.org/10.2210/pdb6PBK/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Sulfolobus acidocaldarius DSM 639
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-14 Released: 2019-11-20 
• Deposition Author(s): Tsai, C.-L., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Models: experimental

Literature

The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility.

Tsai, C.L., Tripp, P., Sivabalasarma, S., Zhang, C., Rodriguez-Franco, M., Wipfler, R.L., Chaudhury, P., Banerjee, A., Beeby, M., Whitaker, R.J., Tainer, J.A., Albers, S.V.

(2020) Nat Microbiol 5: 216-225

• PubMed: 31844299 
• DOI: https://doi.org/10.1038/s41564-019-0622-3
• Primary Citation Related Structures: 
  5TUG, 5TUH, 6PBK


• PubMed Abstract: 
  

  Motility structures are vital in all three domains of life. In Archaea, motility is mediated by the archaellum, a rotating type IV pilus-like structure that is a unique nanomachine for swimming motility in nature. Whereas periplasmic FlaF binds the surface layer (S-layer), the structure, assembly and roles of other periplasmic components remain enigmatic, limiting our knowledge of the archaellum's functional interactions. Here, we find that the periplasmic protein FlaG and the association with its paralogue FlaF are essential for archaellation and motility. Therefore, we determine the crystal structure of Sulfolobus acidocaldarius soluble FlaG (sFlaG), which reveals a β-sandwich fold resembling the S-layer-interacting FlaF soluble domain (sFlaF). Furthermore, we solve the sFlaG ₂ -sFlaF ₂ co-crystal structure, define its heterotetrameric complex in solution by small-angle X-ray scattering and find that mutations that disrupt the complex abolish motility. Interestingly, the sFlaF and sFlaG of Pyrococcus furiosus form a globular complex, whereas sFlaG alone forms a filament, indicating that FlaF can regulate FlaG filament assembly. Strikingly, Sulfolobus cells that lack the S-layer component bound by FlaF assemble archaella but cannot swim. These collective results support a model where a FlaG filament capped by a FlaG-FlaF complex anchors the archaellum to the S-layer to allow motility.

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Organizational Affiliation: 
• Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Cell Biology, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
Molecular Biology Program, Sloan-Kettering Institute, New York, NY, USA.
Department of Life Sciences, Imperial College London, London, UK.
Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. [e-mail].
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany. [e-mail].
Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 63.48 kDa 
• Atom Count: 4,073 
• Modeled Residue Count: 490 
• Deposited Residue Count: 562 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saci FlaG soluble domain	A, C	135	Sulfolobus acidocaldarius DSM 639	Mutation(s): 1  Gene Names: Saci_1176
UniProt
Find proteins for Q4J9K7 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4J9K7  Go to UniProtKB:  Q4J9K7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved flagellar protein F	B, D	146	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0  Gene Names: Saci_1175
UniProt
Find proteins for Q4J9K8 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4J9K8  Go to UniProtKB:  Q4J9K8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth A], I [auth B], K [auth C], L [auth C], R [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD	O [auth D], P [auth D], Q [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	H [auth B], N [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	G [auth A], J [auth B], M [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.038	α = 90
b = 120.038	β = 90
c = 152.138	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Tsai, C.-L., Tainer, J.A.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Derived calculations
• Version 1.2: 2020-06-10
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description