5YHF

Crystal structure of SecDF in Super-membrane-facing form

• PDB DOI: https://doi.org/10.2210/pdb5YHF/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2017-09-28 Released: 2018-02-14 
• Deposition Author(s): Tanaka, Y., Tsukazaki, T., Yoshikaie, K., Furukawa, A.
• Funding Organization(s): JSPS/MEXT KAKENHI, Mitsubishi Foundation, Noguchi Institute, Naito Foundation, Mochida Memorial Foundation for Medical and Pharmaceutical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 

Literature

Remote Coupled Drastic beta-Barrel to beta-Sheet Transition of the Protein Translocation Motor.

Furukawa, A., Nakayama, S., Yoshikaie, K., Tanaka, Y., Tsukazaki, T.

(2018) Structure 26: 485-489.e2

• PubMed: 29398525 
• DOI: https://doi.org/10.1016/j.str.2018.01.002
• Primary Citation of Related Structures:  
  5YHF


• PubMed Abstract: 
  

  The membrane protein SecDF, belonging to the RND superfamily, enhances protein translocation at the extracytoplasmic side using a proton gradient. Here, we report the crystal structure of SecDF in a form we named Super-membrane-facing (Super F) form, demonstrating a β-barrel architecture instead of the previously reported β-sheet structure. Through this structural insight and supporting results of an in vivo crosslinking experiment, we propose a remote coupling model in which a structural change of the transmembrane region drives a functional, extracytoplasmic conformational transition.

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Organizational Affiliation: 

Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82.48 kDa 
• Atom Count: 5,790 
• Modelled Residue Count: 734 
• Deposited Residue Count: 741 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein translocase subunit SecDF	A	741	Thermus thermophilus HB8	Mutation(s): 1  Gene Names: secDF, TTHA0697 Membrane Entity: Yes
UniProt
Find proteins for Q5SKE6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKE6  Go to UniProtKB:  Q5SKE6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.207 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.19	α = 75.11
b = 65.64	β = 75.23
c = 79.98	γ = 80.83

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MoRDa	phasing
PDB_EXTRACT	data extraction
XDS	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Tanaka, Y., Tsukazaki, T., Yoshikaie, K., Furukawa, A.

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Funding Organization	Location	Grant Number
JSPS/MEXT KAKENHI	Japan	JP26119007, JP26291023, JP17H05669, JP16K14713, JP15H01537, JP15J08235, 15K14490, JP15K06972
Mitsubishi Foundation	Japan	--
Noguchi Institute	Japan	--
Naito Foundation	Japan	--
Mochida Memorial Foundation for Medical and Pharmaceutical Research	Japan	--

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Database references, Structure summary
• Version 1.2: 2018-03-21
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description