2YXR | pdb_00002yxr

The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal

• PDB DOI: https://doi.org/10.2210/pdb2YXR/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2007-04-27 Released: 2007-08-14 
• Deposition Author(s): Li, W., Schulman, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.335 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.300 (Depositor) 

Starting Model: experimental

Literature

The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal

Li, W., Schulman, S., Boyd, D., Erlandson, K., Beckwith, J., Rapoport, T.A.

(2007) Mol Cell 26: 511-521

• PubMed: 17531803 
• DOI: https://doi.org/10.1016/j.molcel.2007.05.003
• Primary Citation Related Structures: 
  2YXQ, 2YXR

---

Organizational Affiliation: 
• Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158-2330, USA. [e-mail] <[e-mail]>

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 60.62 kDa 
• Atom Count: 3,999 
• Modeled Residue Count: 519 
• Deposited Residue Count: 553 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Preprotein translocase subunit secY	A	426	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: secY Membrane Entity: Yes
UniProt
Find proteins for Q60175 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q60175  Go to UniProtKB:  Q60175

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Preprotein translocase subunit secE	B	74	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: secE Membrane Entity: Yes
UniProt
Find proteins for Q57817 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57817  Go to UniProtKB:  Q57817

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Preprotein translocase secG subunit	C	53	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: secG Membrane Entity: Yes
UniProt
Find proteins for P60460 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P60460  Go to UniProtKB:  P60460

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.335 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.300 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.51	α = 90
b = 150.36	β = 90
c = 79.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Li, W., Schulman, S.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description