2QCZ | pdb_00002qcz

Structure of N-terminal domain of E. Coli YaeT

• PDB DOI: https://doi.org/10.2210/pdb2QCZ/pdb

• Classification: MEMBRANE PROTEIN, PROTEIN TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2007-06-20 Released: 2007-08-28 
• Deposition Author(s): Kim, S., Malinverni, J.C., Sliz, P., Silhavy, T.J., Harrison, S.C., Kahne, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.329 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.258 (DCC) 

Literature

Structure and function of an essential component of the outer membrane protein assembly machine.

Kim, S., Malinverni, J.C., Sliz, P., Silhavy, T.J., Harrison, S.C., Kahne, D.

(2007) Science 317: 961-964

• PubMed: 17702946 
• DOI: https://doi.org/10.1126/science.1143993
• Primary Citation Related Structures: 
  2QCZ, 2QDF


• PubMed Abstract: 
  

  Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

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.

Macromolecule Content 

• Total Structure Weight: 74.91 kDa 
• Atom Count: 4,834 
• Modeled Residue Count: 620 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor yaeT	A, B	335	Escherichia coli K-12	Mutation(s): 0  Gene Names: yaeT Membrane Entity: Yes
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940  Go to UniProtKB:  P0A940

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.329 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.258 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.721	α = 90
b = 94.048	β = 90
c = 109.176	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Kim, S., Malinverni, J.C., Sliz, P., Silhavy, T.J., Harrison, S.C., Kahne, D.

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references