1L0Q

Tandem YVTN beta-propeller and PKD domains from an archaeal surface layer protein

• PDB DOI: https://doi.org/10.2210/pdb1L0Q/pdb

• Classification: PROTEIN BINDING
• Organism(s): Methanosarcina mazei S-6
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2002-02-12 Released: 2002-11-06 
• Deposition Author(s): Jing, H., Takagi, J., Liu, J.-H., Lindgren, S., Zhang, R.-G., Joachimiak, A., Wang, J.-H., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.263 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Archaeal Surface Layer Proteins Contain beta Propeller, PKD, and beta Helix Domains and Are Related to Metazoan Cell Surface Proteins.

Jing, H., Takagi, J., Liu, J., Lindgren, S., Zhang, R., Joachimiak, A., Wang, J., Springer, T.

(2002) Structure 10: 1453-1464

• PubMed: 12377130 
• DOI: https://doi.org/10.1016/s0969-2126(02)00840-7
• Primary Citation of Related Structures:  
  1L0Q


• PubMed Abstract: 
  

  The surface layer of archaeobacteria protects cells from extreme environments and, in Methanosarcina, may regulate cell adhesion. We identify three domain types that account for the complete architecture of numerous Methanosarcina surface layer proteins (SLPs). We solve the crystal structure for two of these domains, which correspond to the two N-terminal domains of an M. mazei SLP. One domain displays a unique, highly symmetrical, seven-bladed beta propeller fold, and the other belongs to the polycystic kidney disease (PKD) superfamily fold. The third domain is predicted to adopt a beta helix fold. These domains have homologs in metazoan cell surface proteins, suggesting remarkable relationships between domains in archaeal SLPs and metazoan cell surface proteins.

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Organizational Affiliation: 

Center for Blood Research and Department of Pathology, Harvard Medical School, Boston, MA 02115, 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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 163.19 kDa 
• Atom Count: 12,764 
• Modelled Residue Count: 1,564 
• Deposited Residue Count: 1,564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface layer protein	A, B, C, D	391	Methanosarcina mazei S-6	Mutation(s): 6  Membrane Entity: Yes
UniProt
Find proteins for Q50245 (Methanosarcina mazei) Explore Q50245  Go to UniProtKB:  Q50245

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
YCM	A, B, C, D	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.263 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.181	α = 90
b = 65.885	β = 124.25
c = 140.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Jing, H., Takagi, J., Liu, J.-H., Lindgren, S., Zhang, R.-G., Joachimiak, A., Wang, J.-H., Springer, T.A.

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance