1L0Q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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 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 prote ...

    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.

    Related Citations: 
    • An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components
      Springer, T.A.
      (1998) J.Mol.Biol. 283: 837
    • Implications for familial hypercholesterolemia from structure of the LDL receptor YWTD-EGF doman pair
      Jeon, H.,Meng, W.,Takagi, J.,Eck, M.J.,Springer, T.A.,Blacklow, S.C.
      (2001) Nat.Struct.Mol.Biol. 8: 499
    • The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity
      Galagan, J.E.,Nusbaum, C.,Roy, A.,Endrizzi, M.G.,Macdonald, P.,FitzHugh, W.,Calvo, S.,Engels, R.,Smirnov, S.
      () TO BE PUBLISHED --: --
    • The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease
      Bycroft, M.,Bateman, A.,Clarke, J.,Hamill, S.J.,Sandford, R.,Thomas, R.L.,Chothia, C.
      (1999) Embo J. 18: 297
    • Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6
      Mayerhofer, L.E.,Conway de Macario, E.,Yao, R.,Macario, A.J.L.
      (1998) Arch.Microbiol. 169: 339

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Surface layer protein
A, B, C, D
391Methanosarcina mazeiMutation(s): 0 
Find proteins for Q50245 (Methanosarcina mazei)
Go to UniProtKB:  Q50245
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A, B, C, D
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 188.181α = 90.00
b = 65.885β = 124.25
c = 140.030γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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