Macromolecule Content

Total Structure Weight: 163.19 kDa
Atom Count: 12764
Modelled Residue Count: 1564
Deposited Residue Count: 1564
Unique protein chains: 1

1L0Q

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

PDB DOI: 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.

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

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: 12377130 Search on PubMed
DOI: 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.

Related Citations:

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 Biol 8: 499

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

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 --: --

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50245
Protein Feature View Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
YCM Query on 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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2002-02-12
Released Date: 2002-11-06

Deposition Author(s):

Revision History (Full details and data files)

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