3PLT | pdb_00003plt

Crystal structure of Lsp1 from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb3PLT/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-15 Released: 2011-06-22
Deposition Author(s): Ziolkowska, N.E., Walther, T.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.296 (Depositor), 0.284 (DCC)
R-Value Work:
0.236 (Depositor), 0.232 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3PLT

This is version 1.3 of the entry. See complete history.

Literature

Eisosome-driven plasma membrane organization is mediated by BAR domains.

Ziolkowska, N.E., Karotki, L., Rehman, M., Huiskonen, J.T., Walther, T.C.

(2011) Nat Struct Mol Biol 18: 854-856

PubMed: 21685922 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.2080
Primary Citation Related Structures:
3PLT

PubMed Abstract:
Plasma membranes are organized into domains of different protein and lipid composition. Eisosomes are key complexes for yeast plasma membrane organization, containing primarily Pil1 and Lsp1. Here we show that both proteins consist mostly of a banana-shaped BAR domain common to membrane sculpting proteins, most similar to the ones of amphiphysin, arfaptin 2 and endophilin 2. Our data reveal a previously unrecognized family of BAR-domain proteins involved in plasma membrane organization.

Organizational Affiliation

Max Planck Institute of Biochemistry, Organelle Architecture and Dynamics, Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 78.24 kDa
Atom Count: 5,037
Modeled Residue Count: 634
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingolipid long chain base-responsive protein LSP1	A, B, C	234	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: LSP1, YPL004C
UniProt
Find proteins for Q12230 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12230 Go to UniProtKB: Q12230
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12230
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.296 (Depositor), 0.284 (DCC)
R-Value Work: 0.236 (Depositor), 0.232 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 273.16	α = 90
b = 38.753	β = 99.349
c = 75.509	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Ziolkowska, N.E.

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.