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- PDB-8qb8: Lsp1 in native eisosome lattice bound to plasma membrane microdomain -

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Basic information

Entry
Database: PDB / ID: 8qb8
TitleLsp1 in native eisosome lattice bound to plasma membrane microdomain
ComponentsSphingolipid long chain base-responsive protein LSP1
KeywordsLIPID BINDING PROTEIN / BAR domain / plasma membrane microdomain / membrane curvature / native biochemistry
Function / homology
Function and homology information


eisosome filament / eisosome assembly / eisosome / cell periphery / negative regulation of protein kinase activity / endocytosis / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion ...eisosome filament / eisosome assembly / eisosome / cell periphery / negative regulation of protein kinase activity / endocytosis / response to heat / mitochondrial outer membrane / lipid binding / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
Eisosome component PIL1/LSP1 / Eisosome component PIL1 / AH/BAR domain superfamily
Similarity search - Domain/homology
Sphingolipid long chain base-responsive protein LSP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKefauver, J.M. / Zou, L. / Loewith, R.J. / Defosses, A.
Funding supportEuropean Union, Switzerland, 4items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionIF-2020-101026765-MEMTOREuropean Union
European Research Council (ERC)AdG TENDOEuropean Union
Swiss National Science FoundationCRSII5_189996 METEORIC Switzerland
Swiss National Science Foundation310030_207754 Switzerland
Citation
Journal: To Be Published
Title: CryoEM architecture of a native stretch-sensitive membrane microdomain
Authors: Kefauver, J.M. / Hakala, M. / Zou, L. / Alba, J. / Espadas Moreno, J. / Tettamanti, M.G. / Estrozi, L. / Vanni, S. / Roux, A. / Desfosses, A. / Loewith, R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sphingolipid long chain base-responsive protein LSP1
B: Sphingolipid long chain base-responsive protein LSP1
C: Sphingolipid long chain base-responsive protein LSP1
I: Sphingolipid long chain base-responsive protein LSP1
D: Sphingolipid long chain base-responsive protein LSP1
J: Sphingolipid long chain base-responsive protein LSP1
E: Sphingolipid long chain base-responsive protein LSP1
K: Sphingolipid long chain base-responsive protein LSP1
F: Sphingolipid long chain base-responsive protein LSP1
L: Sphingolipid long chain base-responsive protein LSP1
G: Sphingolipid long chain base-responsive protein LSP1
M: Sphingolipid long chain base-responsive protein LSP1
H: Sphingolipid long chain base-responsive protein LSP1
N: Sphingolipid long chain base-responsive protein LSP1


Theoretical massNumber of molelcules
Total (without water)533,62514
Polymers533,62514
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DE
d_5EG
d_6FI
d_7GK
d_8HM
d_9ID
d_10JF
d_11KH
d_12LJ
d_13ML
d_14NN

NCS oper:
IDCodeMatrixVector
1given(-0.999974342254, -0.00460483161765, 0.00548729079344), (0.00458046042094, -0.999979627311, -0.00444571084608), (0.00550765075244, -0.00442046246086, 0.999975062336)339.859164837, 339.583646577, -0.174344729376
2given(0.975690386589, -0.0100071613698, 0.218924932887), (-0.00935394426676, 0.996144956115, 0.0872223029578), (-0.218953815324, -0.0871497741129, 0.971835450901)-38.3473186847, -58.5730529068, 59.8123279473
3given(0.813141755351, -0.0650726827985, -0.578416832101), (-0.0739827762336, 0.974116916664, -0.213594900429), (0.577344814236, 0.216475815328, 0.787280881803)210.56667255, 48.9651984028, -76.8372056082
4given(0.672268254835, -0.133769068568, -0.728121713613), (-0.131968707736, 0.946131759391, -0.295666964759), (0.728450172434, 0.294856796031, 0.618401015616)272.698971455, 120.214493843, -69.5630687759
5given(0.976252222027, -0.00856689103052, -0.216467566543), (-0.0114090123521, 0.995798015331, -0.0908633429929), (0.216336389505, 0.0911752216382, 0.972052285392)49.2875344599, 63.8499119314, -44.6401596128
6given(0.816764499065, -0.0619077818867, 0.573640287644), (-0.074628570756, 0.974539559902, 0.2114313662), (-0.572124400365, -0.215499588696, 0.791349226182)-125.660431636, -14.7071240523, 191.378245595
7given(0.676376562455, -0.126260487402, 0.725653522752), (-0.133667887532, 0.947797773241, 0.289503500639), (-0.724325646104, -0.292809956047, 0.624191227138)-117.651235346, -56.3177056362, 276.660275366
8given(-0.9746304784, 0.00354678723835, 0.223791981253), (0.0155717749445, -0.996377099156, 0.0836073926278), (0.223277742729, 0.0849711514411, 0.971044259045)290.095825579, 276.207247305, -44.4690674293
9given(-0.816375290223, 0.0623911588933, -0.574141732332), (0.0785726580964, -0.972904479645, -0.217447030069), (-0.572151835541, -0.222630224314, 0.789352937733)465.224891294, 354.359825055, 192.811910658
10given(-0.676650080418, 0.132437163317, -0.724296255991), (0.135987558739, -0.944290399657, -0.299704896497), (-0.723638067364, -0.301290621972, 0.62094436834)456.16576333, 396.408901723, 278.120633136
11given(-0.977351193739, 0.00365032393837, -0.21159234209), (0.0167389768473, -0.995385085005, -0.0944898894252), (-0.210960780123, -0.0958916455413, 0.972779698372)378.514537164, 397.856717024, 59.6514182398
12given(-0.814244013117, 0.0551099550605, 0.577901012248), (0.0813379641599, -0.974833793797, 0.207564953827), (0.574796331486, 0.216013812809, 0.789270048834)131.027883188, 290.509393233, -76.5422833596
13given(-0.6734749561, 0.11974009918, 0.729447593837), (0.140605723612, -0.948027300397, 0.285436977614), (0.725714485175, 0.294799162737, 0.621636501226)69.4111899107, 219.724981442, -69.2233099659

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Components

#1: Protein
Sphingolipid long chain base-responsive protein LSP1


Mass: 38116.039 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50 / References: UniProt: Q12230

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Helical lattice of native Pil1/Lsp1 protein bound to plasma membrane microdomain
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: TB50
Buffer solutionpH: 7 / Details: 50mM PIPES pH 7, 300mM NaCl, 1mM CHAPS, 0.5mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.0.8particle selection
4Gctf1.06CTF correction
7UCSF Chimera1.16model fitting
8Coot0.8.9.2model fitting
10RELION3.0.8initial Euler assignment
11cryoSPARC4.1.2final Euler assignment
13cryoSPARC4.1.23D reconstruction
14PHENIX1.20-4459model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2423944 / Symmetry type: POINT
Atomic model buildingAccession code: P53252 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002830254
ELECTRON MICROSCOPYf_angle_d0.631140866
ELECTRON MICROSCOPYf_chiral_restr0.0314564
ELECTRON MICROSCOPYf_plane_restr0.0065348
ELECTRON MICROSCOPYf_dihedral_angle_d3.91174158
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints9.02435274813E-11
ens_1d_3AAELECTRON MICROSCOPYNCS constraints4.95790153265E-13
ens_1d_4AAELECTRON MICROSCOPYNCS constraints7.50591463668E-13
ens_1d_5AAELECTRON MICROSCOPYNCS constraints6.46913540982E-13
ens_1d_6AAELECTRON MICROSCOPYNCS constraints1.08584947403E-12
ens_1d_7AAELECTRON MICROSCOPYNCS constraints5.97560670724E-13
ens_1d_8AAELECTRON MICROSCOPYNCS constraints2.30523146903E-10
ens_1d_9AAELECTRON MICROSCOPYNCS constraints2.6783042044E-10
ens_1d_10AAELECTRON MICROSCOPYNCS constraints6.4885652071E-13
ens_1d_11AAELECTRON MICROSCOPYNCS constraints6.66958379974E-13
ens_1d_12AAELECTRON MICROSCOPYNCS constraints5.0169448514E-13
ens_1d_13AAELECTRON MICROSCOPYNCS constraints3.50861427097E-12
ens_1d_14AAELECTRON MICROSCOPYNCS constraints3.93377887767E-13

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