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- PDB-3plt: Crystal structure of Lsp1 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3plt
TitleCrystal structure of Lsp1 from Saccharomyces cerevisiae
ComponentsSphingolipid long chain base-responsive protein LSP1
KeywordsSTRUCTURAL PROTEIN / eisosomes / Lsp1 / Pil1 / bar domain / plasma membrane / self-assembly / phosphoprotein
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 / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Sphingolipid long chain base-responsive protein LSP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZiolkowska, N.E. / Walther, T.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Eisosome-driven plasma membrane organization is mediated by BAR domains.
Authors: Ziolkowska, N.E. / Karotki, L. / Rehman, M. / Huiskonen, J.T. / Walther, T.C.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)78,2443
Polymers78,2443
Non-polymers00
Water1086
1
A: Sphingolipid long chain base-responsive protein LSP1
B: Sphingolipid long chain base-responsive protein LSP1


Theoretical massNumber of molelcules
Total (without water)52,1632
Polymers52,1632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-41 kcal/mol
Surface area21920 Å2
MethodPISA
2
C: Sphingolipid long chain base-responsive protein LSP1

C: Sphingolipid long chain base-responsive protein LSP1


Theoretical massNumber of molelcules
Total (without water)52,1632
Polymers52,1632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6000 Å2
ΔGint-45 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.1600, 38.7530, 75.5090
Angle α, β, γ (deg.)90.0000, 99.3490, 90.0000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 52 - 264 / Label seq-ID: 19 - 231

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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


Mass: 26081.361 Da / Num. of mol.: 3 / Fragment: UNP residues 36-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LSP1, YPL004C / Plasmid: PNZ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12230
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11
Details: 0.2M NaCl, 20mM phenol, 20% PEG 8000, 0.1M CAPS, pH 11, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17725 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 18.75
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1.91 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→37.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 46.745 / SU ML: 0.395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 905 5.1 %RANDOM
Rwork0.236 ---
obs0.239 16807 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.921 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å2-1.92 Å2
2--2.49 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 0 6 5037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225098
X-RAY DIFFRACTIONr_bond_other_d0.0010.023530
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9916877
X-RAY DIFFRACTIONr_angle_other_deg0.81438639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7815630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35325.041244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04115971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0071538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
X-RAY DIFFRACTIONr_mcbond_it0.3511.53161
X-RAY DIFFRACTIONr_mcbond_other0.0561.51273
X-RAY DIFFRACTIONr_mcangle_it0.69725072
X-RAY DIFFRACTIONr_scbond_it1.0331937
X-RAY DIFFRACTIONr_scangle_it1.9114.51805
Refine LS restraints NCS

Ens-ID: 1 / Number: 2791 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.930.5
2Bmedium positional0.760.5
3Cmedium positional0.720.5
1Amedium thermal0.272
2Bmedium thermal0.272
3Cmedium thermal0.272
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 52 -
Rwork0.325 1146 -
obs--91.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.0659-0.39386.14321.3317-0.17384.1354-0.52870.71791.6971-0.1784-0.3172-0.1142-0.19190.21060.84590.32870.05120.03980.13740.03880.368956.26637.21646.116
213.55370.04322.24960.010.01750.8967-0.3107-0.02330.4325-0.0171-0.04850.0251-0.1826-0.06110.35920.3340.05170.0130.2912-0.03430.39571.38635.37156.813
39.98280.86456.56950.4610.66145.96150.18590.11950.0656-0.1769-0.26540.01850.2462-0.22040.07950.3460.08890.05410.2582-0.11230.290443.54726.82539.832
429.4842.77497.48653.4202-0.61038.92340.4872-1.8545-0.79380.5707-0.37310.22330.541-0.074-0.11410.41370.0360.15950.45650.08710.144267.02624.39470.187
59.1003-2.43810.59921.9533-3.900317.7283-0.32570.4960.9498-0.0177-0.4692-0.1668-0.49930.95810.79490.32380.0150.0850.12630.01470.1799-0.20220.438.492
63.3298-1.46455.16041.2504-2.445210.33270.02970.23820.3425-0.034-0.1243-0.00470.20070.21720.09460.3080.01740.11510.14920.03330.212-9.35515.7322.302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 125
2X-RAY DIFFRACTION2A126 - 264
3X-RAY DIFFRACTION3B52 - 222
4X-RAY DIFFRACTION4B223 - 264
5X-RAY DIFFRACTION5C52 - 109
6X-RAY DIFFRACTION6C110 - 264

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