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- PDB-6byd: Crystal structure of the second StART domain of yeast Lam4 -

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Basic information

Entry
Database: PDB / ID: 6byd
TitleCrystal structure of the second StART domain of yeast Lam4
ComponentsMembrane-anchored lipid-binding protein LAM4
KeywordsLIPID TRANSPORT / Sterol Transport
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / sterol transport / cortical endoplasmic reticulum / endoplasmic reticulum membrane / mitochondrion / plasma membrane
Similarity search - Function
VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / : / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / PH-like domain superfamily
Similarity search - Domain/homology
Membrane-anchored lipid-binding protein LAM4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.195 Å
AuthorsJentsch, J.A. / Kiburu, I.N. / Wu, J. / Pandey, K. / Boudker, O. / Menon, A.K.
Funding support Germany, Qatar, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)Graduiertenkolleg 2098, Project 11 Germany
Qatar National Research FundNPRP 7-082-1-014Qatar
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of sterol binding and transport by a yeast StARkin domain.
Authors: Jentsch, J.A. / Kiburu, I. / Pandey, K. / Timme, M. / Ramlall, T. / Levkau, B. / Wu, J. / Eliezer, D. / Boudker, O. / Menon, A.K.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-anchored lipid-binding protein LAM4


Theoretical massNumber of molelcules
Total (without water)23,0401
Polymers23,0401
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.601, 67.923, 132.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Membrane-anchored lipid-binding protein LAM4 / Lipid transfer at contact site protein 3 / Lipid transfer protein anchored at membrane contact sites 1


Mass: 23040.311 Da / Num. of mol.: 1 / Fragment: LAM4 (YHR080C)-StARkin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LAM4, LTC3, YHR080C / Production host: Escherichia coli (E. coli) / References: UniProt: P38800
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.5M Lithium Chloride 30% PEG 6000 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97494 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97494 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 11009 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 30.88 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.037 / Rrim(I) all: 0.137 / Χ2: 0.981 / Net I/σ(I): 7.3 / Num. measured all: 153681
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.19-2.2712.80.66410830.9680.1890.6910.614
2.27-2.36140.51110860.9860.1410.5310.492
2.36-2.4714.40.41710590.9790.1140.4320.556
2.47-2.614.50.30611030.9910.0840.3180.639
2.6-2.7614.40.24410730.9910.0670.2540.855
2.76-2.9714.40.18310900.9920.050.1891.092
2.97-3.2714.20.13411100.9960.0370.1391.338
3.27-3.7414.10.1210980.9960.0330.1251.381
3.74-4.7213.60.0911110.9950.0250.0941.423
4.72-5013.30.07811960.9970.0220.0811.376

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL2Mapphasing
RefinementResolution: 2.195→43.103 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 544 5.02 %
Rwork0.1857 10293 -
obs0.189 10837 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.23 Å2 / Biso mean: 45.1961 Å2 / Biso min: 18.41 Å2
Refinement stepCycle: final / Resolution: 2.195→43.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 0 48 1601
Biso mean---42.04 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081582
X-RAY DIFFRACTIONf_angle_d0.9012141
X-RAY DIFFRACTIONf_chiral_restr0.056248
X-RAY DIFFRACTIONf_plane_restr0.006273
X-RAY DIFFRACTIONf_dihedral_angle_d3.585979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1946-2.41550.28021260.21552506263299
2.4155-2.76490.28911360.20925302666100
2.7649-3.48330.27461340.200525742708100
3.4833-43.11130.21761480.16526832831100
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)
12.2687-0.25830.13191.7386-1.08531.071-0.19060.19190.1046-0.2350.14890.256-0.2675-0.88340.06840.3740.0587-0.04590.788-0.01980.360814.295635.2951.5139
21.8194-0.2522-0.46032.27460.63773.55210.12750.012-0.233-0.2193-0.19570.05220.1351-0.60860.0130.2111-0.0015-0.020.28150.00030.254422.116931.146451.4533
34.6853-1.3567-0.79472.9526-0.18752.30170.10110.0503-0.0747-0.1229-0.19720.21770.07360.31750.09570.1884-0.0005-0.01310.3650.00060.197337.669634.980556.0051
43.9064-0.4139-0.34092.01660.07013.43930.12110.1730.0265-0.299-0.1770.02780.04340.40910.01670.30330.03640.01820.2219-0.00490.201237.306335.520446.3725
52.3783-2.43471.28363.7245-0.21352.5551-0.9033-1.07380.34880.28970.6908-0.0044-0.3554-0.10960.08370.28260.0566-0.00170.2764-0.03690.200232.214136.4544.1685
66.601-0.5543-0.94142.9015-0.22153.09280.40290.09760.8459-0.5569-0.1449-0.13590.0387-0.9833-0.04180.22880.1164-0.02150.35150.02690.305921.864335.892545.0863
73.9834-0.9155-0.39261.20891.07263.58950.0016-0.1279-0.0615-0.0715-0.12260.09190.412-0.42960.00790.2983-0.0043-0.03520.21620.01010.262226.316529.420546.2041
80.82441.2734-0.36322.0262-0.86095.0175-0.3710.1482-0.5395-0.262-0.2152-0.38831.05780.49260.17440.47610.14930.05930.2977-0.03670.347934.381524.175433.4529
91.6457-0.3963-1.26661.81840.63414.04980.0796-0.3211-0.1417-0.1965-0.0612-0.08490.56250.04080.00710.35280.0591-0.01430.19240.05450.2929.490426.673154.8422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )A4 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 50 )A24 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 70 )A51 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 98 )A71 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 111 )A99 - 111
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 124 )A112 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 153 )A125 - 153
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 166 )A154 - 166
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 200 )A167 - 200

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