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- PDB-6bym: Crystal structure of the sterol-bound second StART domain of yeas... -

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Basic information

Entry
Database: PDB / ID: 6bym
TitleCrystal structure of the sterol-bound second StART domain of yeast Lam4
ComponentsSterol-binding protein
KeywordsLIPID TRANSPORT / Sterol Transport
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / 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
25-HYDROXYCHOLESTEROL / : / Membrane-anchored lipid-binding protein LAM4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Jan 31, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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
Revision 1.5Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.6Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sterol-binding protein
B: Sterol-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3234
Polymers45,5182
Non-polymers8052
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-2 kcal/mol
Surface area17680 Å2
Unit cell
Length a, b, c (Å)38.179, 47.301, 55.996
Angle α, β, γ (deg.)111.210, 101.630, 100.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 196)
21(chain B and resid 4 through 196)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 196 / Label seq-ID: 4 - 196

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 4 through 196)AA
2(chain B and resid 4 through 196)BB

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Components

#1: Protein Sterol-binding protein


Mass: 22758.939 Da / Num. of mol.: 2 / Fragment: LAM4 (YHR080C)-StARkin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LAM4, SCKG_4597 / Production host: Escherichia Coli (E. coli) / References: UniProt: A0A250WL92, UniProt: P38800*PLUS
#2: Chemical ChemComp-HC3 / 25-HYDROXYCHOLESTEROL / (3BETA)-CHOLEST-5-ENE-3,25-DIOL


Mass: 402.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Lithium Chloride 0.7M 0.1M HEPES pH 7.5 24% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17147 / % possible obs: 98.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 26.06 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.105 / Χ2: 1.353 / Net I/σ(I): 9.6 / Num. measured all: 66375
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.283.80.25916820.9520.1530.3010.78797.1
2.28-2.373.90.21117230.9710.1240.2450.77897.6
2.37-2.483.90.18316720.9740.1070.2120.89797.5
2.48-2.613.90.15917070.9790.0930.1841.09797.9
2.61-2.773.90.13817470.9810.0810.161.24598.1
2.77-2.993.90.11516990.9850.0680.1341.63598.1
2.99-3.293.90.09817180.990.0580.1141.70598.6
3.29-3.763.90.08817150.990.0520.1031.71499
3.76-4.743.80.0717510.9920.0420.0811.80299.2
4.74-503.90.0617330.9950.0350.071.83599.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.381 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 870 5.08 %
Rwork0.1655 16261 -
obs0.1688 17131 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.05 Å2 / Biso mean: 30.5521 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 2.2→42.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 150 143 3400
Biso mean--29.56 30.64 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083231
X-RAY DIFFRACTIONf_angle_d0.9994393
X-RAY DIFFRACTIONf_chiral_restr0.058514
X-RAY DIFFRACTIONf_plane_restr0.006548
X-RAY DIFFRACTIONf_dihedral_angle_d14.2271976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1830X-RAY DIFFRACTION11.976TORSIONAL
12B1830X-RAY DIFFRACTION11.976TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.33790.31851360.19042661279796
2.3379-2.51840.27891480.19042704285298
2.5184-2.77180.26751360.18752734287098
2.7718-3.17280.25151540.18472707286198
3.1728-3.99690.20171540.15772696285099
3.9969-42.38920.19331420.14112759290199

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