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- PDB-6ser: Crystal structure of human STARD10 -

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Basic information

Entry
Database: PDB / ID: 6ser
TitleCrystal structure of human STARD10
ComponentsSTART domain-containing protein 10
KeywordsLIPID TRANSPORT / STARD10 / lipid transporter / Type 2 diabetes
Function / homology
Function and homology information


intercellular canaliculus / motile cilium / lipid transport / Synthesis of PC / microvillus / lipid binding / membrane / cytosol
Similarity search - Function
STARD10, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / START domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.299 Å
AuthorsCheng, K. / Wigley, D.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N009258/1 United Kingdom
CitationJournal: To Be Published
Title: The crystal structure of human STARD10
Authors: Cheng, K. / Wigley, D.B.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: START domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0649
Polymers33,0941
Non-polymers9708
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint26 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.336, 101.199, 125.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-301-

PO4

21A-454-

HOH

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Components

#1: Protein START domain-containing protein 10 / StARD10 / Antigen NY-CO-28 / PCTP-like protein / PCTP-L / Serologically defined colon cancer ...StARD10 / Antigen NY-CO-28 / PCTP-like protein / PCTP-L / Serologically defined colon cancer antigen 28 / StAR-related lipid transfer protein 10


Mass: 33093.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STARD10, SDCCAG28, CGI-52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y365
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50% (v/v) PEG 200, 100 mM Sodium phosphate dibasic/ Potassium phosphate monobasic (pH 6.2), 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.29→60.043 Å / Num. obs: 19758 / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 2.29→2.34 Å / Rmerge(I) obs: 0.44 / Num. unique obs: 925

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→60.043 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1010 5.11 %
Rwork0.2098 18741 -
obs0.2117 19751 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.87 Å2 / Biso mean: 44.8853 Å2 / Biso min: 19.49 Å2
Refinement stepCycle: final / Resolution: 2.299→60.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 63 68 2120
Biso mean--60.41 43.89 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072098
X-RAY DIFFRACTIONf_angle_d0.9972826
X-RAY DIFFRACTIONf_chiral_restr0.063299
X-RAY DIFFRACTIONf_plane_restr0.006350
X-RAY DIFFRACTIONf_dihedral_angle_d18.0041273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.299-2.42030.30461270.245261699
2.4203-2.57190.28421380.24312644100
2.5719-2.77050.29931360.24672646100
2.7705-3.04930.27581530.24542665100
3.0493-3.49050.24641650.22782655100
3.4905-4.39740.22151280.18282713100
4.3974-600.22331630.18562802100

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