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- PDB-13ft: START domain of Caenorhabditis elegans StAR-related lipid transfe... -

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Basic information

Entry
Database: PDB / ID: 13ft
TitleSTART domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3)
ComponentsSTART domain-containing protein
KeywordsLIPID TRANSPORT / cholesterol / cholesterol traffic / cholesterol metabolism / physical biochemistry / STARD3 / START domain / NPC1/NPC2
Function / homology
Function and homology information


: / endoplasmic reticulum-endosome membrane contact site / late endosome membrane / lipid binding
Similarity search - Function
MENTAL domain / Cholesterol-capturing domain / MENTAL domain profile. / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily
Similarity search - Domain/homology
START domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBattista, B. / Sambrailo, A. / Biglione, F.A. / Lombardo, V.A. / Mansilla, M.C. / Albanesi, D. / Lisa, M.N. / de Mendoza, D. / Binolfi, A.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2018-02572 Argentina
CitationJournal: To Be Published
Title: Cholesterol complex of the START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3)
Authors: Battista, B. / Sambrailo, A. / Biglione, F.A. / Lombardo, V.A. / Mansilla, M.C. / Albanesi, D. / Lisa, M.N. / de Mendoza, D. / Binolfi, A.
History
DepositionMay 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3699
Polymers52,5122
Non-polymers8577
Water4,252236
1
A: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5423
Polymers26,2561
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8276
Polymers26,2561
Non-polymers5715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.774, 79.249, 72.512
Angle α, β, γ (deg.)90.000, 90.270, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 232 through 412 or resid 420 through 443))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGLYSLYSAA232 - 41213 - 193
d_12VALVALTYRTYRAA420 - 443201 - 224
d_21ARGARGTYRTYRBB232 - 44313 - 224

NCS oper: (Code: givenMatrix: (-0.759133646489, -0.0210041238965, 0.650595829642), (-0.0205699491886, -0.998206028408, -0.0562281249953), (0.650609701709, -0.056067384721, 0.757339728531)Vector: 95. ...NCS oper: (Code: given
Matrix: (-0.759133646489, -0.0210041238965, 0.650595829642), (-0.0205699491886, -0.998206028408, -0.0562281249953), (0.650609701709, -0.056067384721, 0.757339728531)
Vector: 95.3980618548, 61.6341419029, -32.9710688433)

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Components

#1: Protein START domain-containing protein


Mass: 26255.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tag-340, CELE_F26F4.4, F26F4.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): E. coli C41 / References: UniProt: Q19819
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM sodium citrate tribasic dihydrate pH 5.0, 200 mM lithium sulfate; 22% v/v PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.01→29.67 Å / Num. obs: 33445 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Net I/σ(I): 17
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2250 / CC1/2: 0.724 / Rpim(I) all: 0.337 / Rrim(I) all: 0.742

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→29.67 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 1599 4.78 %
Rwork0.1804 31824 -
obs0.1821 33423 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.56 Å2
Refinement stepCycle: LAST / Resolution: 2.01→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 54 236 3689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693528
X-RAY DIFFRACTIONf_angle_d0.90334756
X-RAY DIFFRACTIONf_chiral_restr0.0566509
X-RAY DIFFRACTIONf_plane_restr0.0082601
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851325
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.05851472429 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.080.29081190.23112674X-RAY DIFFRACTION91.39
2.08-2.150.23951480.20592905X-RAY DIFFRACTION99.93
2.15-2.240.23671440.18582917X-RAY DIFFRACTION99.97
2.24-2.340.25331060.18682932X-RAY DIFFRACTION100
2.34-2.460.25181190.19112909X-RAY DIFFRACTION100
2.46-2.620.23691510.18972917X-RAY DIFFRACTION99.97
2.62-2.820.24861660.19082878X-RAY DIFFRACTION100
2.82-3.10.24461720.18982880X-RAY DIFFRACTION99.97
3.1-3.550.18651500.16972920X-RAY DIFFRACTION100
3.55-4.470.18571420.15552963X-RAY DIFFRACTION100
4.47-29.670.19461820.18492929X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 60.4189036133 Å / Origin y: 29.2825853714 Å / Origin z: 17.4157205886 Å
111213212223313233
T0.187410214646 Å2-0.0111385977785 Å20.00157318064014 Å2-0.231754359321 Å20.00289914534857 Å2--0.171965997222 Å2
L0.442951308861 °2-0.123853527998 °20.0655310668657 °2-1.33936422101 °2-0.0412489942583 °2--0.676377850193 °2
S0.0306606595155 Å °-0.0109543464117 Å °-0.0211825861259 Å °-0.178037069977 Å °-0.0181522668946 Å °0.126416335005 Å °0.0832327148493 Å °-0.0565782019105 Å °-0.00955726428444 Å °
Refinement TLS groupSelection details: all

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