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- PDB-13fr: Cholesterol complex of the START domain of Caenorhabditis elegans... -

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Basic information

Entry
Database: PDB / ID: 13fr
TitleCholesterol complex of the START 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
CHOLESTEROL / START domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
C: START domain-containing protein
D: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0739
Polymers105,0244
Non-polymers1,0505
Water7,224401
1
A: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3482
Polymers26,2561
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4403
Polymers26,2561
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6432
Polymers26,2561
Non-polymers3871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: START domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6432
Polymers26,2561
Non-polymers3871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.512, 77.667, 85.294
Angle α, β, γ (deg.)90.000, 116.166, 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 233 through 374 or resid 379 through 409 or resid 411 through 444))
d_2ens_1(chain "B" and (resid 233 through 335 or resid 342...
d_3ens_1(chain "C" and (resid 233 through 335 or resid 342...
d_4ens_1(chain "D" and (resid 233 through 335 or resid 342...

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_11LEULEUPROPROAA233 - 37414 - 155
d_12PROPROTHRTHRAA379 - 409160 - 190
d_13LEULEUHISHISAA411 - 444192 - 225
d_21LEULEUPROPROBB233 - 33514 - 116
d_22SERSERPROPROBB342 - 374123 - 155
d_23PROPROTHRTHRBB379 - 409160 - 190
d_24LEULEUGLYGLYBB411 - 413192 - 194
d_25METMETHISHISBB424 - 444205 - 225
d_31LEULEUPROPROCC233 - 33514 - 116
d_32SERSERPROPROCC342 - 374123 - 155
d_33PROPROTHRTHRCC379 - 409160 - 190
d_34LEULEUGLYGLYCC411 - 413192 - 194
d_35METMETHISHISCC424 - 444205 - 225
d_41LEULEUPROPRODD233 - 33514 - 116
d_42SERSERPROPRODD342 - 374123 - 155
d_43PROPROTHRTHRDD379 - 409160 - 190
d_44LEULEUGLYGLYDD411 - 413192 - 194
d_45METMETHISHISDD424 - 444205 - 225

NCS oper:
IDCodeMatrixVector
1given(0.997323975481, -0.0143722811989, 0.0716821139728), (0.0132225251339, 0.999776622406, 0.0164884844404), (-0.0719030789296, -0.0154965422981, 0.997291233501)19.8257849282, -0.737087817744, 37.039031243
2given(-0.15512618244, -0.0509655616353, -0.986579129644), (0.0217356997407, -0.998602675188, 0.0481690405159), (-0.98765552035, -0.0139717083653, 0.156017192921)17.4064088861, 59.7244553965, 13.7474144609
3given(-0.262268093609, -0.0939500805839, -0.960410760786), (0.0722067248822, -0.994369940672, 0.0775539165292), (-0.962289787931, -0.0490081977379, 0.267575336303)38.9733089453, 58.8721091139, 49.0218525496

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Components

#1: Protein
START domain-containing protein


Mass: 26255.965 Da / Num. of mol.: 4
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM sodium cacodylate pH 6.5, 100 mM magnesium acetate, 200 mM potassium chloride, 14% w/v PEG 8000

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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: 2.09→29.37 Å / Num. obs: 57282 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.125 / Net I/σ(I): 9.7
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4398 / CC1/2: 0.73 / Rpim(I) all: 0.422 / Rrim(I) all: 0.768 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→29.37 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 2821 4.93 %
Rwork0.2102 54400 -
obs0.2119 57221 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.53 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 74 401 7402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327190
X-RAY DIFFRACTIONf_angle_d0.64219732
X-RAY DIFFRACTIONf_chiral_restr0.04451054
X-RAY DIFFRACTIONf_plane_restr0.00511232
X-RAY DIFFRACTIONf_dihedral_angle_d11.29272795
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.881439921951
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.46020373259
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.44230413581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.36111280.32472694X-RAY DIFFRACTION96.98
2.13-2.160.2871080.28562752X-RAY DIFFRACTION97.48
2.16-2.210.28061380.26822706X-RAY DIFFRACTION97.4
2.21-2.250.30561270.26062714X-RAY DIFFRACTION97.29
2.25-2.30.28111050.26492742X-RAY DIFFRACTION96.97
2.3-2.350.28631340.2652693X-RAY DIFFRACTION96.91
2.35-2.410.31520.25522656X-RAY DIFFRACTION96.3
2.41-2.480.3311320.25092688X-RAY DIFFRACTION96.54
2.48-2.550.29681360.24042696X-RAY DIFFRACTION96.75
2.55-2.630.29221590.25012685X-RAY DIFFRACTION97.16
2.63-2.730.33721440.24792723X-RAY DIFFRACTION96.99
2.73-2.840.29721110.2392704X-RAY DIFFRACTION96.94
2.84-2.970.27991250.22682734X-RAY DIFFRACTION97.24
2.97-3.120.241430.21612722X-RAY DIFFRACTION97.28
3.12-3.320.28681630.21122701X-RAY DIFFRACTION98.12
3.32-3.570.23481500.19022756X-RAY DIFFRACTION98.18
3.57-3.930.22822050.18392690X-RAY DIFFRACTION98.2
3.93-4.50.17881280.1582791X-RAY DIFFRACTION98.38
4.5-5.660.1731300.16312793X-RAY DIFFRACTION98.32
5.66-29.370.20072030.20052760X-RAY DIFFRACTION97.76
Refinement TLS params.Method: refined / Origin x: 5.1840271307 Å / Origin y: 30.8014770709 Å / Origin z: 42.1310202756 Å
111213212223313233
T0.178122428181 Å2-0.00386297956096 Å20.0429342698743 Å2-0.196372620022 Å20.0123580983888 Å2--0.237300796519 Å2
L0.351086354071 °20.0161270423127 °20.153669176218 °2-0.220093797266 °20.0164643617629 °2--0.447643032365 °2
S-0.00801462375229 Å °0.0257257191885 Å °-0.0106003637265 Å °-0.0338306208198 Å °-0.0378424392932 Å °-0.0398548348959 Å °0.0405567940281 Å °0.0337413164118 Å °0.0463842932783 Å °
Refinement TLS groupSelection details: all

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