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- PDB-3p0l: Human steroidogenic acute regulatory protein -

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Basic information

Entry
Database: PDB / ID: 3p0l
TitleHuman steroidogenic acute regulatory protein
ComponentsSteroidogenic acute regulatory protein, mitochondrial
KeywordsTRANSPORT PROTEIN / Structural Genomics Consortium / SGC / START domain / cholesterol transport / cholesterol / mitochondria
Function / homology
Function and homology information


positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / Mitochondrial protein degradation ...positive regulation of bile acid biosynthetic process / cellular lipid metabolic process / regulation of steroid biosynthetic process / intracellular cholesterol transport / glucocorticoid metabolic process / Pregnenolone biosynthesis / steroid biosynthetic process / cholesterol transfer activity / cholesterol binding / Mitochondrial protein degradation / cholesterol metabolic process / mitochondrial intermembrane space / mitochondrial matrix
Similarity search - Function
Steroidogenic acute regulatory protein / Steroidogenic acute regulatory protein-like / 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
Steroidogenic acute regulatory protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLehtio, L. / Siponen, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Siponen, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Comparative structural analysis of lipid binding START domains.
Authors: Thorsell, A.G. / Lee, W.H. / Persson, C. / Siponen, M.I. / Nilsson, M. / Busam, R.D. / Kotenyova, T. / Schuler, H. / Lehtio, L.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroidogenic acute regulatory protein, mitochondrial
B: Steroidogenic acute regulatory protein, mitochondrial
C: Steroidogenic acute regulatory protein, mitochondrial
D: Steroidogenic acute regulatory protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)98,8224
Polymers98,8224
Non-polymers00
Water00
1
A: Steroidogenic acute regulatory protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)24,7051
Polymers24,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Steroidogenic acute regulatory protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)24,7051
Polymers24,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Steroidogenic acute regulatory protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)24,7051
Polymers24,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Steroidogenic acute regulatory protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)24,7051
Polymers24,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.130, 144.130, 101.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 65:66 or resseq 68:173 or resseq 177:249 or resseq 251:276 )
211chain B and (resseq 64:172 or resseq 178:276 )
311chain C and (resseq 64:92 or resseq 94:172 or resseq 178:213 or resseq 216:276 )
411chain D and (resseq 64:101 or resseq 107:171 or resseq...

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Components

#1: Protein
Steroidogenic acute regulatory protein, mitochondrial / StAR / START domain-containing protein 1 / StARD1


Mass: 24705.393 Da / Num. of mol.: 4 / Fragment: START domain, UNP residues 66-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAR, STARD1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE / References: UniProt: P49675

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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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 200 mM Ca-acetate, 40 % PEG-300, 100 mM Na-Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.4→15 Å / Num. all: 16316 / Num. obs: 16316 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.6 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 19.78
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 22.8 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 4.75 / Num. unique all: 1363 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EM2

1em2


Resolution: 3.4→14.908 Å / σ(F): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1641 10.06 %random
Rwork0.2565 ---
all0.2598 16316 --
obs0.2598 16316 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.061 Å2 / ksol: 0.265 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.3389 Å20 Å2-0 Å2
2--18.3389 Å20 Å2
3----36.6779 Å2
Refinement stepCycle: LAST / Resolution: 3.4→14.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6373 0 0 0 6373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026472
X-RAY DIFFRACTIONf_angle_d0.5128704
X-RAY DIFFRACTIONf_dihedral_angle_d12.8492478
X-RAY DIFFRACTIONf_chiral_restr0.044977
X-RAY DIFFRACTIONf_plane_restr0.0021114
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1609X-RAY DIFFRACTIONPOSITIONAL
12B1609X-RAY DIFFRACTIONPOSITIONAL0.009
13C1589X-RAY DIFFRACTIONPOSITIONAL0.008
14D1451X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4013-3.50.40031390.33171211X-RAY DIFFRACTION90
3.5-3.61130.32911380.30821226X-RAY DIFFRACTION90
3.6113-3.73820.29541340.28931206X-RAY DIFFRACTION90
3.7382-3.88510.29231340.27571211X-RAY DIFFRACTION90
3.8851-4.05820.28671380.26111212X-RAY DIFFRACTION90
4.0582-4.26690.26631390.2421210X-RAY DIFFRACTION90
4.2669-4.52650.25781330.23091230X-RAY DIFFRACTION90
4.5265-4.86370.25461350.23321213X-RAY DIFFRACTION90
4.8637-5.33070.2821360.25481230X-RAY DIFFRACTION90
5.3307-6.0520.34921350.2791223X-RAY DIFFRACTION90
6.052-7.44730.35421370.27661219X-RAY DIFFRACTION90
7.4473-14.45880.24451410.21591258X-RAY DIFFRACTION90

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