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- PDB-2pso: Human StarD13 (DLC2) lipid transfer and protein localization domain -

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Basic information

Entry
Database: PDB / ID: 2pso
TitleHuman StarD13 (DLC2) lipid transfer and protein localization domain
ComponentsStAR-related lipid transfer protein 13
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha and beta protein / lipid binding / helix swapping / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


endothelial tube lumen extension / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / endothelial cell migration / RHOA GTPase cycle / lipid droplet ...endothelial tube lumen extension / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / endothelial cell migration / RHOA GTPase cycle / lipid droplet / GTPase activator activity / mitochondrial membrane / actin cytoskeleton organization / lipid binding / signal transduction / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1870 / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / START domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1870 / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Rho GTPase activation protein / START-like domain superfamily / SAM domain (Sterile alpha motif) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
StAR-related lipid transfer protein 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLehtio, L. / Busam, R. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. ...Lehtio, L. / Busam, R. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Ogg, D. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van den Berg, S. / Weigelt, J. / Welin, M. / Persson, C. / 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
DepositionMay 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 21, 2011Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: StAR-related lipid transfer protein 13
B: StAR-related lipid transfer protein 13
C: StAR-related lipid transfer protein 13


Theoretical massNumber of molelcules
Total (without water)80,8733
Polymers80,8733
Non-polymers00
Water00
1
A: StAR-related lipid transfer protein 13


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: StAR-related lipid transfer protein 13


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: StAR-related lipid transfer protein 13


Theoretical massNumber of molelcules
Total (without water)26,9581
Polymers26,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.240, 78.240, 212.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Detailseach monomers represents biological unit

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Components

#1: Protein StAR-related lipid transfer protein 13 / StARD13 / START domain-containing protein 13 / 46H23.2 / Deleted in liver cancer protein 2 / Rho ...StARD13 / START domain-containing protein 13 / 46H23.2 / Deleted in liver cancer protein 2 / Rho GTPase-activating protein


Mass: 26957.654 Da / Num. of mol.: 3 / Fragment: START domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STARD13, DLC2, GT650 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9Y3M8

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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: 4.08 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 % MPD, 100 mM Tris-HCl, 125 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.03992 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2006 / Details: mirrors
RadiationMonochromator: Si(111), Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03992 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 31213 / Num. obs: 31213 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 86.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.69
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.52 / Num. unique all: 3157 / Rsym value: 0.554 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JSS

1jss


Resolution: 2.8→19.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 25.808 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Phenix program has also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.24446 1572 5 %RANDOM
Rwork0.20973 ---
all0.2115 29640 --
obs0.2115 29640 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.487 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4477 0 0 0 4477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9386251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42423.795195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13915716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4111526
X-RAY DIFFRACTIONr_chiral_restr0.0960.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.151809
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.53024
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.3207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.1533
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.34
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.40622945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.94334647
X-RAY DIFFRACTIONr_scbond_it2.21421863
X-RAY DIFFRACTIONr_scangle_it3.36131604
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 96 -
Rwork0.304 2191 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.282.74420.63073.3810.33682.4533-0.27580.55950.0212-0.3663-0.11960.59771.4724-0.83890.39541.02910.0410.0020.48520.13070.180231.34014.4918-30.0522
20.41930.0305-0.24412.9075-1.26812.5195-0.0083-0.1369-0.0157-0.3323-0.0554-0.0277-0.1033-0.15160.06370.49410.0656-0.03880.3428-0.00960.314832.8212-9.8153-0.6681
32.49842.21771.3112.98960.9063.1555-0.07140.00440.2193-0.5049-0.16670.12490.0941-0.02040.23810.49820.0878-0.07810.3314-0.0420.341730.2062-17.72311.7226
42.12912.54591.9283.97050.96213.69430.1688-0.19930.1722-1.13850.1880.2871-0.7465-0.3502-0.35680.86080.2205-0.19640.4120.06320.374627.4291-9.4067-8.7337
54.6231-0.05126.69460.6574-1.53912.9607-0.4042-0.24210.41770.0740.0334-0.0098-0.768-0.63280.37070.64060.0184-0.12180.31870.00650.322430.6489-2.28353.5878
615.4305-11.9186-6.895613.60767.00269.0849-0.60.0896-0.8612-0.38170.42990.97590.61770.12230.17010.4429-0.2142-0.14050.5178-0.15220.318256.1676-43.733547.98
70.708-0.19151.53670.1277-0.63213.9526-0.1076-0.0759-0.02030.0233-0.03890.0348-0.51330.20440.14650.44530.0075-0.01850.51590.01030.353941.2289-18.09431.9452
81.73311.44040.83722.03930.57053.4128-0.0893-0.2835-0.09980.0317-0.02920.0196-0.2661-0.26290.11850.42430.10290.00130.51320.00880.26434.5472-19.019729.7039
91.17660.03290.7710.6641-0.42263.0940.1346-0.4079-0.33710.4193-0.3569-0.0934-0.05060.47070.22220.3809-0.0094-0.03980.6170.02990.324643.6615-25.067233.5402
100.9944-0.267-0.113316.8061-0.74530.0489-0.34970.20340.1283-0.44530.3457-0.5806-0.01061.21310.0040.532-0.2311-0.05620.65770.05680.314550.4641-15.960829.2199
114.1272-10.0268-2.074424.35925.03971.04271.6212-0.6673-1.82823.0452-0.22162.58242.1746-2.7484-1.39960.9951-0.6389-0.05491.3645-0.01950.161434.0322-15.708947.1187
125.19094.1767-1.17123.3663-1.0020.88480.0702-0.20210.21660.47630.03130.2073-0.0819-0.2827-0.10150.38330.10150.06960.7238-0.03360.241421.4465-26.849134.4606
137.4186-0.0909-0.71512.39760.46635.5251-0.41741.0655-1.601-0.05590.1271-0.11120.5815-0.00340.29030.2731-0.13710.19490.5269-0.38520.455310.8022-47.431329.5776
147.65542.6411-5.25631.3231-2.31678.4231-0.65360.6157-1.0209-0.04440.3215-0.37090.508-0.31090.33210.342-0.08210.12670.6674-0.24570.35776.562-42.822833.1479
157.11660.9806-1.47131.7136-0.1070.97160.14150.1503-0.80910.3056-0.2909-0.45290.0562-0.46580.14940.3105-0.06210.08550.5852-0.06210.334819.7944-40.672934.66
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA908 - 92332 - 47
2X-RAY DIFFRACTION2AA924 - 99148 - 115
3X-RAY DIFFRACTION3AA992 - 1064116 - 188
4X-RAY DIFFRACTION4AA1065 - 1084189 - 208
5X-RAY DIFFRACTION5AA1085 - 1104209 - 228
6X-RAY DIFFRACTION6BB907 - 92331 - 47
7X-RAY DIFFRACTION7BB924 - 100248 - 126
8X-RAY DIFFRACTION8BB1003 - 1059127 - 183
9X-RAY DIFFRACTION9BB1060 - 1084184 - 208
10X-RAY DIFFRACTION10BB1085 - 1104209 - 228
11X-RAY DIFFRACTION11CC909 - 91733 - 41
12X-RAY DIFFRACTION12CC918 - 95042 - 74
13X-RAY DIFFRACTION13CC951 - 102575 - 149
14X-RAY DIFFRACTION14CC1026 - 1064150 - 188
15X-RAY DIFFRACTION15CC1065 - 1102189 - 226

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