[English] 日本語
Yorodumi
- PDB-2pso: Human StarD13 (DLC2) lipid transfer and protein localization domain -

+
Open data


ID or keywords:

Loading...

-
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 / RHOA GTPase cycle / endothelial cell migration / 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 / RHOA GTPase cycle / endothelial cell migration / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more