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- PDB-2jw2: Validation of inter-helical orientation of the steril-alpha-motif... -

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Basic information

Entry
Database: PDB / ID: 2jw2
TitleValidation of inter-helical orientation of the steril-alpha-motif of human deleted in liver cancer 2 by residual dipolar couplings
ComponentsStAR-related lipid transfer protein 13
KeywordsLIPID BINDING PROTEIN / DLC2-SAM / RDC refinement / Alternative splicing / Anti-oncogene / Cell cycle / Cytoplasm / GTPase activation / Polymorphism
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 / GTPase activator activity ...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 / GTPase activator activity / lipid droplet / mitochondrial membrane / actin cytoskeleton organization / lipid binding / signal transduction / cytosol
Similarity search - Function
Helix Hairpins - #2070 / 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 / Rho GTPase activation protein ...Helix Hairpins - #2070 / 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 / Rho GTPase activation protein / START-like domain superfamily / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
StAR-related lipid transfer protein 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsrefinment of structures of DLC2-SAM using RDCs
AuthorsLi, H. / Sze, K. / Fung, K.
CitationJournal: To be Published
Title: Validation of inter-helical orientation of the steril-alpha-motif of human deleted in liver cancer 2 by residual dipolar couplings
Authors: Li, H. / Sze, K. / Fung, K. / Sun, H.
History
DepositionOct 3, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: StAR-related lipid transfer protein 13


Theoretical massNumber of molelcules
Total (without water)9,3401
Polymers9,3401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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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: 9339.574 Da / Num. of mol.: 1 / Fragment: DLC2-SAM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3M8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: refinment of structures of DLC2-SAM using RDCs
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2212D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 5% DMPC/DHPC 0.8 mM TTAB bicelles
SampleConc.: 1 mM / Component: sample_1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.02 7.1 ambient 298 K
20.02 7.1 ambient 311 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Version: 2.17.2 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 16

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