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- PDB-1sn6: NMR solution structure of human Saposin C in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 1sn6
TitleNMR solution structure of human Saposin C in SDS micelles
ComponentsProactivator polypeptide
KeywordsMEMBRANE PROTEIN / 3 disulfide bridges / all alpha-helices / alpha-helices connected by turns
Function / homology
Function and homology information


positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / lysosomal lumen / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / regulation of autophagy / phospholipid binding / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / protease binding / collagen-containing extracellular matrix / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 ...Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsHawkins, C.A. / de Alba, E. / Tjandra, N.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Solution structure of human saposin C in a detergent environment.
Authors: Hawkins, C.A. / Alba, E. / Tjandra, N.
#1: Journal: Biochemistry / Year: 2003
Title: Solution structure of human saposin C: pH-dependent interaction with phospholipid vesicles
Authors: de Alba, E. / Weiler, S. / Tjandra, N.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proactivator polypeptide


Theoretical massNumber of molelcules
Total (without water)9,4251
Polymers9,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Proactivator polypeptide


Mass: 9424.898 Da / Num. of mol.: 1 / Fragment: Saposin C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP / Plasmid: pET-30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07602
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1214D 13C/15N-separated NOESY
2334D 13C-separated NOESY
141CBCA(CO)NH
151CBCANH
161HNCO
17215N-HSQC
NMR detailsText: The structure was determined in the presence of detergent micelles.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D2090% H20, 10% D20
21mM saposin C U-15N; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 90% H20, 10% D2090% H20, 10% D20
31mM saposin C U-15N, U-13C; 25mM sodium dodecyl sulfate U-2H; 0.01% sodium azide; 100% D20100% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM sodium dodecyl sulfate U-2H; 0.01% sodium azide 6.8ambient 298 K
225mM sodium dodecyl sulfate U-2H; 0.01% sodium azide 6.4ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
NMRPipe2.1Delaglio, Grzesiek, Zhu, Vuister, Pfeifer, Baxprocessing
PIPP4.2.8Garrettdata analysis
XPLOR-NIH2.9.3Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on 1854 NOE-derived distance restraints, 117 dihedral angle restraints, and 56 distance restraints derived from hydrogen bond.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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