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- PDB-1rg3: SP-B C-terminal peptide in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 1rg3
TitleSP-B C-terminal peptide in SDS micelles
ComponentsPulmonary surfactant-associated protein B
KeywordsSURFACE ACTIVE PROTEIN / lung / surfactant / SP-B
Function / homology
Function and homology information


Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism / multivesicular body / animal organ morphogenesis / lysosome / endoplasmic reticulum membrane / extracellular region
Similarity search - Function
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 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.
Similarity search - Domain/homology
Pulmonary surfactant-associated protein B
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsBooth, V. / Waring, A.J. / Walther, F.J. / Keough, K.M.
CitationJournal: Biochemistry / Year: 2004
Title: NMR Structures of the C-Terminal Segment of Surfactant Protein B in Detergent Micelles and Hexafluoro-2-propanol.
Authors: Booth, V. / Waring, A.J. / Walther, F.J. / Keough, K.M.
History
DepositionNov 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pulmonary surfactant-associated protein B


Theoretical massNumber of molelcules
Total (without water)1,8471
Polymers1,8471
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)10 / 40structures with favorable non-bond energy
Representative

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Components

#1: Protein/peptide Pulmonary surfactant-associated protein B / SP-B / 6 kDa protein / Pulmonary surfactant-associated proteolipid SPLPhe / 18 kDa pulmonary- ...SP-B / 6 kDa protein / Pulmonary surfactant-associated proteolipid SPLPhe / 18 kDa pulmonary-surfactant protein


Mass: 1847.344 Da / Num. of mol.: 1 / Fragment: C-terminal helix / Source method: obtained synthetically
Details: The peptide was synthesized with N15 isotope labels on all valine and leucine residues. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P07988

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1313D 15N-separated NOESY

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Sample preparation

DetailsContents: 2 mM SP-B63-78, 200 mM deuterated sodium dodecyl sulfate
Solvent system: 200 mM deuterated sodium dodecyl sulfate; 90% H2O; 10% D2O; 2 mM DSS
Sample conditionsIonic strength: 0 / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CNS1.2Brungerstructure solution
ENSEMBLE1Forman-Kaydata analysis
CNS1.2Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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