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(-) Description

Title :  NMR STRUCTURE OF MINI-B, AN N-TERMINAL- C-TERMINAL CONSTRUCT FROM HUMAN SURFACTANT PROTEIN B (SP-B), IN SODIUM DODECYL SULFATE (SDS) MICELLES
 
Authors :  V. Booth, M. Sarker, A. J. Waring, K. M. W. Keough
Date :  11 Aug 06  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Mini-B, Sp-B, Surfactant Protein B, Lipid Associated Protein, Surface Active Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Booth, M. Sarker, A. J. Waring, K. M. W. Keough
Nmr Structure Of Mini-B, An N-Terminal - C-Terminal Construct From Human Surfactant Protein B (Sp-B), In Sodium Dodecyl Sulfate (Sds) Micelles
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PULMONARY SURFACTANT-ASSOCIATED PROTEIN B
    ChainsA
    EngineeredYES
    FragmentMINI-B
    Other DetailsTHIS SEQUENCE IS A BIOLOGICALLY ACTIVE FRAGMENT OF THE PROTEIN SP-B WHICH OCCURS NATURALLY IN HUMANS.
    SynonymSP-B, 6 KDA PROTEIN, PULMONARY SURFACTANT- ASSOCIATED PROTEOLIPID SPLPHE, 18 KDA PULMONARY-SURFACTANT PROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DWF)

(-) Sites  (0, 0)

(no "Site" information available for 2DWF)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:1 -A:33
2A:4 -A:27

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DWF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013100R272HPSPB_HUMANPolymorphism3024809AR28H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DWF)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003938222bENSE00002197707chr2:85895312-8589524073PSPB_HUMAN1-23230--
1.3bENST000003938223bENSE00001135296chr2:85894929-85894802128PSPB_HUMAN23-65430--
1.4ENST000003938224ENSE00001135287chr2:85894300-8589422972PSPB_HUMAN66-89240--
1.5aENST000003938225aENSE00001135279chr2:85893865-85893740126PSPB_HUMAN90-131420--
1.6ENST000003938226ENSE00001135274chr2:85892917-85892729189PSPB_HUMAN132-194630--
1.7ENST000003938227ENSE00001135266chr2:85892501-8589241290PSPB_HUMAN195-224301A:1-1717
1.8ENST000003938228ENSE00001135259chr2:85890970-85890787184PSPB_HUMAN225-286621A:18-34 (gaps)54
1.9bENST000003938229bENSE00001135249chr2:85890614-85890469146PSPB_HUMAN286-334490--
1.11ENST0000039382211ENSE00001135239chr2:85889232-8588915281PSPB_HUMAN335-361270--
1.12aENST0000039382212aENSE00001154897chr2:85888658-8588857782PSPB_HUMAN362-381200--
1.13aENST0000039382213aENSE00001516582chr2:85886805-858844372369PSPB_HUMAN-00--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:34
 aligned with PSPB_HUMAN | P07988 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:71
                                   217       227       237       247       257       267       277 
           PSPB_HUMAN   208 CWLCRALIKRIQAMIPKGALAVAVAQVCRVVPLVAGGICQCLAERYSVILLDTLLGRMLPQLVCRLVLRCS 278
               SCOP domains d2dwfa1 A:1-34                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...-------------------------------------....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------H------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.7         Exon 1.8  PDB: A:18-34 (gaps) UniProt: 225-286         Transcript 1
                 2dwf A   1 CWLCRALIKRIQAMIPKG-------------------------------------GRMLPQLVCRLVLRCS  34
                                    10       | -         -         -         -     |  23        33 
                                            18                                    19               

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DWF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DWF)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (PSPB_HUMAN | P07988)
molecular function
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
    GO:0006665    sphingolipid metabolic process    The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
cellular component
    GO:0097208    alveolar lamellar body    A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.
    GO:0045334    clathrin-coated endocytic vesicle    A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0042599    lamellar body    A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0005771    multivesicular body    A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0097486    multivesicular body lumen    The volume enclosed by the outermost membrane of a multivesicular body.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PSPB_HUMAN | P079881dfw 1kmr 1rg3 1rg4 1ssz 2jou 2m0h 2m1t

(-) Related Entries Specified in the PDB File

1rg3 THIS PEPTIDE CONSISTS OF THE C-TERMINAL HALF OF MINI-B. THE STRUCTURE WAS DETERMINED IN SDS MICELLES.
1rg4 THIS PEPTIDE CONSISTS OF THE C-TERMINAL HALF OF MINI-B. THE STRUCTURE WAS DETERMINED IN HFIP.
2a2h THIS IS AN IDENTICAL PEPTIDE. THE STRUCTURE WAS DETERMINED IN HFIP.