Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE COILED-COIL TRIMERIZATION DOMAIN FROM LUNG SURFACTANT PROTEIN D
 
Authors :  H. Kovacs, S. I. O'Donoghue, H. -J. Hoppe, D. Comfort, K. B. M. Reid, I. D. Campbell, M. Nilges
Date :  22 Jul 02  (Deposition) - 27 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (21x)
Keywords :  Coiled Coil, Lung Surfactant Protein, Trimer, Ambiguous Distance Restraints, Nmr-Spectroscopy, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Kovacs, S. I. O'Donoghue, H. -J. Hoppe, D. Comfort, K. B. M. Reid, I. D. Campbell, M. Nilges
Solution Structure Of The Coiled-Coil Trimerization Domain From Lung Surfactant Protein D
J. Biomol. Nmr V. 24 89 2002
PubMed-ID: 12495025  |  Reference-DOI: 10.1023/A:1020980006628
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PULMONARY SURFACTANT-ASSOCIATED PROTEIN D
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTRIMERIC COILED-COIL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (21x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1M7L)

(-) Sites  (0, 0)

(no "Site" information available for 1M7L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M7L)

(-) Exons   (3, 9)

NMR Structure (3, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003722922ENSE00001457451chr10:81708859-8170882238SFTPD_HUMAN-00--
1.3ENST000003722923ENSE00001679030chr10:81706418-81706217202SFTPD_HUMAN1-67670--
1.4ENST000003722924ENSE00001388162chr10:81702635-81702519117SFTPD_HUMAN67-106400--
1.5ENST000003722925ENSE00000909268chr10:81702260-81702144117SFTPD_HUMAN106-145400--
1.6ENST000003722926ENSE00000909267chr10:81701826-81701710117SFTPD_HUMAN145-184400--
1.7bENST000003722927bENSE00002173050chr10:81701270-81701154117SFTPD_HUMAN184-223403A:1-4
B:41-44
C:81-84
4
4
4
1.8ENST000003722928ENSE00001708197chr10:81700544-8170046184SFTPD_HUMAN223-251293A:4-32
B:44-72
C:84-112
29
29
29
1.9ENST000003722929ENSE00001920473chr10:81697984-81697496489SFTPD_HUMAN251-3751253A:32-40 (gaps)
B:72-80 (gaps)
C:112-120 (gaps)
20
20
20

(-) 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:40
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:51
                                   229       239       249       259       269 
          SFTPD_HUMAN   220 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGF 270
               SCOP domains d1m7la_ A: Surfactant protein                       SCOP domains
               CATH domains 1m7lA00 A:1-40                                      CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......-----------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
           Transcript 1 (1) 1.7b---------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.8  PDB: A:4-32        ------------------- Transcript 1 (2)
                 1m7l A   1 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNG-----------GI  40
                                    10        20        30       | -        39 
                                                                38          39 

Chain B from PDB  Type:PROTEIN  Length:40
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:51
                                   229       239       249       259       269 
          SFTPD_HUMAN   220 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGF 270
               SCOP domains d1m7lb_ B: Surfactant protein                       SCOP domains
               CATH domains 1m7lB00 B:41-80                                     CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......-----------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
           Transcript 1 (1) 1.7b---------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.8  PDB: B:44-72       ------------------- Transcript 1 (2)
                 1m7l B  41 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNG-----------GI  80
                                    50        60        70       | -        79 
                                                                78          79 

Chain C from PDB  Type:PROTEIN  Length:40
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:51
                                   229       239       249       259       269 
          SFTPD_HUMAN   220 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGF 270
               SCOP domains d1m7lc_ C: Surfactant protein                       SCOP domains
               CATH domains 1m7lC00 C:81-120                                    CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......-----------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
           Transcript 1 (1) 1.7b---------------------------Exon 1.9             Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.8  PDB: C:84-112      ------------------- Transcript 1 (2)
                 1m7l C  81 GLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNG-----------GI 120
                                    90       100       110       | -       119 
                                                               118         119 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 3)

NMR Structure

(-) CATH Domains  (1, 3)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M7L)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A,B,C   (SFTPD_HUMAN | P35247)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0048286    lung alveolus development    The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
    GO:0048246    macrophage chemotaxis    The movement of a macrophage in response to an external stimulus.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0045085    negative regulation of interleukin-2 biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0001817    regulation of cytokine production    Any process that modulates the frequency, rate, or extent of production of a cytokine.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    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:0043129    surfactant homeostasis    Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli.
cellular component
    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:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1m7l)
 
  Sites
(no "Sites" information available for 1m7l)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m7l)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1m7l
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SFTPD_HUMAN | P35247
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SFTPD_HUMAN | P35247
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SFTPD_HUMAN | P352471b08 1pw9 1pwb 2ggu 2ggx 2orj 2ork 2os9 2ria 2rib 2ric 2rid 2rie 3dbz 3g81 3g83 3g84 3ikn 3ikp 3ikq 3ikr 4e52 4m17 4m18

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1M7L)