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(-) Description

Title :  STRUCTURE OF PORCINE SURFACTANT PROTEIN D NECK AND CARBOHYDRATE RECOGNITION DOMAIN COMPLEXED WITH MANNOSE
 
Authors :  M. Van Eijk, M. J. Rynkiewicz, M. R. White, K. L. Hartshorn, X. Zou, K. Sc D. Luo, E. C. Crouch, T. M. Cafarella, J. F. Head, H. P. Haagsman, B. A. Se
Date :  08 Feb 12  (Deposition) - 20 Jun 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Collectin, Lectin, Carbohydrate/Sugar Binding, Lung Surfactant, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Van Eijk, M. J. Rynkiewicz, M. R. White, K. L. Hartshorn, X. Zou, K. Schulten, D. Luo, E. C. Crouch, T. R. Cafarella, J. F. Head, H. P. Haagsman, B. A. Seaton
A Unique Sugar-Binding Site Mediates The Distinct Anti-Influenza Activity Of Pig Surfactant Protein D.
J. Biol. Chem. V. 287 26666 2012
PubMed-ID: 22685299  |  Reference-DOI: 10.1074/JBC.M112.368571

(-) Compounds

Molecule 1 - PULMONARY SURFACTANT-ASSOCIATED PROTEIN D
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System PlasmidPUPE105.03
    Expression System StrainHEK293
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentNECK AND CARBOHYDRATE RECOGNITION DOMAIN, UNP RESIDUES 223- 378
    GeneSFTPD
    MutationYES
    Organism CommonPIGS,SWINE,WILD BOAR
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    SynonymPSP-D, SP-D, LUNG SURFACTANT PROTEIN D

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:297 , GLU A:301 , ASN A:324 , GLU A:329 , ASN A:330BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:321 , ASN A:323 , GLU A:329 , ASN A:341 , ASP A:342 , BMA A:403BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREGLU A:321 , ASN A:323 , ASN A:325 , GLU A:329 , ASN A:341 , LYS A:343 , CA A:402BINDING SITE FOR RESIDUE BMA A 403

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:261 -A:353
2A:331 -A:345

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:234 -Pro A:235
2Glu A:321 -Pro A:322

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DN8)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SFTPD_PIG272-377  1A:252-354
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SFTPD_PIG354-376  1A:331-353
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SFTPD_PIG272-377  3A:252-354
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SFTPD_PIG354-376  3A:331-353

(-) Exons   (0, 0)

(no "Exon" information available for 4DN8)

(-) Sequences/Alignments

Asymmetric Unit
   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:155
 aligned with SFTPD_PIG | Q9N1X4 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:155
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373     
           SFTPD_PIG    224 ITALRQQVETLQGQVQRLQKAFSQYKKVELFPNGRGVGEKIFKTGGFEKTFQDAQQVCTQAGGQMASPRSETENEALSQLVTAQNKAAFLSMTDIKTEGNFTYPTGEPLVYANWAPGEPNNNGGSSGAENCVEIFPNGKWNDKACGELRLVICEF  378
               SCOP domains -------------------------------d4dn8a1 A:235-355 Surfactant protein, lectin domain                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..eeeeee.............................hhhhh...eeee.....eeee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------C_TYPE_LECTIN_2  PDB: A:252-354 UniProt: 272-377                                                          - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        -- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4dn8 A  204 ITALRQQVETLQGQVQRLQKAFSQYKKVELFPNGRGVGEKIFKTGGFEKTFQDAQQVCTQAGGQMASPRSETENEALSQLVTAQNKAAFLSMTDIKTEGQFTYPTGEPLVYANWAPGEPNNNGGSSGAENCVEIFPNGKWNDKACGELRLVICEF  355
                                   213       223       233       243       253       263       273       283       293       303       313       323   ||| 330       340       350     
                                                                                                                                                    326A||                             
                                                                                                                                                     326B|                             
                                                                                                                                                      326C                             

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DN8)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (SFTPD_PIG | Q9N1X4)
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.
biological process
    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: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: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: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: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.

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