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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT SURFACTANT PROTEIN A NECK AND CARBOHYDRATE RECOGNITION DOMAIN (NCRD) COMPLEXED WITH MANNOSE
 
Authors :  F. Shang, M. J. Rynkiewicz, F. X. Mccormack, H. Wu, T. M. Cafarella, J. He B. A. Seaton
Date :  19 Oct 10  (Deposition) - 03 Nov 10  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Collectin, Sugar Binding Protein, Mannose (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Shang, M. J. Rynkiewicz, F. X. Mccormack, H. Wu, T. M. Cafarella, J. F. Head, B. A. Seaton
Crystallographic Complexes Of Surfactant Protein A And Carbohydrates Reveal Ligand-Induced Conformational Change.
J. Biol. Chem. V. 286 757 2011
PubMed-ID: 21047777  |  Reference-DOI: 10.1074/JBC.M110.175265

(-) Compounds

Molecule 1 - PULMONARY SURFACTANT-ASSOCIATED PROTEIN A
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA
    Expression System PlasmidPVL 1392
    Expression System Taxid7110
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 101-248
    GeneSFTP-1, SFTP1, SFTPA, SFTPA1
    MutationYES
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPSAP, PSP-A, SP-A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MAN1Ligand/IonALPHA-D-MANNOSE
3NA1Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MAN3Ligand/IonALPHA-D-MANNOSE
3NA-1Ligand/IonSODIUM ION
4SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:195 , GLU A:202 , ASN A:214 , ASP A:215 , MAN A:500 , HOH A:518BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWAREGLU A:171 , GLY A:198 , GLY A:200 , LYS A:201 , GLU A:202 , ASP A:215BINDING SITE FOR RESIDUE NA A 301
3AC3SOFTWAREARG A:216 , GLN A:220 , ARG A:222 , HOH A:564BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWAREGLU A:149 , GLU A:195 , ARG A:197 , GLU A:202 , TYR A:208 , ASN A:214 , ASP A:215 , ARG A:216 , CA A:300 , HOH A:518 , HOH A:519BINDING SITE FOR RESIDUE MAN A 500

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:135 -A:226
2A:204 -A:218

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:195 -Pro A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PAK)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SFTPA_RAT134-247  1A:114-227
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SFTPA_RAT224-246  1A:204-226
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SFTPA_RAT134-247  3A:114-227
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SFTPA_RAT224-246  3A:204-226

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000478701ENSRNOE00000343643chr16:17570887-1757091731SFTPA_RAT-00--
1.2ENSRNOT000000478702ENSRNOE00000317514chr16:17571511-17571707197SFTPA_RAT1-58580--
1.3ENSRNOT000000478703ENSRNOE00000108375chr16:17571895-17572014120SFTPA_RAT58-98410--
1.4ENSRNOT000000478704ENSRNOE00000108787chr16:17572890-1757296778SFTPA_RAT98-124271A:84-10421
1.5ENSRNOT000000478705ENSRNOE00000109185chr16:17573209-175743891181SFTPA_RAT124-2481251A:104-228125

(-) 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:145
 aligned with SFTPA_RAT | P08427 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:145
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243     
            SFTPA_RAT   104 DEELQTELYEIKHQILQTMGVLSLQGSMLSVGDKVFSTNGQSVNFDTIKEMCTRAGGNIAVPRTPEENEAIASIAKKYNNYVYLGMIEDQTPGDFHYLDGASVNYTNWYPGEPRGQGKEKCVEMYTDGTWNDRGCLQYRLAVCEF 248
               SCOP domains d3paka1 A:84-109          d3paka2 A:110-228 Surfactant protein, lectin domain                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------Lectin_C-3pakA01 A:124-228                                                                                Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..eeeeeee......eee.......................eeee.....eeee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------C_TYPE_LECTIN_2  PDB: A:114-227 UniProt: 134-247                                                                  - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        -- PROSITE (2)
           Transcript 1 (1) Exon 1.4 [INCOMPLETE]---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.5  PDB: A:104-228 UniProt: 124-248                                                                                     Transcript 1 (2)
                 3pak A  84 DEELQTELYEIKHQILQTMGVLSLQGSMLSVGDKVFSTNGQSVNFDTIKEMCTRAGGNIAVPRTPEENEAIASIAKKYNNYVYLGMIEDQTPGDFHYLDGASVSYTNWYPGEPRGQGKEKCVEMYTDGTWNDRGCLQYRLAVCEF 228
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223     

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PAK)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (SFTPA_RAT | P08427)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0071732    cellular response to nitric oxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    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:0070849    response to epidermal growth factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0009725    response to hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
    GO:0055093    response to hyperoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0070741    response to interleukin-6    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0033189    response to vitamin A    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus.
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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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: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: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.
    GO:0005791    rough endoplasmic reticulum    The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SFTPA_RAT | P084271gie 1r13 1r14 3paq 3par 3pbf 4wr9 4wrc 4wre 4wrf 4wuw 4wux 5ffr 5ffs 5fft

(-) Related Entries Specified in the PDB File

1r13 SURFACTANT PROTEIN A NCRD
1r14 SAMARIUM SOAKED SURFACTANT PROTEIN A NCRD
3paq SURFACTANT PROTEIN-A NCRD COMPLEXED WITH ALPHA-METHYLMANNOSE
3par UNLIGANDED SURFACTANT PROTEIN-A NCRD
3pbf SURFACTANT PROTEIN-A NCRD COMPLEXED WITH GLYCEROL