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(-) Description

Title :  STRUCTURE OF THE CALCIUM-DEPENDENT LECTIN DOMAIN FROM A RAT MANNOSE-BINDING PROTEIN DETERMINED BY MAD PHASING
 
Authors :  W. I. Weis, K. Drickamer, W. A. Hendrickson
Date :  23 Sep 91  (Deposition) - 15 Jan 92  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hepatic Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. I. Weis, R. Kahn, R. Fourme, K. Drickamer, W. A. Hendrickson
Structure Of The Calcium-Dependent Lectin Domain From A Rat Mannose-Binding Protein Determined By Mad Phasing.
Science V. 254 1608 1991
PubMed-ID: 1721241
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-BINDING PROTEIN-A
    ChainsA, B
    EngineeredYES
    Organism CommonBLACK RAT
    Organism ScientificRATTUS RATTUS
    Organism Taxid10117

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1HO4Ligand/IonHOLMIUM ATOM

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:161 , GLU A:165 , ASP A:188 , GLU A:193 , ASP A:194 , HOH A:222BINDING SITE FOR RESIDUE HO A 1
2AC2SOFTWAREGLU A:185 , ASN A:187 , GLU A:193 , ASN A:205 , ASP A:206 , HOH A:223BINDING SITE FOR RESIDUE HO A 2
3AC3SOFTWAREHOH B:31 , ASP B:161 , GLU B:165 , ASP B:188 , GLU B:193 , ASP B:194BINDING SITE FOR RESIDUE HO B 1
4AC4SOFTWAREHOH B:32 , GLU B:185 , ASN B:187 , GLU B:193 , ASN B:205 , ASP B:206BINDING SITE FOR RESIDUE HO B 2
5HO1UNKNOWNASP A:161 , GLU A:165 , ASP A:188 , GLU A:193 , ASP A:194 , HOH A:222NULL
6HO2UNKNOWNGLU A:185 , ASN A:187 , GLU A:193 , ASN A:205 , ASP A:206 , HOH A:223NULL
7HO3UNKNOWNASP B:161 , GLU B:165 , ASP B:188 , GLU B:193 , ASP B:194 , HOH B:31NULL
8HO4UNKNOWNGLU B:185 , ASN B:187 , GLU B:193 , ASN B:205 , ASP B:206 , HOH B:32NULL

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:128 -A:217
2A:195 -A:209
3B:128 -B:217
4B:195 -B:209

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:185 -Pro A:186
2Glu B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.MBL1_RAT212-234
 
  2A:195-217
B:195-217

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000157231ENSRNOE00000411163chr16:17591820-1759188162MBL1_RAT-00--
1.2ENSRNOT000000157232ENSRNOE00000110617chr16:17593783-17593943161MBL1_RAT1-51510--
1.3ENSRNOT000000157233ENSRNOE00000110943chr16:17594301-17594417117MBL1_RAT51-90400--
1.4ENSRNOT000000157234ENSRNOE00000111237chr16:17596168-1759624275MBL1_RAT90-115260--
1.5ENSRNOT000000157235ENSRNOE00000111555chr16:17597083-17597859777MBL1_RAT115-2381242A:107-221
B:107-221
115
115

(-) Sequences/Alignments

Asymmetric/Biological 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:115
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:115
                                   133       143       153       163       173       183       193       203       213       223       233     
             MBL1_RAT   124 SGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d1msba_ A: Mannose-binding protein A, C-lectin domain                                                               SCOP domains
               CATH domains 1msbA00 A:107-221 Mannose-Binding Protein A, subunit A                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhh..eeeeee........ee........................eeee.hhh.eeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE
               Transcript 1 Exon 1.5  PDB: A:107-221 UniProt: 115-238 [INCOMPLETE]                                                              Transcript 1
                 1msb A 107 SGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 221
                                   116       126       136       146       156       166       176       186       196       206       216     

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:115
                                   133       143       153       163       173       183       193       203       213       223       233     
             MBL1_RAT   124 SGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d1msbb_ B: Mannose-binding protein A, C-lectin domain                                                               SCOP domains
               CATH domains 1msbB00 B:107-221 Mannose-Binding Protein A, subunit A                                                              CATH domains
           Pfam domains (1) ----------Lectin_C-1msbB01 B:117-219                                                                             -- Pfam domains (1)
           Pfam domains (2) ----------Lectin_C-1msbB02 B:117-219                                                                             -- Pfam domains (2)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh..eeeeee........ee........................eeee.hhh.eeee........eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE
               Transcript 1 Exon 1.5  PDB: B:107-221 UniProt: 115-238 [INCOMPLETE]                                                              Transcript 1
                 1msb B 107 SGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPNDHGSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 221
                                   116       126       136       146       156       166       176       186       196       206       216     

   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: C_Lectin (98)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MBL1_RAT | P19999)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    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:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0001867    complement activation, lectin pathway    Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive 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:0051873    killing by host of symbiont cells    Any process mediated by an organism that results in the death of cells in the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MBL1_RAT | P199991afa 1afb 1afd 1bch 1bcj 1buu 1fif 1fih 1kmb 1kwt 1kwu 1kwv 1kww 1kwx 1kwy 1kwz 1kx0 1kx1 1rtm 1ytt 2kmb 2msb 3kmb 4kmb

(-) Related Entries Specified in the PDB File

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