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(-) Description

Title :  CRYSTAL STRUCTURE OF MASP-1 CUB2 DOMAIN BOUND TO METHYLAMINE
 
Authors :  A. R. Gingras, P. C. E. Moody, R. Wallis
Date :  22 Nov 10  (Deposition) - 24 Aug 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (3x),B (3x)
Biol. Unit 4:  A (3x),B (3x)
Biol. Unit 5:  A  (3x)
Biol. Unit 6:  B  (3x)
Keywords :  Cub Domain, Ca2+ Binding Site, Complex With Methylamine, Complement Protein, Lectin Pathway Of Complement, Mbl, Mbp, Ficolins, Bloodstream, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. R. Gingras, U. V. Girija, A. H. Keeble, R. Panchal, D. A. Mitchell, P. C. Moody, R. Wallis
Structural Basis Of Mannan-Binding Lectin Recognition By It Associated Serine Protease Masp-1: Implications For Complement Activation.
Structure V. 19 1635 2011
PubMed-ID: 22078562  |  Reference-DOI: 10.1016/J.STR.2011.08.014

(-) Compounds

Molecule 1 - MANNAN-BINDING LECTIN SERINE PROTEASE 1
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypeVECTOR
    FragmentMASP-1 CUB2 DOMAIN (UNP RESIDUES 188-301)
    GeneCRARF, MASP-1/-3, MASP1, MASP3
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymCOMPLEMENT FACTOR MASP-3, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR, MANNOSE-BINDING LECTIN-ASSOCIATED SERINE PROTEASE 1, MASP-1, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE, RA- REACTIVE FACTOR SERINE PROTEASE P100, RARF, SERINE PROTEASE 5, MANNAN-BINDING LECTIN SERINE PROTEASE 1 HEAVY CHAIN, MANNAN-BINDING LECTIN SERINE PROTEASE 1 LIGHT CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (3x)A (3x)B (3x)
Biological Unit 4 (3x)A (3x)B (3x)
Biological Unit 5 (3x)A 
Biological Unit 6 (3x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NME1Ligand/IonMETHYLAMINE
3SO42Ligand/IonSULFATE ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME1Ligand/IonMETHYLAMINE
3SO41Ligand/IonSULFATE ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME-1Ligand/IonMETHYLAMINE
3SO41Ligand/IonSULFATE ION
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 3 (3, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME3Ligand/IonMETHYLAMINE
3SO43Ligand/IonSULFATE ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 4 (3, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME3Ligand/IonMETHYLAMINE
3SO43Ligand/IonSULFATE ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 5 (3, 9)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME3Ligand/IonMETHYLAMINE
3SO43Ligand/IonSULFATE ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NME-1Ligand/IonMETHYLAMINE
3SO43Ligand/IonSULFATE ION
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , HOH A:14 , GLU A:216 , ASP A:226 , ASP A:263 , SER A:265BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREGLU A:216 , TYR A:225 , ASP A:263 , SER A:265BINDING SITE FOR RESIDUE NME A 2
3AC3SOFTWAREHOH A:31 , ARG A:269 , HOH A:303BINDING SITE FOR RESIDUE SO4 A 278
4AC4SOFTWAREHOH A:34 , HOH A:158 , HOH A:161 , ASP A:182 , TYR A:183 , ASN A:185 , PHE A:209 , GLU A:210 , ASP A:211 , SER A:245 , THR B:175 , ARG B:276BINDING SITE FOR RESIDUE TRS A 279
5AC5SOFTWAREHOH B:4 , HOH B:8 , GLU B:216 , ASP B:226 , ASP B:263 , SER B:265BINDING SITE FOR RESIDUE CA B 1
6AC6SOFTWAREHOH B:30 , HOH B:62 , ARG B:269BINDING SITE FOR RESIDUE SO4 B 2

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:166 -A:193
2A:223 -A:241
3B:166 -B:193
4B:223 -B:241

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:183 -Pro A:184
2Gly A:238 -Pro A:239
3Tyr B:183 -Pro B:184
4Gly B:238 -Pro B:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  2A:166-277
B:166-277
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  1A:166-277
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  1-
B:166-277
-
Biological Unit 3 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  6A:166-277
B:166-277
-
Biological Unit 4 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  6A:166-277
B:166-277
-
Biological Unit 5 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  3A:166-277
-
-
Biological Unit 6 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_RAT190-302
 
16-143
  3-
B:166-277
-

(-) Exons   (0, 0)

(no "Exon" information available for 3POI)

(-) 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:113
 aligned with MASP1_RAT | Q8CHN8 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:113
                                   198       208       218       228       238       248       258       268       278       288       298   
            MASP1_RAT   189 ECSGNLFTQRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIEDHPEVPCPYDYIKIKAGSKVWGPFCGEKSPEPISTQSHSIQILFRSDNSGENRGWRLSYRA 301
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeee............eeeeeee.......eeee.................eeeeee..eeeeee........ee....eeeeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CUB  PDB: A:166-277 UniProt: 190-302                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3poi A 165 ECSGNLFTQRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIEDHPEVPCPYDYIKIKAGSKVWGPFCGEKSPEPISTQSHSIQILFRSDNSGENRGWRLSYRA 277
                                   174       184       194       204       214       224       234       244       254       264       274   

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with MASP1_RAT | Q8CHN8 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:114
                                   197       207       217       227       237       247       257       267       277       287       297    
            MASP1_RAT   188 VECSGNLFTQRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIEDHPEVPCPYDYIKIKAGSKVWGPFCGEKSPEPISTQSHSIQILFRSDNSGENRGWRLSYRA 301
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeee............eeeeeee.......eeee.................eeeeee..eeeeee........ee....eeeeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --CUB  PDB: B:166-277 UniProt: 190-302                                                                             PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3poi B 164 VECSGNLFTQRTGTITSPDYPNPYPKSSECSYTIDLEEGFMVTLQFEDIFDIEDHPEVPCPYDYIKIKAGSKVWGPFCGEKSPEPISTQSHSIQILFRSDNSGENRGWRLSYRA 277
                                   173       183       193       203       213       223       233       243       253       263       273    

   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  (0, 0)

(no "SCOP Domain" information available for 3POI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3POI)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MASP1_RAT | Q8CHN8)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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
        MASP1_RAT | Q8CHN83pob 3poe 3pof 3pog 3poj 5ckq

(-) Related Entries Specified in the PDB File

3pob CUB DOMAIN IN COMPLEX WITH MBL PEPTIDE
3pof SEARCH MODEL