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(-) Description

Title :  CUB1-EGF-CUB2 DOMAIN OF HUMAN MASP-1/3
 
Authors :  C. Gaboriaud
Date :  10 Jun 08  (Deposition) - 01 Jul 08  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complement System, Innate Immunity, Calcium Binding Sites, Complement Pathway, Egf-Like Domain, Glycoprotein, Hydrolase, Hydroxylation, Immune Response, Protease, Serine Protease, Sushi, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Teillet, C. Gaboriaud, M. Lacroix, L. Martin, G. J. Arlaud, N. M. Thielens
Crystal Structure Of The Cub1-Egf-Cub2 Domain Of Human Masp-1/3 And Identification Of Its Interaction Sites With Mannan-Binding Lectin And Ficolins
J. Biol. Chem. V. 283 25715 2008
PubMed-ID: 18596036  |  Reference-DOI: 10.1074/JBC.M803551200

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR MASP-3
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression System Cell LineHIGH FIVE CELLS
    Expression System Vector TypeBACULOVIRUS
    FragmentCUB1-EGF-CUB2 DOMAIN
    GeneMASP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsBACULOVIRUS/INSECT CELL SYSTEM
    SynonymMASP-1/3, MANNAN-BINDING LECTIN SERINE PEPTIDASE 1 (C4/C2 ACTIVATING COMPONENT OF RA-REACTIVE FACTOR), ISOFORM CRA_D, MANNAN- BINDING LECTIN SERINE PEPTIDASE 1, C4/C2 ACTIVATING COMPONENT OF RA- REACTIVE FACTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:159 , HOH A:8067BINDING SITE FOR RESIDUE NAG A 1001
2AC2SOFTWAREASP A:120 , VAL A:121 , GLU A:123 , ASN A:140 , TYR A:141 , GLY A:144 , HOH A:8005BINDING SITE FOR RESIDUE CA A 3001
3AC3SOFTWAREGLU A:49 , ASP A:57 , ASP A:102 , SER A:104 , HOH A:8009 , HOH A:8097BINDING SITE FOR RESIDUE CA A 5001
4AC4SOFTWAREGLU A:216 , ASP A:226 , ASP A:263 , SER A:265 , HOH A:8002 , HOH A:8021BINDING SITE FOR RESIDUE CA A 8001
5AC5SOFTWAREASP B:120 , VAL B:121 , GLU B:123 , ASN B:140 , TYR B:141 , GLY B:144 , HOH B:7008BINDING SITE FOR RESIDUE CA B 4001
6AC6SOFTWAREGLU B:49 , ASP B:57 , ASP B:102 , SER B:104BINDING SITE FOR RESIDUE CA B 6001
7AC7SOFTWAREGLU B:216 , ASP B:226 , ASP B:263 , SER B:265 , HOH B:7016 , HOH B:7020BINDING SITE FOR RESIDUE CA B 7001

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:72
2A:124 -A:138
3A:134 -A:147
4A:149 -A:162
5A:166 -A:193
6A:223 -A:241
7B:54 -B:72
8B:124 -B:138
9B:134 -B:147
10B:149 -B:162
11B:166 -B:193
12B:223 -B:241

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Tyr A:17 -Pro A:18
2Phe A:183 -Pro A:184
3Gly A:238 -Pro A:239
4Tyr B:17 -Pro B:18
5Phe B:183 -Pro B:184
6Gly B:238 -Pro B:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.MASP1_HUMAN11-138
185-297
 
  2-
A:166-278
B:166-278
2EGF_CAPS01187 Calcium-binding EGF-like domain signature.MASP1_HUMAN139-166
 
  2A:120-147
B:120-147
3ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.MASP1_HUMAN157-168
 
  2A:138-149
B:138-149
4EGF_2PS01186 EGF-like domain signature 2.MASP1_HUMAN166-181
 
  2A:147-162
B:147-162

(-) Exons   (0, 0)

(no "Exon" information available for 3DEM)

(-) 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:267
 aligned with MASP1_HUMAN | P48740 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:272
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
          MASP1_HUMAN    26 NMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTDTEQTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKEREDEELSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAA 297
               SCOP domains d3dema1 A:7-120 automated matches                                                                                 d3dema     2 A:121-165 automated matches     d3dema3 A:166-278 automated matches                                                                               SCOP domains
               CATH domains 3demA01 A:7-120  [code=2.60.120.290, no name defined]                                                             3demA0     2 A:121-164 Laminin              3demA03 A:165-278  [code=2.60.120.290, no name defined]                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........eeeeeeee....eeeeeeeeeee...hhhhh..eeeee....eeeee................ee....eeeeeeee.........eeeeeeeeee......-----.....eeeee..eeeee.....ee......ee...........eeeee............eeeeeee.....eeeeee.................eeeeee..eeeeee........ee....eeeeeee..........eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CUB  PDB: - UniProt: 11-138                                                                                      EGF_CA  PDB: A:120-147      ------------------CUB  PDB: A:166-278 UniProt: 185-297                                                                              PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL--------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------EGF_2           -------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dem A   7 NMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTDTEQTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKE-----LSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAA 278
                                    16        26        36        46        56        66        76        86        96       106       116       126     | 136       146       156       166       176       186       196       206       216       226       236       246       256       266       276  
                                                                                                                                                 126   132                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with MASP1_HUMAN | P48740 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:272
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
          MASP1_HUMAN    26 NMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTDTEQTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKEREDEELSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAA 297
               SCOP domains d3demb1 B:7-120 automated matches                                                                                 d3demb     2 B:121-165 automated matches     d3demb3 B:166-278 automated matches                                                                               SCOP domains
               CATH domains 3demB01 B:7-120  [code=2.60.120.290, no name defined]                                                             3demB0     2 B:121-164 Laminin              3demB03 B:165-278  [code=2.60.120.290, no name defined]                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........eeeeeeee....eeeeeeeeeee...hhhhh..eeeee....eeeee.......--.......ee....eeeeeeee.........eeeeeeeeee......-----.....eeeee..eeeee.....ee......ee...........eeeee............eeeeeee......eeeeeeeeee............eeeeee..eeeeee........ee....eeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CUB  PDB: - UniProt: 11-138                                                                                      EGF_CA  PDB: B:120-147      ------------------CUB  PDB: B:166-278 UniProt: 185-297                                                                              PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL--------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------EGF_2           -------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dem B   7 NMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTD--QTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKE-----LSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAA 278
                                    16        26        36        46        56        66        76 |  |   86        96       106       116       126     | 136       146       156       166       176       186       196       206       216       226       236       246       256       266       276  
                                                                                                  78 81                                          126   132                                                                                                                                                  

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MASP1_HUMAN | P48740)
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: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.
    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:0045916    negative regulation of complement activation    Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.
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_HUMAN | P487403gov 4aqb 4djz 4igd 4iw4 4kkd

(-) Related Entries Specified in the PDB File

1nt0 CRYSTAL STRUCTURE OF THE CUB1-EGF-CUB2 REGION OF MASP2
1nzi CRYSTAL STRUCTURE OF THE CUB1-EGF INTERACTION DOMAIN OF COMPLEMENT PROTEASE C1S