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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC REGION OF HUMAN MASP-1
 
Authors :  V. Harmat, J. Dobo, L. Beinrohr, E. Sebestyen, P. Zavodszky, P. Gal
Date :  20 Mar 09  (Deposition) - 09 Jun 09  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complement, Serine Protease, Beta Barrel, Hydrolase, Hydroxylation, Immune Response, Innate Immunity, Sushi, Coagulation, Complement Pathway, Disulfide Bond, Egf-Like Domain, Glycoprotein, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Dobo, V. Harmat, L. Beinrohr, E. Sebestyen, P. Zavodszky, P. Gal
Masp-1, A Promiscuous Complement Protease: Structure Of Its Catalytic Region Reveals The Basis Of Its Broad Specificity
J. Immunol. V. 183 1207 2009
PubMed-ID: 19564340  |  Reference-DOI: 10.4049/JIMMUNOL.0901141

(-) Compounds

Molecule 1 - MASP-1
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSUSHI-1 AND SUSHI-2 DOMAINS, CCP1-CCP2, RESIDUES 298-448
    GeneCRARF, CRARF1, MASP1, PRSS5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRA-REACTIVE FACTOR SERINE PROTEASE P100, RARF, MANNAN- BINDING LECTIN SERINE PROTEASE 1, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE, MASP-1, SERINE PROTEASE 5, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR HEAVY CHAIN, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR LIGHT CHAIN
 
Molecule 2 - MASP-1
    ChainsB
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSERINE PROTEASE DOMAIN, RESIDUES 449-699
    GeneCRARF, CRARF1, MASP1, PRSS5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRA-REACTIVE FACTOR SERINE PROTEASE P100, RARF, MANNAN- BINDING LECTIN SERINE PROTEASE 1, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE, MASP-1, SERINE PROTEASE 5, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR HEAVY CHAIN, COMPLEMENT-ACTIVATING COMPONENT OF RA-REACTIVE FACTOR LIGHT CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:313 , LEU A:326 , SER A:328 , SER A:442 , HOH B:5 , LYS B:457BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREMET A:342 , ASP A:343 , THR A:344 , HOH B:12BINDING SITE FOR RESIDUE GOL B 2

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:301 -A:349
2A:329 -A:362
3A:367 -A:414
4A:397 -A:432
5A:436 -B:572
6B:475 -B:491
7B:614 -B:631
8B:642 -B:672

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:313 -Pro A:314
2Glu A:399 -Pro A:400
3Ala B:619 -Pro B:620
4Arg B:655 -Glu B:656

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051832V568AMASP1_HUMANPolymorphism13322090BV568A
2UniProtVAR_051833G679RMASP1_HUMANPolymorphism3774266BG679R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 5)

Asymmetric/Biological Unit (4, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.MASP1_HUMAN299-364
365-434
  2A:299-364
A:365-434
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.MASP1_HUMAN449-696  1B:449-696
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.MASP1_HUMAN486-491  1B:486-491
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.MASP1_HUMAN640-651  1B:640-651

(-) Exons   (0, 0)

(no "Exon" information available for 3GOV)

(-) 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:147
 aligned with MASP1_HUMAN | P48740 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:147
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       
          MASP1_HUMAN   298 GNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNNNTGIYTCSAQGVWMNKVLGRSLPTCLPVCGLPKFSRK 444
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eeee.....ee...eeeeee...eeeee..eee.eeeee............eeee...........eeeee...........eeeeee....eee......eeee.....ee..........eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SUSHI  PDB: A:299-364 UniProt: 299-364                            SUSHI  PDB: A:365-434 UniProt: 365-434                                ---------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gov A 298 GNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNNNTGIYTCSAQGVWMNKVLGRSLPTCLPVCGLPKFSRK 444
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with MASP1_HUMAN | P48740 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:251
                                   458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698 
          MASP1_HUMAN   449 IFNGRPAQKGTTPWIAMLSHLNGQPFCGGSLLGSSWIVTAAHCLHQSLDPEDPTLRDSDLLSPSDFKIILGKHWRLRSDENEQHLGVKHTTLHPQYDPNTFENDVALVELLESPVLNAFVMPICLPEGPQQEGAMVIVSGWGKQFLQRFPETLMEIEIPIVDHSTCQKAYAPLKKKVTRDMICAGEKEGGKDACAGDSGGPMVTLNRERGQWYLVGTVSWGDDCGKKDRYGVYSYIHHNKDWIQRVTGVRN 699
               SCOP domains d3govb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 3govB01     3govB02 B:461-570,B:687-699 Trypsin-like serine proteases                                                     3govB01 B:449-460,B:571-686 Trypsin-like serine proteases                                                           3govB02       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee...eeeehhhhhh..........hhhhh.hhh.eeeee............eee.eeeeee.............eeeee........................eeeeee.............eeeeeeeehhhhhhhhh..........eeee................eeeee......eeeeeeeee..........eeeee...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------R-------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:449-696 UniProt: 449-696                                                                                                                                                                                                            --- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gov B 449 IFNGRPAQKGTTPWIAMLSHLNGQPFCGGSLLGSSWIVTAAHCLHQSLDPKDPTLRDSDLLSPSDFKIILGKHWRLRSDENEQHLGVKHTTLHPQYDPNTFENDVALVELLESPVLNAFVMPICLPEGPQQEGAMVIVSGWGKQFLQRFPETLMEIEIPIVDHSTCQKAYAPLKKKVTRDMICAGEKEGGKDACAGDSGGPMVTLNRERGQWYLVGTVSWGDDCGKKDRYGVYSYIHHNKDWIQRVTGVRN 699
                                   458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698 

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P487403dem 4aqb 4djz 4igd 4iw4 4kkd

(-) Related Entries Specified in the PDB File

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