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(-) Description

Title :  COMPARATIVE ANALYSES OF PENTRAXINS: IMPLICATIONS FOR PROTOMER ASSEMBLY AND LIGAND BINDING
 
Authors :  N. Srinivasan, H. E. White, J. Emsley, S. P. Wood, M. B. Pepys, T. L. Blundell
Date :  06 Apr 95  (Deposition) - 15 Oct 95  (Release) - 15 Oct 95  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E
Keywords :  Pentraxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Srinivasan, H. E. White, J. Emsley, S. P. Wood, M. B. Pepys, T. L. Blundell
Comparative Analyses Of Pentraxins: Implications For Protomer Assembly And Ligand Binding.
Structure V. 2 1017 1994
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-REACTIVE PROTEIN
    ChainsA, B, C, D, E
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCRP

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Theoretical Model (1, 10)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 1CRV)

(-) SS Bonds  (5, 5)

Theoretical Model
No.Residues
1A:36 -A:95
2B:36 -B:95
3C:36 -C:95
4D:36 -D:95
5E:36 -E:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CRV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 10)

Theoretical Model (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTX_2PS51828 Pentraxin (PTX) domain profile.CRP_HUMAN23-224
 
 
 
 
  5A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
2PTX_1PS00289 Pentraxin domain signature.CRP_HUMAN113-120
 
 
 
 
  5A:93-100
B:93-100
C:93-100
D:93-100
E:93-100

(-) Exons   (2, 10)

Theoretical Model (2, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002550301bENSE00001328381chr1:159684379-159684215165CRP_HUMAN1-21215A:1-3
B:1-3
C:1-3
D:1-3
E:1-3
3
3
3
3
3
1.2cENST000002550302cENSE00001287766chr1:159683928-1596820791850CRP_HUMAN21-2242045A:3-204 (gaps)
B:3-204 (gaps)
C:3-204 (gaps)
D:3-204 (gaps)
E:3-204 (gaps)
205
205
205
205
205

(-) Sequences/Alignments

Theoretical Model
   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:206
 aligned with CRP_HUMAN | P02741 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:206
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
            CRP_HUMAN    19 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee........eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee......eee..........eeeee..................eeee..eee.....hhhhhhhhh..............eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: A:5-204 UniProt: 23-224                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2c  PDB: A:3-204 (gaps) UniProt: 21-224                                                                                                                                                               Transcript 1 (2)
                 1crv A   1 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 204
                                    10        20        30        40    ||  48        58        68        78        88||      98       108       118       128       138       148       158       168       178       188       198      
                                                                      44A|                                          88A|                                                                                                                  
                                                                       44B                                            90                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with CRP_HUMAN | P02741 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:206
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
            CRP_HUMAN    19 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee........eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee......eee..........eeeee..................eeee..eee.....hhhhhhhhh..............eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: B:5-204 UniProt: 23-224                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2c  PDB: B:3-204 (gaps) UniProt: 21-224                                                                                                                                                               Transcript 1 (2)
                 1crv B   1 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 204
                                    10        20        30        40    ||  48        58        68        78        88||      98       108       118       128       138       148       158       168       178       188       198      
                                                                      44A|                                          88A|                                                                                                                  
                                                                       44B                                            90                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with CRP_HUMAN | P02741 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:206
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
            CRP_HUMAN    19 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee........eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee......eee..........eeeee..................eeee..eee.....hhhhhhhhh..............eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: C:5-204 UniProt: 23-224                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2c  PDB: C:3-204 (gaps) UniProt: 21-224                                                                                                                                                               Transcript 1 (2)
                 1crv C   1 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 204
                                    10        20        30        40    ||  48        58        68        78        88||      98       108       118       128       138       148       158       168       178       188       198      
                                                                      44A|                                          88A|                                                                                                                  
                                                                       44B                                            90                                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:206
 aligned with CRP_HUMAN | P02741 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:206
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
            CRP_HUMAN    19 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee........eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee......eee..........eeeee..................eeee..eee.....hhhhhhhhh..............eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: D:5-204 UniProt: 23-224                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2c  PDB: D:3-204 (gaps) UniProt: 21-224                                                                                                                                                               Transcript 1 (2)
                 1crv D   1 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 204
                                    10        20        30        40    ||  48        58        68        78        88||      98       108       118       128       138       148       158       168       178       188       198      
                                                                      44A|                                          88A|                                                                                                                  
                                                                       44B                                            90                                                                                                                  

Chain E from PDB  Type:PROTEIN  Length:206
 aligned with CRP_HUMAN | P02741 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:206
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
            CRP_HUMAN    19 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeee........eeeeeeeee........eeeeeeee......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee......eee..........eeeee..................eeee..eee.....hhhhhhhhh..............eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: E:5-204 UniProt: 23-224                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2c  PDB: E:3-204 (gaps) UniProt: 21-224                                                                                                                                                               Transcript 1 (2)
                 1crv E   1 QTDMSRKAFVFPKESDTSYVSLKAPLTKPLKAFTVCLHFYTELSSTRGYSIFSYATKRQDNEILIFWSKDIGYSFTVGGSEILFEVPEVTVAPVHICTSWESASGIVEFWVDGKPRVRKSLKKGYTVGAEASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEINTIYLGGPFSPNVLNWRALKYEVQGEVFTKPQLWP 204
                                    10        20        30        40    ||  48        58        68        78        88||      98       108       118       128       138       148       158       168       178       188       198      
                                                                      44A|                                          88A|                                                                                                                  
                                                                       44B                                            90                                                                                                                  

   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 1CRV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1CRV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CRV)

(-) Gene Ontology  (20, 20)

Theoretical Model(hide GO term definitions)
Chain A,B,C,D,E   (CRP_HUMAN | P02741)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0033265    choline binding    Interacting selectively and non-covalently with choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium.
    GO:0001849    complement component C1q binding    Interacting selectively and non-covalently with the C1q component of the classical complement cascade.
    GO:0030169    low-density lipoprotein particle binding    Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0046790    virion binding    Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
biological process
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0010888    negative regulation of lipid storage    Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0010745    negative regulation of macrophage derived foam cell differentiation    Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:0008228    opsonization    The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032930    positive regulation of superoxide anion generation    Any process that activates or increases the frequency, rate or extent of enzymatic generation of superoxide by a cell.
    GO:2000482    regulation of interleukin-8 secretion    Any process that modulates the frequency, rate or extent of interleukin-8 secretion.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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
        CRP_HUMAN | P027411b09 1gnh 1lj7 3l2y 3pvn 3pvo

(-) Related Entries Specified in the PDB File

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