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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  MODEL OF RAT CRRY DETERMINED BY SOLUTION SCATTERING, CURVE FITTING AND HOMOLOGY MODELLING
 
Authors :  M. Aslam, J. M. Guthridge, B. K. Hack, R. J. Quigg, V. M. Holers, S. J. Perkins
Date :  30 Jan 03  (Deposition) - 03 Feb 04  (Release) - 07 Apr 10  (Revision)
Method :  SOLUTION SCATTERING
Resolution :  NOT APPLICABLE
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunology, Complement, Glycoprotein, Scr, Ccp, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Aslam, J. M. Guthridge, B. K. Hack, R. J. Quigg, V. M. Holers, S. J. Perkins
The Extended Multidomain Solution Structures Of The Complement Protein Crry And Its Chimeric Conjugate Crry-Ig By Scattering, Analytical Ultracentrifugation And Constrained Modelling: Implications For Function And Therapy
J. Mol. Biol. V. 329 525 2003
PubMed-ID: 12767833  |  Reference-DOI: 10.1016/S0022-2836(03)00492-3

(-) Compounds

Molecule 1 - COMPLEMENT RECEPTOR RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: SCR-1 TO SCR-5
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NTJ)

(-) Sites  (0, 0)

(no "Site" information available for 1NTJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NTJ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 5)

Asymmetric/Biological Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CR1L_RAT36-96
97-158
159-229
231-290
292-354
355-415
417-477		  5A:3-63
A:64-125
A:126-196
A:198-257
A:259-320
-
-

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000107991ENSRNOE00000344752chr13:111057427-111057067361CR1L_RAT1-36361A:1-33
1.2ENSRNOT000000107992ENSRNOE00000259154chr13:111054088-111053909180CR1L_RAT36-96611A:3-6361
1.3ENSRNOT000000107993ENSRNOE00000259145chr13:111053179-111053080100CR1L_RAT96-129341A:63-9634
1.4ENSRNOT000000107994ENSRNOE00000258717chr13:111047369-11104728486CR1L_RAT129-158301A:96-12530
1.5ENSRNOT000000107995ENSRNOE00000258708chr13:111032883-111032485399CR1L_RAT158-2911341A:125-258134
1.6ENSRNOT000000107996ENSRNOE00000258698chr13:111029696-111029594103CR1L_RAT291-325351A:258-29235
1.7ENSRNOT000000107997ENSRNOE00000258691chr13:111028340-11102825586CR1L_RAT325-354301A:292-32029
1.8ENSRNOT000000107998ENSRNOE00000258677chr13:111025811-111025626186CR1L_RAT354-416630--
1.9ENSRNOT000000107999ENSRNOE00000362867chr13:111021835-111021650186CR1L_RAT416-478630--
1.10ENSRNOT0000001079910ENSRNOE00000258669chr13:111019296-11101927324CR1L_RAT478-48690--
1.11ENSRNOT0000001079911ENSRNOE00000258661chr13:111018067-11101799276CR1L_RAT486-511260--
1.12ENSRNOT0000001079912ENSRNOE00000281590chr13:111013671-111013567105CR1L_RAT511-546360--
1.13ENSRNOT0000001079913ENSRNOE00000076758chr13:111010497-111010302196CR1L_RAT546-559140--

(-) 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:320
 aligned with CR1L_RAT | Q63135 from UniProtKB/Swiss-Prot  Length:559

    Alignment length:320
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
             CR1L_RAT    34 TLGQCPAPPLFPYAKPINPTDESTFPVGTSLKYECRPGYIKRQFSITCEVNSVWTSPQDVCIRKQCETPLDPQNGIVHVNTDIRFGSSITYTCNEGYRLIGSSSAMCIISDQSVAWDAEAPICESIPCEIPPSIPNGDFFSPNREDFHYGMVVTYQCNTDARGKKLFNLVGEPSIHCTSIDGQVGVWSGPPPQCIELNKCTPPHVENAVIVSKNKSLFSLRDMVEFRCQDGFMMKGDSSVYCRSLNRWEPQLPSCFKVKSCGAFLGELPNGHVFVPQNLQLGAKVTFVCNTGYQLKGNSSSHCVLDGVESIWNSSVPVCE 353
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................................................................................................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SUSHI  PDB: A:3-63 UniProt: 36-96                            SUSHI  PDB: A:64-125 UniProt: 97-158                          SUSHI  PDB: A:126-196 UniProt: 159-229                                 -SUSHI  PDB: A:198-257 UniProt: 231-290                      -SUSHI  PDB: A:259-320 UniProt: 292-354                         PROSITE
           Transcript 1 (1) 1.1-----------------------------------------------------------Exon 1.3  PDB: A:63-96            ----------------------------Exon 1.5  PDB: A:125-258 UniProt: 158-291                                                                                             ---------------------------------Exon 1.7  PDB: A:292-320      Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:3-63 UniProt: 36-96                         --------------------------------Exon 1.4  PDB: A:96-125       ------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:258-292           ---------------------------- Transcript 1 (2)
                 1ntj A   1 TLGQCPAPPLFPYAKPINPTDESTFPVGTSLKYECRPGYIKRQFSITCEVNSVWTSPQDVCIRKQCETPLDPQNGIVHVNTDIRFGSSITYTCNEGYRLIGSSSAMCIISDQSVAWDAEAPICESIPCEIPPSIPNGDFFSPNREDFHYGMVVTYQCNTDARGKKLFNLVGEPSIHCTSIDGQVGVWSGPPPQCIELNKCTPPHVENAVIVSKNKSLFSLRDMVEFRCQDGFMMKGDSSVYCRSLNRWEPQLPSCFKVKSCGAFLGELPNGHVFVPQNLQLGAKVTFVCNTGYQLKGNSSSHCVLDGVESIWNSSVPVCE 320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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  (0, 0)

(no "SCOP Domain" information available for 1NTJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CR1L_RAT | Q63135)
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:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045916    negative regulation of complement activation    Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  CR1L_RAT | Q63135
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 Related Entries

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

UniProtKB/Swiss-Prot
        CR1L_RAT | Q63135: 2xrb 2xrd

(-) Related Entries Specified in the PDB File

1gkg COMPLEMENT RECEPTOR TYPE 1 SCR-17 WAS USED AS A TEMPLATE FOR ONE SCR DOMAIN
1qub B2 GLYCOPROTEIN I WAS USED AS A TEMPLATE FOR THREE SCR DOMAINS
1vvc VACCINIA COAT PROTEIN SCR-4 WAS USED AS A TEMPLATE FOR ONE SCR DOMAIN