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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED HUMAN CD21 SCR1-SCR2 (COMPLEMENT RECEPTOR TYPE 2)
 
Authors :  A. E. Prota, D. R. Sage, T. Stehle, J. D. Fingeroth
Date :  06 Jun 02  (Deposition) - 05 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Complement Receptor; Epstein Barr Virus; Regulator Of Complement Activation; Short Consensus Repeat; Viral Receptor; Complement Control Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. E. Prota, D. R. Sage, T. Stehle, J. D. Fingeroth
The Crystal Structure Of Human Cd21: Implications For Epstein-Barr Virus And C3D Binding.
Proc. Natl. Acad. Sci. Usa V. 99 10641 2002
PubMed-ID: 12122212  |  Reference-DOI: 10.1073/PNAS.162360499

(-) Compounds

Molecule 1 - COMPLEMENT RECEPTOR TYPE 2
    ChainsA
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System StrainX-33
    Expression System Taxid4922
    Expression System VectorPICZA (INVITROGEN) SECRETED PROTEIN
    GeneCR2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD21;
EPSTEIN-BARR VIRUS RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:87 , ASN A:101 , ILE A:129BINDING SITE FOR RESIDUE NAG A 1001
2AC2SOFTWARETYR A:16 , ASP A:56 , LYS A:57 , PRO A:58 , GLY A:106 , ASN A:107 , HOH A:1023 , HOH A:1040 , HOH A:1049 , HOH A:1133BINDING SITE FOR RESIDUE NAG A 1002

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:45
2A:31 -A:62
3A:71 -A:112
4A:98 -A:126

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:19 -Pro A:20
2Thr A:86 -Pro A:87
3Gly A:119 -Pro A:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LY2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CR2_HUMAN21-84
89-148
152-212
213-273
274-344
408-468
349-407
469-524
525-595
600-659
660-716
717-781
786-845
849-909
910-970
  2A:2-64
A:69-128
-
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003670581aENSE00001952555chr1:207627575-207627821247CR2_HUMAN1-20201A:0-01
1.3bENST000003670583bENSE00001069650chr1:207639871-207640257387CR2_HUMAN20-1491301A:0-129130
1.4bENST000003670584bENSE00000882434chr1:207641872-207642060189CR2_HUMAN149-212641A:129-1291
1.5ENST000003670585ENSE00000882436chr1:207642145-207642244100CR2_HUMAN212-245340--
1.6ENST000003670586ENSE00000791926chr1:207642495-20764257783CR2_HUMAN245-273290--
1.7bENST000003670587bENSE00000882439chr1:207643040-207643447408CR2_HUMAN273-4091370--
1.8ENST000003670588ENSE00000882440chr1:207644085-207644261177CR2_HUMAN409-468600--
1.9aENST000003670589aENSE00000882441chr1:207644342-20764443291CR2_HUMAN468-498310--
1.10ENST0000036705810ENSE00001167936chr1:207644768-20764484477CR2_HUMAN498-524270--
1.12bENST0000036705812bENSE00001381764chr1:207646117-207646524408CR2_HUMAN524-6601370--
1.14ENST0000036705814ENSE00001167916chr1:207647146-20764723085CR2_HUMAN660-688290--
1.15ENST0000036705815ENSE00001167908chr1:207647586-20764766883CR2_HUMAN688-716290--
1.16aENST0000036705816aENSE00001167899chr1:207648169-207648561393CR2_HUMAN716-8471320--
1.17ENST0000036705817ENSE00001167890chr1:207649579-207649764186CR2_HUMAN847-909630--
1.18ENST0000036705818ENSE00001167878chr1:207651230-207651415186CR2_HUMAN909-971630--
1.19ENST0000036705819ENSE00001167866chr1:207652602-20765262524CR2_HUMAN971-97990--
1.20ENST0000036705820ENSE00001167855chr1:207653323-20765339876CR2_HUMAN979-1004260--
1.21bENST0000036705821bENSE00001246608chr1:207658809-207658917109CR2_HUMAN1004-1033300--
1.22bENST0000036705822bENSE00001841611chr1:207662487-207663240754CR2_HUMAN-00--

(-) 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:130
 aligned with CR2_HUMAN | P20023 from UniProtKB/Swiss-Prot  Length:1033

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
            CR2_HUMAN    20 GISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPTCVSV 149
               SCOP domains d1ly2a1 A:0-66 Complement receptor 2, cr2                          d1ly2a2 A:67-129 Complement receptor 2, cr2                     SCOP domains
               CATH domains 1ly2A01 A:0-64 Complement Module, domain 1                       -----1ly2A02 A:70-128 Complement Module, domain 1               - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------Sushi-1ly2A01 A:71-126                                  --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------Sushi-1ly2A02 A:71-126                                  --- Pfam domains (2)
         Sec.struct. author ..ee........eee......ee...eeeeee...eeee...eeeee.......ee.....eeee.....ee.......eeeee....ee...eeeeee...eeee...eeee.....ee.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SUSHI  PDB: A:2-64 UniProt: 21-84                               ----SUSHI  PDB: A:69-128 UniProt: 89-148                        - PROSITE
           Transcript 1 (1) 1--------------------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) Exon 1.3b  PDB: A:0-129 UniProt: 20-149                                                                                            Transcript 1 (2)
                 1ly2 A   0 EASCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPTCVSI 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CR2_HUMAN | P20023)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001848    complement binding    Interacting selectively and non-covalently with any component or product of the complement cascade.
    GO:0004875    complement receptor activity    Combining with any component or product of the complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    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:0002430    complement receptor mediated signaling pathway    A series of molecular signals generated as a consequence of a component of the complement pathway binding to a complement receptor. Such components include both whole complement proteins and fragments of complement proteins generated through the activity of the complement pathway.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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: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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CR2_HUMAN | P200231ghq 1w2r 1w2s 2aty 2gsx 3oed

(-) Related Entries Specified in the PDB File

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