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(-) Description

Title :  EGF DOMAINS 1,2,5 OF HUMAN EMR2, A 7-TM IMMUNE SYSTEM MOLECULE, IN COMPLEX WITH STRONTIUM.
 
Authors :  R. J. M. Abbott, I. Spendlove, P. Roversi, P. Teriete, V. Knott, P. A. Han J. M. Mcdonnell, S. M. Lea
Date :  14 Apr 05  (Deposition) - 18 Oct 06  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Cd97, Cd55, 7Tm, Calcium-Binding, Cell Adhesion, Egf-Like Domain, G-Protein Coupled Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. J. M. Abbott, I. Spendlove, P. Roversi, H. Fitzgibbon, V. Knott, P. Teriete, J. M. Mcdonnell, P. A. Handford, S. M. Lea
Structural And Functional Characterization Of A Novel T Cell Receptor Co-Regulatory Protein Complex, Cd97-Cd55.
J. Biol. Chem. V. 282 22023 2007
PubMed-ID: 17449467  |  Reference-DOI: 10.1074/JBC.M702588200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainNM554
    Expression System Taxid562
    Expression System VariantPREP4
    Expression System Vector TypePLASMID
    FragmentEGF DOMAINS 1,2 AND 5,RESIDUES 25-118,212-260
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEGF-LIKE MODULE EMR2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2CL1Ligand/IonCHLORIDE ION
3SR2Ligand/IonSTRONTIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:95 , VAL A:96 , GLU A:98 , ASN A:114 , THR A:115 , SER A:118 , HOH A:2076BINDING SITE FOR RESIDUE SR A1144
2AC2SOFTWAREASP A:43 , ILE A:44 , GLU A:46 , ASN A:63 , THR A:64 , SER A:67 , CL A:1146BINDING SITE FOR RESIDUE SR A1145
3AC3SOFTWAREGLY A:26 , ASP A:43 , ILE A:44 , GLU A:46 , GLY A:66 , SER A:67 , SR A:1145BINDING SITE FOR RESIDUE CL A1146
4AC4SOFTWAREGLY A:56 , SER A:59 , ASP A:60BINDING SITE FOR RESIDUE CAC A1147

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:15
2A:9 -A:21
3A:23 -A:41
4A:47 -A:61
5A:55 -A:70
6A:72 -A:93
7A:99 -A:112
8A:106 -A:121
9A:123 -A:142

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BOX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BOX)

(-) PROSITE Motifs  (3, 7)

Asymmetric/Biological Unit (3, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.AGRE2_HUMAN67-106
119-162
163-201
212-250
  3A:43-82
A:95-99
-
A:100-133
2EGF_CAPS01187 Calcium-binding EGF-like domain signature.AGRE2_HUMAN67-94
119-145
163-189
212-238
  3A:43-70
A:95-99
-
A:100-121
3ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.AGRE2_HUMAN85-96
136-147
180-191
229-240
  2A:61-72
-
-
A:112-123

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003155761ENSE00001693849chr19:14889353-14889069285AGRE2_HUMAN-00--
1.2ENST000003155762ENSE00002191167chr19:14887739-14887538202AGRE2_HUMAN1-11110--
1.3ENST000003155763ENSE00001651719chr19:14885118-1488506851AGRE2_HUMAN11-28181A:3-42
1.4ENST000003155764ENSE00001682173chr19:14884866-14884750117AGRE2_HUMAN28-67401A:4-4340
1.5ENST000003155765ENSE00001686069chr19:14883309-14883154156AGRE2_HUMAN67-119531A:43-95 (gaps)53
1.6ENST000003155766ENSE00001661372chr19:14877921-14877790132AGRE2_HUMAN119-163451A:95-995
1.7aENST000003155767aENSE00001701230chr19:14877193-14877047147AGRE2_HUMAN163-212500--
1.8ENST000003155768ENSE00001618574chr19:14876616-14876470147AGRE2_HUMAN212-261501A:100-143 (gaps)44
1.9ENST000003155769ENSE00001789199chr19:14876382-1487633647AGRE2_HUMAN261-276160--
1.10ENST0000031557610ENSE00001310171chr19:14876209-1487613278AGRE2_HUMAN277-302260--
1.11ENST0000031557611ENSE00000873228chr19:14875422-14875245178AGRE2_HUMAN303-362600--
1.12ENST0000031557612ENSE00001274234chr19:14867157-14867050108AGRE2_HUMAN362-398370--
1.13aENST0000031557613aENSE00001273581chr19:14866689-14866466224AGRE2_HUMAN398-472750--
1.14ENST0000031557614ENSE00001781176chr19:14865939-14865766174AGRE2_HUMAN473-530580--
1.15ENST0000031557615ENSE00001702606chr19:14863338-14863141198AGRE2_HUMAN531-596660--
1.16ENST0000031557616ENSE00001724318chr19:14862483-14862248236AGRE2_HUMAN597-675790--
1.17ENST0000031557617ENSE00001711017chr19:14857774-1485770867AGRE2_HUMAN675-697230--
1.18ENST0000031557618ENSE00001639863chr19:14857135-1485704492AGRE2_HUMAN698-728310--
1.19ENST0000031557619ENSE00001597079chr19:14854596-14854428169AGRE2_HUMAN728-784570--
1.20ENST0000031557620ENSE00001592248chr19:14854342-14854232111AGRE2_HUMAN785-821370--
1.21ENST0000031557621ENSE00001737543chr19:14847056-148432053852AGRE2_HUMAN822-82320--

(-) 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:135
 aligned with AGRE2_HUMAN | Q9UHX3 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:234
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256    
          AGRE2_HUMAN    27 RGCARWCPQDSSCVNATACRCNPGFSSFSEIITTPMETCDDINECATLSKVSCGKFSDCWNTEGSYDCVCSPGYEPVSGAKTFKNESENTCQDVDECQQNPRLCKSYGTCVNTLGSYTCQCLPGFKLKPEDPKLCTDVNECTSGQNPCHSSTHCLNNVGSYQCRCRPGWQPIPGSPNGPNNTVCEDVDECSSGQHQCDSSTVCFNTVGSYSCRCRPGWKPRHGIPNNQKDTVCE 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee.....eee...ee.............ee.hhhhh----.....eeeeee..eeeeee...eee........hhhhh.eee....---------------------------------------------------------------------------------------------...........eeeee..eeeee.--.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------EGF_3  PDB: A:43-82 UniProt: 67-106     ------------EGF_3  PDB: A:95-99 UniProt: 119-162        EGF_3  PDB: - UniProt: 163-201         ----------EGF_3  PDB: A:100-133 UniProt: 212-250 ---------- PROSITE (1)
                PROSITE (2) ----------------------------------------EGF_CA  PDB: A:43-70        ------------------------EGF_CA  PDB: A:95-99       -----------------EGF_CA  PDB: -             ----------------------EGF_CA  PDB: A:100-121     ---------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------ASX_HYDROXYL---------------------------------------ASX_HYDROXYL--------------------------------ASX_HYDROXYL-------------------------------------ASX_HYDROXYL-------------------- PROSITE (3)
           Transcript 1 (1) 1.--------------------------------------Exon 1.5  PDB: A:43-95 (gaps) UniProt: 67-119        -------------------------------------------Exon 1.7a  PDB: - UniProt: 163-212                ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: A:4-43 UniProt: 28-67    ---------------------------------------------------Exon 1.6  PDB: A:95-99 UniProt: 119-163      ------------------------------------------------Exon 1.8  PDB: A:100-143 (gaps) UniProt: 212-261  Transcript 1 (2)
                 2box A   3 RGCARWCPQDSSCVNATACRCNPGFSSFSEIITTPMETCDDINECAT----SCGKFSDCWNTEGSYDCVCSPGYEPVSGAKTFKNESENTCQDVDEC---------------------------------------------------------------------------------------------SSGQHQCDSSTVCFNTVGSYSCRC--GWKPRHGIPNNQKDTVCE 143
                                    12        22        32        42      |  - |      62        72        82        92      |  -         -         -         -         -         -         -         -         -         -|      109       119   |  |129       139    
                                                                         49   54                                           99                                                                                           100                    123  |                 
                                                                                                                                                                                                                                                  126                 

   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 2BOX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BOX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BOX)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGRE2_HUMAN | Q9UHX3)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0035374    chondroitin sulfate binding    Interacting selectively and non-covalently with chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    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.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071621    granulocyte chemotaxis    The movement of a granulocyte in response to an external stimulus.
    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: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.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0031256    leading edge membrane    The portion of the plasma membrane surrounding the leading edge of a motile cell.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGRE2_HUMAN | Q9UHX32bo2 2bou

(-) Related Entries Specified in the PDB File

2bo2 EGF DOMAINS 1,2,5 OF HUMAN EMR2, A 7-TM IMMUNE SYSTEM MOLECULE, IN COMPLEX WITH CALCIUM.
2bou EGF DOMAINS 1,2,5 OF HUMAN EMR2, A 7-TM IMMUNE SYSTEM MOLECULE, IN COMPLEX WITH BARIUM.