Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF EMILIN-1 C1Q-LIKE DOMAIN
 
Authors :  G. Verdone, S. A. Colebrooke, A. Corazza, D. O. Cicero, T. Eliseo, P. Viglino, I. D. Campbell, A. Colombatti, G. Esposito
Date :  11 Jan 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
Keywords :  Emilin-1, C1Q-Like Domain, Homotrimeric Protein Complex, Beta-Sandwich, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Verdone, S. A. Colebrooke, A. Corazza, D. O. Cicero, T. Eliseo, P. Viglino, I. D. Campbell, A. Colombatti, G. Esposito
The Solution Structure Of The C-Terminal Domain Of Emilin-1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EMILIN-1
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineM15 CELLS
    Expression System Taxid562
    Expression System Vector TypePQE-30
    FragmentC-TERMINAL DOMAIN, C1Q DOMAIN
    GeneEMILIN1, EMI
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymELASTIN MICROFIBRIL INTERFACE-LOCATED PROTEIN 1, ELASTIN MICROFIBRIL INTERFACER 1

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2OII)

(-) Sites  (0, 0)

(no "Site" information available for 2OII)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OII)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

NMR Structure (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046097E903KEMIL1_HUMANPolymorphism36045790A/B/CE882K

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OII)

(-) Exons   (2, 6)

NMR Structure (2, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003803201ENSE00001484569chr2:27301435-27302103669EMIL1_HUMAN1-57570--
1.2ENST000003803202ENSE00000732220chr2:27303019-27303138120EMIL1_HUMAN57-97410--
1.3ENST000003803203ENSE00000732221chr2:27303600-27303820221EMIL1_HUMAN97-171750--
1.4aENST000003803204aENSE00000809129chr2:27304951-273068791929EMIL1_HUMAN171-8146440--
1.5ENST000003803205ENSE00000732225chr2:27307283-27307399117EMIL1_HUMAN814-853400--
1.6ENST000003803206ENSE00001802271chr2:27307859-2730787618EMIL1_HUMAN853-85970--
1.7ENST000003803207ENSE00000809130chr2:27308028-27308165138EMIL1_HUMAN859-905473A:846-884
B:846-884
C:846-884
39
39
39
1.8ENST000003803208ENSE00001669474chr2:27308546-27309271726EMIL1_HUMAN905-10161123A:884-995 (gaps)
B:884-995 (gaps)
C:884-995 (gaps)
112
112
112

(-) Sequences/Alignments

NMR Structure
   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:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2oiia_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..............eeee.....ee....eee....eeeeeee..........eeee..........ee..-------------------...............eeeee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: A:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2oii A  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946                                                 

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2oiib_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..............eeee.....ee....eee....eeeeeee..........eeee..........ee..-------------------...............eeeee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: B:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: B:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2oii B  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946                                                 

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with EMIL1_HUMAN | Q9Y6C2 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:150
                                   876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016
         EMIL1_HUMAN    867 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGGYEPEGLENKPVAESQPSPGTLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA 1016
               SCOP domains d2oiic_ C: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----C1q-2oiiC01 C:851-986                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) -----C1q-2oiiC02 C:851-986                                                                                                                   --------- Pfam domains (2)
           Pfam domains (3) -----C1q-2oiiC03 C:851-986                                                                                                                   --------- Pfam domains (3)
         Sec.struct. author .....eeeee..............ee.......ee....ee.....eeeeeee.........eeeee..........eee.-------------------.................eee...............eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------K----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7  PDB: C:846-884 [INCOMPLETE]  --------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8  PDB: C:884-995 (gaps) UniProt: 905-1016                                                                Transcript 1 (2)
                2oii C  846 PVPQVAFSAALSLPRSEPGTVPFDRVLLNDGGYYDPETGVFTAPLAGRYLLSAVLTGHRHEKVEAVLSRSNQGVARVDSGG-------------------TLGVFSLILPLQAGDTVCVDLVMGQLAHSEEPLTIFSGALLYGDPELEHA  995
                                   855       865       875       885       895       905       915       925|        -         -|      955       965       975       985       995
                                                                                                          926                 946                                                 

   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, 3)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

NMR Structure
(-)
Clan: C1q_TNF (45)
(-)
Family: C1q (8)
1aC1q-2oiiC01C:851-986
1bC1q-2oiiC02C:851-986
1cC1q-2oiiC03C:851-986

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A,B,C   (EMIL1_HUMAN | Q9Y6C2)
molecular function
    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).
biological process
    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.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2oii)
 
  Sites
(no "Sites" information available for 2oii)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oii)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2oii
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EMIL1_HUMAN | Q9Y6C2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  EMIL1_HUMAN | Q9Y6C2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EMIL1_HUMAN | Q9Y6C22ka3

(-) Related Entries Specified in the PDB File

1c28 ACRP-30 CHAIN A