Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CLEC9A C-TYPE LECTIN-LIKE DOMAIN
 
Authors :  P. E. Czabotar, J. G. Zhang, A. N. Policheni, K. Shortman, M. H. Lahoud, P
Date :  07 Mar 12  (Deposition) - 25 Apr 12  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dendritic Cell, C-Type Lectin-Like Domain, Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Zhang, P. E. Czabotar, A. N. Policheni, I. Caminschi, S. S. Wan, S. Kitsoulis, K. M. Tullett, A. Y. Robin, R. Brammananth, M. F. Van Delft, J. Lu, L. A. O'Reilly, E. C. Josefsson, B. T. Kile, W. J. Chin, J. D. Mintern, M. A. Olshina, W. Wong, J. Baum, M. D. Wright, D. C. Huang, N. Mohandas, R. L. Coppel, P. M. Colman, N. A. Nicola, K. Shortman, M. H. Lahoud
The Dendritic Cell Receptor Clec9A Binds Damaged Cells Via Exposed Actin Filaments.
Immunity V. 36 646 2012
PubMed-ID: 22483802  |  Reference-DOI: 10.1016/J.IMMUNI.2012.03.009

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 9 MEMBER A
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Fragment: C-TYPE LECTIN-LIKE DOMAIN, UNP RESIDUES 110-241
    Gene: CLEC9A, UNQ9341/PRO34046
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:150 , GLU A:152 , GLU A:156 , GLU A:233 , HOH A:403 , HOH A:428BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREGLN B:150 , GLU B:152 , GLU B:156 , GLU B:233 , HOH B:407 , HOH B:412BINDING SITE FOR RESIDUE CA B 301

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:113 -A:124
2A:141 -A:232
3A:211 -A:224
4B:113 -B:124
5B:141 -B:232
6B:211 -B:224

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VPP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VPP)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC9A_HUMAN120-233
 		  2A:120-233
B:120-233
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC9A_HUMAN211-232
 		  2A:211-232
B:211-232
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC9A_HUMAN120-233
 		  1A:120-233
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC9A_HUMAN211-232
 		  1A:211-232
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC9A_HUMAN120-233
 		  1-
B:120-233
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC9A_HUMAN211-232
 		  1-
B:211-232

(-) Exons   (0, 0)

(no "Exon" information available for 3VPP)

(-) Sequences/Alignments

Asymmetric 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:121
 aligned with CLC9A_HUMAN | Q6UXN8 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:127
                                   120       130       140       150       160       170       180       190       200       210       220       230       
          CLC9A_HUMAN   111 SPCPNNWIQNRESCYYVSEIWSIWHTSQENCLKEGSTLLQIESKEEMDFITGSLRKIKGSYDYWVGLSQDGHSGRWLWQDGSSPSPGLLPAERSQSANQVCGYVKSNSLLSSNCSTWKYFICEKYAL 237
               SCOP domains d3vppa_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh......eeeeeeee......eee..............------.eeeeee..eeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------C_TYPE_LECTIN_2  PDB: A:120-233 UniProt: 120-233                                                                  ---- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpp A 111 SPCPNNWIQNRESCYYVSEIWSIWHTSQENCLKEGSTLLQIESKEEMDFITGSLRKIKGSYDYWVGLSQDGHSGRWLWQDGSSPSPGLLPAE------QVCGYVKSNSLLSSNCDTWKYFICEKYAL 237
                                   120       130       140       150       160       170       180       190       200 |     210       220       230       
                                                                                                                     202    209                            


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with CLC9A_HUMAN | Q6UXN8 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:127
                                   120       130       140       150       160       170       180       190       200       210       220       230       
          CLC9A_HUMAN   111 SPCPNNWIQNRESCYYVSEIWSIWHTSQENCLKEGSTLLQIESKEEMDFITGSLRKIKGSYDYWVGLSQDGHSGRWLWQDGSSPSPGLLPAERSQSANQVCGYVKSNSLLSSNCSTWKYFICEKYAL 237
               SCOP domains d3vppb_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh......eeeeeeee......eee..............-----..eeeeee..eeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------C_TYPE_LECTIN_2  PDB: B:120-233 UniProt: 120-233                                                                  ---- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpp B 111 SPCPNNWIQNRESCYYVSEIWSIWHTSQENCLKEGSTLLQIESKEEMDFITGSLRKIKGSYDYWVGLSQDGHSGRWLWQDGSSPSPGLLPAE-----NQVCGYVKSNSLLSSNCDTWKYFICEKYAL 237
                                   120       130       140       150       160       170       180       190       200 |     210       220       230       
                                                                                                                     202   208
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VPP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VPP)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CLC9A_HUMAN | Q6UXN8)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0050715    positive regulation of cytokine secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vpp)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3vpp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CLC9A_HUMAN | Q6UXN8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CLC9A_HUMAN | Q6UXN8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3VPP)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VPP)