Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE NK CELL LIGAND RAE-1 BETA
 
Authors :  P. Li, R. K. Strong
Date :  21 Jun 01  (Deposition) - 20 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Murine Nk Cell Ligand, Rae-1 Beta, Nkg2D, Mhc-I Platform, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Li, G. Mcdermott, R. K. Strong
Crystal Structures Of Rae-1Beta And Its Complex With The Activating Immunoreceptor Nkg2D.
Immunity V. 16 77 2002
PubMed-ID: 11825567  |  Reference-DOI: 10.1016/S1074-7613(02)00258-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOIC ACID EARLY TRANSCRIPT BETA
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RAE-1BETA
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: RAE-1 BETA

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1JFM)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:7 -A:26
2A:60 -A:160
3B:7 -B:26
4B:60 -B:160
5C:7 -C:26
6C:60 -C:160
7D:7 -D:26
8D:60 -D:160
9E:7 -E:26
10E:60 -E:160

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JFM)

(-) Exons   (0, 0)

(no "Exon" information available for 1JFM)

(-) 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:174
 aligned with RAE1B_MOUSE | O08603 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
          RAE1B_MOUSE    31 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 204
               SCOP domains d1jfma_ A: NK cell ligand RAE-1 beta                                                                                                                                           SCOP domains
               CATH domains 1jfmA00 A:1-174 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..........eeeeeee..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.........eeeeee...eeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jfm A   1 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with RAE1B_MOUSE | O08603 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
          RAE1B_MOUSE    31 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 204
               SCOP domains d1jfmb_ B: NK cell ligand RAE-1 beta                                                                                                                                           SCOP domains
               CATH domains 1jfmB00 B:1-174 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee...........eeeeee..eeeeeee..eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeee..........eeeeee...eeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jfm B   1 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with RAE1B_MOUSE | O08603 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
          RAE1B_MOUSE    31 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 204
               SCOP domains d1jfmc_ C: NK cell ligand RAE-1 beta                                                                                                                                           SCOP domains
               CATH domains 1jfmC00 C:1-174 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee...........eeeeee..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeee.........eeeeee...eeeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jfm C   1 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain D from PDB  Type:PROTEIN  Length:174
 aligned with RAE1B_MOUSE | O08603 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
          RAE1B_MOUSE    31 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 204
               SCOP domains d1jfmd_ D: NK cell ligand RAE-1 beta                                                                                                                                           SCOP domains
               CATH domains 1jfmD00 D:1-174 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..........eeeeee....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee.........eeeeee...eeeeee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jfm D   1 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain E from PDB  Type:PROTEIN  Length:174
 aligned with RAE1B_MOUSE | O08603 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:174
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
          RAE1B_MOUSE    31 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 204
               SCOP domains d1jfme_ E: NK cell ligand RAE-1 beta                                                                                                                                           SCOP domains
               CATH domains 1jfmE00 E:1-174 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee...........eeeeee..eeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeee..........eeeeee...eeeeee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jfm E   1 DAHSLRCNLTIKDPTPADPLWYEAKCFVGEILILHLSNINKTMTSGDPGETANATEVKKCLTQPLKNLCQKLRNKVSNTKVDTHKTNGYPHLQVTMIYPQSQGRTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWKDDGEFVKQLKFLIHECSQKMDEFLKQSKEK 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RAE1B_MOUSE | O08603)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0046703    natural killer cell lectin-like receptor binding    Interacting selectively and non-covalently with a lectin-like natural killer cell receptor.
    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:0001913    T cell mediated cytotoxicity    The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0071360    cellular response to exogenous dsRNA    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0002839    positive regulation of immune response to tumor cell    Any process that activates or increases the frequency, rate, or extent of an immune response to tumor cell.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0043032    positive regulation of macrophage activation    Any process that stimulates, induces or increases the rate of macrophage activation.
    GO:0032816    positive regulation of natural killer cell activation    Any process that activates or increases the frequency, rate or extent of natural killer cell activation.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0042271    susceptibility to natural killer cell mediated cytotoxicity    The process of causing a cell to become susceptible to natural killer cell mediated cytotoxicity.
cellular component
    GO:0031362    anchored component of external side of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0046658    anchored component of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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.

 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
(no "Ligands, Modified Residues, Ions" information available for 1jfm)
 
  Sites
(no "Sites" information available for 1jfm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jfm)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  1jfm
    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
  RAE1B_MOUSE | O08603
    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
  RAE1B_MOUSE | O08603
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RAE1B_MOUSE | O08603: 4pp8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JFM)