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(-) Description

Title :  THE CRYSTAL STRUCTURE OF NATURAL KILLER CELL RECEPTOR LY49C
 
Authors :  L. Deng, R. A. Mariuzza
Date :  12 Feb 08  (Deposition) - 15 Apr 08  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Natural Killer Cell Receptor, Mhc, Virus, Crystal Structure, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Deng, S. Cho, E. L. Malchiodi, M. C. Kerzic, J. Dam, R. A. Mariuzza
Molecular Architecture Of The Major Histocompatibility Complex Class I-Binding Site Of Ly49 Natural Killer Cell Receptors.
J. Biol. Chem. V. 283 16840 2008
PubMed-ID: 18426793  |  Reference-DOI: 10.1074/JBC.M801526200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NATURAL KILLER CELL RECEPTOR LY49C
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET21A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 65-266
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3C8J)

(-) Sites  (0, 0)

(no "Site" information available for 3C8J)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:145 -A:150
2A:163 -A:251
3A:167 -A:253
4A:232 -A:245
5B:145 -B:150
6B:163 -B:251
7B:167 -B:253
8B:232 -B:245
9C:145 -C:150
10C:163 -C:251
11C:167 -C:253
12C:232 -C:245
13D:145 -D:150
14D:163 -D:251
15D:167 -D:253
16D:232 -D:245

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 48)

Asymmetric Unit (12, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_KLRA3_MOUSE_013 *Y146HKLRA3_MOUSE  ---  ---A/B/C/DY142H
02UniProtVAR_KLRA3_MOUSE_014 *S151GKLRA3_MOUSE  ---  ---A/B/C/DS147G
03UniProtVAR_KLRA3_MOUSE_015 *Y174FKLRA3_MOUSE  ---  ---A/B/C/DY170F
04UniProtVAR_KLRA3_MOUSE_016 *L179VKLRA3_MOUSE  ---  ---A/B/C/DL175V
05UniProtVAR_KLRA3_MOUSE_017 *F189SKLRA3_MOUSE  ---  ---A/B/C/DF185S
06UniProtVAR_KLRA3_MOUSE_018 *N198SKLRA3_MOUSE  ---  ---A/B/C/DN194S
07UniProtVAR_KLRA3_MOUSE_019 *P219QKLRA3_MOUSE  ---  ---A/B/C/DP215Q
08UniProtVAR_KLRA3_MOUSE_020 *I226TKLRA3_MOUSE  ---  ---A/B/C/DI222T
09UniProtVAR_KLRA3_MOUSE_021 *K232TKLRA3_MOUSE  ---  ---A/B/C/DK228T
10UniProtVAR_KLRA3_MOUSE_022 *I247TKLRA3_MOUSE  ---  ---A/B/C/DI243T
11UniProtVAR_KLRA3_MOUSE_023 *I251TKLRA3_MOUSE  ---  ---A/B/C/DI247T
12UniProtVAR_KLRA3_MOUSE_024 *K260RKLRA3_MOUSE  ---  ---A/B/C/DK256R
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (12, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_KLRA3_MOUSE_013 *Y146HKLRA3_MOUSE  ---  ---A/BY142H
02UniProtVAR_KLRA3_MOUSE_014 *S151GKLRA3_MOUSE  ---  ---A/BS147G
03UniProtVAR_KLRA3_MOUSE_015 *Y174FKLRA3_MOUSE  ---  ---A/BY170F
04UniProtVAR_KLRA3_MOUSE_016 *L179VKLRA3_MOUSE  ---  ---A/BL175V
05UniProtVAR_KLRA3_MOUSE_017 *F189SKLRA3_MOUSE  ---  ---A/BF185S
06UniProtVAR_KLRA3_MOUSE_018 *N198SKLRA3_MOUSE  ---  ---A/BN194S
07UniProtVAR_KLRA3_MOUSE_019 *P219QKLRA3_MOUSE  ---  ---A/BP215Q
08UniProtVAR_KLRA3_MOUSE_020 *I226TKLRA3_MOUSE  ---  ---A/BI222T
09UniProtVAR_KLRA3_MOUSE_021 *K232TKLRA3_MOUSE  ---  ---A/BK228T
10UniProtVAR_KLRA3_MOUSE_022 *I247TKLRA3_MOUSE  ---  ---A/BI243T
11UniProtVAR_KLRA3_MOUSE_023 *I251TKLRA3_MOUSE  ---  ---A/BI247T
12UniProtVAR_KLRA3_MOUSE_024 *K260RKLRA3_MOUSE  ---  ---A/BK256R
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (12, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_KLRA3_MOUSE_013 *Y146HKLRA3_MOUSE  ---  ---C/DY142H
02UniProtVAR_KLRA3_MOUSE_014 *S151GKLRA3_MOUSE  ---  ---C/DS147G
03UniProtVAR_KLRA3_MOUSE_015 *Y174FKLRA3_MOUSE  ---  ---C/DY170F
04UniProtVAR_KLRA3_MOUSE_016 *L179VKLRA3_MOUSE  ---  ---C/DL175V
05UniProtVAR_KLRA3_MOUSE_017 *F189SKLRA3_MOUSE  ---  ---C/DF185S
06UniProtVAR_KLRA3_MOUSE_018 *N198SKLRA3_MOUSE  ---  ---C/DN194S
07UniProtVAR_KLRA3_MOUSE_019 *P219QKLRA3_MOUSE  ---  ---C/DP215Q
08UniProtVAR_KLRA3_MOUSE_020 *I226TKLRA3_MOUSE  ---  ---C/DI222T
09UniProtVAR_KLRA3_MOUSE_021 *K232TKLRA3_MOUSE  ---  ---C/DK228T
10UniProtVAR_KLRA3_MOUSE_022 *I247TKLRA3_MOUSE  ---  ---C/DI243T
11UniProtVAR_KLRA3_MOUSE_023 *I251TKLRA3_MOUSE  ---  ---C/DI247T
12UniProtVAR_KLRA3_MOUSE_024 *K260RKLRA3_MOUSE  ---  ---C/DK256R
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.KLRA3_MOUSE150-258
 
 
 
  4A:146-254
B:146-254
C:146-254
D:146-254
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.KLRA3_MOUSE150-258
 
 
 
  2A:146-254
B:146-254
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.KLRA3_MOUSE150-258
 
 
 
  2-
-
C:146-254
D:146-254

(-) Exons   (0, 0)

(no "Exon" information available for 3C8J)

(-) 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:127
 aligned with KLRA3_MOUSE | Q64329 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:127
                                   149       159       169       179       189       199       209       219       229       239       249       259       
          KLRA3_MOUSE   140 TGRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYSVPILKIEDEDELKFLQRHVIPENYWIGLSYDKKKKEWAWIDNGPSKLDMKIRKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 266
               SCOP domains d3c8ja_ A: automated matches                                                                                                    SCOP domains
               CATH domains 3c8jA00 A:136-262 Mannose-Binding Protein A, subunit A                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.eeeeeeeeeehhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeeee....eeee.......hhhhhhh.......eeee....eeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------H----G----------------------F----V---------S--------S--------------------Q------T-----T--------------T---T--------R------ SAPs(SNPs)
                    PROSITE ----------C_TYPE_LECTIN_2  PDB: A:146-254 UniProt: 150-258                                                             -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8j A 136 TGRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYGVPILKIEDEDELKFLQRHVIPGNYWIGLSYDKKKKEWAWIDNGPSKLDMKIKKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 262
                                   145       155       165       175       185       195       205       215       225       235       245       255       

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with KLRA3_MOUSE | Q64329 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:126
                                   150       160       170       180       190       200       210       220       230       240       250       260      
          KLRA3_MOUSE   141 GRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYSVPILKIEDEDELKFLQRHVIPENYWIGLSYDKKKKEWAWIDNGPSKLDMKIRKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 266
               SCOP domains d3c8jb_ B: automated matches                                                                                                   SCOP domains
               CATH domains 3c8jB00 B:137-262 Mannose-Binding Protein A, subunit A                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.eeeeeeeeeehhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeeee....eeee.......hhhhhhh.......eeee....eeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -----H----G----------------------F----V---------S--------S--------------------Q------T-----T--------------T---T--------R------ SAPs(SNPs)
                    PROSITE ---------C_TYPE_LECTIN_2  PDB: B:146-254 UniProt: 150-258                                                             -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c8j B 137 GRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYGVPILKIEDEDELKFLQRHVIPGNYWIGLSYDKKKKEWAWIDNGPSKLDMKIKKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 262
                                   146       156       166       176       186       196       206       216       226       236       246       256      

Chain C from PDB  Type:PROTEIN  Length:126
 aligned with KLRA3_MOUSE | Q64329 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:126
                                   150       160       170       180       190       200       210       220       230       240       250       260      
          KLRA3_MOUSE   141 GRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYSVPILKIEDEDELKFLQRHVIPENYWIGLSYDKKKKEWAWIDNGPSKLDMKIRKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 266
               SCOP domains d3c8jc_ C: automated matches                                                                                                   SCOP domains
               CATH domains 3c8jC00 C:137-262 Mannose-Binding Protein A, subunit A                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.eeeeeeeeeehhhhhhhhhhh.........hhhhhhhhhhhh....eeeeeeee....eeee.......hhhhhhh.......eeee....eeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -----H----G----------------------F----V---------S--------S--------------------Q------T-----T--------------T---T--------R------ SAPs(SNPs)
                    PROSITE ---------C_TYPE_LECTIN_2  PDB: C:146-254 UniProt: 150-258                                                             -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c8j C 137 GRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYGVPILKIEDEDELKFLQRHVIPGNYWIGLSYDKKKKEWAWIDNGPSKLDMKIKKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 262
                                   146       156       166       176       186       196       206       216       226       236       246       256      

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with KLRA3_MOUSE | Q64329 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:130
                                   146       156       166       176       186       196       206       216       226       236       246       256       266
          KLRA3_MOUSE   137 SRDTGRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYSVPILKIEDEDELKFLQRHVIPENYWIGLSYDKKKKEWAWIDNGPSKLDMKIRKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 266
               SCOP domains d3c8jd_ D: automated matches                                                                                                       SCOP domains
               CATH domains 3c8jD00 D:133-262 Mannose-Binding Protein A, subunit A                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.eeeeeeeeeehhhhhhhhhhhh........hhhhhhhhhhhh....eeeeeeee....eeee.......hhhhhhhhh.....eeee....eeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------H----G----------------------F----V---------S--------S--------------------Q------T-----T--------------T---T--------R------ SAPs(SNPs)
                    PROSITE -------------C_TYPE_LECTIN_2  PDB: D:146-254 UniProt: 150-258                                                             -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8j D 133 SRDTGRGVKYWFCYSTKCYYFIMNKTTWSGCKANCQHYGVPILKIEDEDELKFLQRHVIPGNYWIGLSYDKKKKEWAWIDNGPSKLDMKIKKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLDKFPD 262
                                   142       152       162       172       182       192       202       212       222       232       242       252       262

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C8J)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KLRA3_MOUSE | Q64329)
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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KLRA3_MOUSE | Q643291p1z 1p4l 3c8k 5j6g

(-) Related Entries Specified in the PDB File

3c8k