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(-) Description

Title :  STRUCTURE OF THE INTERLEUKIN-15 QUATERNARY COMPLEX
 
Authors :  A. M. Ring, E. Ozkan, D. Feng, K. C. Garcia
Date :  27 Aug 12  (Deposition) - 07 Nov 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cytokine, Cytokine Receptor, Immunoregulatory, Anti-Tumor, Anti- Viral, Reductive Methylation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Ring, J. X. Lin, D. Feng, S. Mitra, M. Rickert, G. R. Bowman, V. S. Pande, P. Li, I. Moraga, R. Spolski, E. Ozkan, W. J. Leonard, K. C. Garcia
Mechanistic And Structural Insight Into The Functional Dichotomy Between Il-2 And Il-15.
Nat. Immunol. V. 13 1187 2012
PubMed-ID: 23104097  |  Reference-DOI: 10.1038/NI.2449

(-) Compounds

Molecule 1 - INTERLEUKIN-15
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL15
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-15
 
Molecule 2 - INTERLEUKIN-2 RECEPTOR SUBUNIT BETA
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: IL2RB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-2 RECEPTOR SUBUNIT BETA, IL-2R SUBUNIT BETA, IL-2RB, HIGH AFFINITY IL-2 RECEPTOR SUBUNIT BETA, P70-75, P75
 
Molecule 3 - CYTOKINE RECEPTOR COMMON SUBUNIT GAMMA
    Chains: C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: IL2RG
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: INTERLEUKIN-2 RECEPTOR SUBUNIT GAMMA, IL-2 RECEPTOR SUBUNIT GAMMA, IL-2R SUBUNIT GAMMA, IL-2RG, GAMMAC, P64
 
Molecule 4 - INTERLEUKIN-15 RECEPTOR SUBUNIT ALPHA
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL15RA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-15 RECEPTOR SUBUNIT ALPHA, IL-15R-ALPHA, IL-15RA, SOLUBLE INTERLEUKIN-15 RECEPTOR SUBUNIT ALPHA, SIL-15 RECEPTOR SUBUNIT ALPHA, SIL-15R-ALPHA, SIL-15RA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MLY11Mod. Amino AcidN-DIMETHYL-LYSINE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:98 , TRP B:38 , ASP B:40 , THR B:79 , HOH B:494BINDING SITE FOR RESIDUE EDO B 301
2AC2SOFTWAREVAL B:115 , ASN B:123 , TRP B:166 , NAG B:303 , HOH B:455 , HOH B:484BINDING SITE FOR RESIDUE NAG B 302
3AC3SOFTWARETRP B:166 , NAG B:302 , HOH B:411 , HOH B:455BINDING SITE FOR RESIDUE NAG B 303
4AC4SOFTWAREASN C:206 , ALA C:212 , GLN C:213BINDING SITE FOR RESIDUE ACT C 301
5AC5SOFTWAREGLU C:136 , ASN C:137 , ASN C:153 , ARG C:155 , HOH C:472BINDING SITE FOR RESIDUE NAG C 302
6AC6SOFTWAREPHE C:43 , TYR C:47 , ASN C:49 , LEU C:84 , GLN C:94 , NAG C:304 , HOH C:427BINDING SITE FOR RESIDUE NAG C 303
7AC7SOFTWARENAG C:303BINDING SITE FOR RESIDUE NAG C 304
8AC8SOFTWAREASN C:62 , ARG C:114 , HOH C:473BINDING SITE FOR RESIDUE NAG C 305

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:85
2A:42 -A:88
3B:10 -B:20
4B:33 -B:84
5B:48 -B:60
6C:40 -C:50
7C:80 -C:93
8C:160 -C:209
9D:3 -D:45
10D:29 -D:63

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn C:206 -Pro C:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GS7)

(-) Exons   (0, 0)

(no "Exon" information available for 4GS7)

(-) 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:114
                                                                                                                                                  
               SCOP domains d4gs7a_ A: Interleukin-15 (IL-15)                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhheeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4gs7 A  -1 MGNWVNVISDLkkIEDLIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEkNIkEFLQSFVHIVQMFIN 112
                                     8 ||     18        28        38        48        58        68        78        88     |  98       108    
                                      10-MLY                                                                              94-MLY              
                                       11-MLY                                                                                97-MLY           


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4gs7b1 B:6-103 Interleukin-2 receptor beta chain                                           d4gs7b2 B:104-207 Interleukin-2 receptor beta chain                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeee...eeeeeee......eeee.ee....eeeeeee..............eeeeeeeee..eeeeeeeeeehhhhh......eeeeeeee....eeeeee....hhhhh..eeeeeeee....hhhhh..eee.....eeee.......eeeeeeeeee..............eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gs7 B   6 SQFTCFYNSRAQISCVWSQTSCQVHAWPDRRRWQQTCELLPVSQASWACNLILGAPDSQkLTTVDIVTLRVLCREGVRWRVMAIQDFKPFENLRLMAPISLQVVHVETHRCNISWEISQASHYFERHLEFEARTLSPGHTWEEAPLLTLkQkQEWICLETLTPDTQYEFQVRVkPLQGEFTTWSPWSQPLAFRTKP 207
                                    15        31        41        51        61        71        81        91       101       111       121       131       141       151       161 |     171       181   |   191       201      
                                             24|                                      71-MLY                                                                                   161-MLY                 185-MLY                  
                                              31                                                                                                                                 163-MLY                                        


Chain C from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4gs7c1 C:32-129 Cytokine receptor common gamma chain                                             d4gs7c2 C:130-227 Cytokine receptor common gamma chain                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...eeeee............eeeeee........ee...eeee..eeeeeeee.hhh.....eeeeee.......eeeeeehhhh.ee....eeeeeeeee..eeeeeee...hhh.eeeeeeeee......eeeee....eeee........eeeeeeeee................eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gs7 C  32 PLPLPEVQCFVFNVEYMNCTWQSSSEPQPTNLTLHYWYkNSDNDkVQKCSHYLFSEEITSGCQLQKKEIHLYQTFVVQLQDPREPRRQATQMLkLQNLVIPWAPENLTLHKLSESQLELNWNNRFLNHCLEHLVQYRTDWDHSWTEQSVDYRHKFSLPSVDGQKRYTFRVRSRFNPLCGSAQHWSEWSHPIHWGSN 227
                                    41        51        61        71    |   81        91       101       111       121   |   131       141       151       161       171       181       191       201       211       221      
                                                                 70-MLY |                                              125-MLY                                                                                                  
                                                                       76-MLY                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains d4gs7d_ D: Interleukin-15 receptor subunit alpha                    SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee..........eee.ee...eee......eeeeee......eee......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 4gs7 D   1 ITCPPPMSVEHADIWVKSYSLYSRERYICNSGFKRKAGTSSLTECVLNKATNVAHWTTPSLKCIRDP  67
                                    10        20        30        40        50        60
   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  (4, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GS7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GS7)

(-) Gene Ontology  (68, 103)

Asymmetric/Biological Unit(hide GO term definitions)

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  I15RA_HUMAN | Q13261
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  IL15_HUMAN | P40933
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  IL2RB_HUMAN | P14784
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 Related Entries

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

UniProtKB/Swiss-Prot
        I15RA_HUMAN | Q13261: 2ers 2z3q 2z3r
        IL15_HUMAN | P40933: 2xqb 2z3q 2z3r
        IL2RB_HUMAN | P14784: 1ilm 1iln 2b5i 2erj 3qaz 5m5e
        IL2RG_HUMAN | P31785: 1ill 1ilm 1iln 1ite 2b5i 2erj 3bpl 3qaz 3qb7 5m5e

(-) Related Entries Specified in the PDB File

2b5i INTERLEUKIN-2 QUATERNARY COMPLEX
2z3q INTERLEUKIN-15 BINARY COMPLEX WITH IL-15RA