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(-) Description

Title :  CRYSTAL STRUCTURE OF A INTERLEUKIN-2 VARIANT IN COMPLEX WITH INTERLEUKIN-2 RECEPTOR
 
Authors :  C. Klein, A. Freimoser-Grundschober, I. Waldhauer, M. Stihle, M. Birk
Date :  21 Oct 16  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  B,C,D
Keywords :  Interleukine-2, Interleukine-2 Receptor, Immune System, Cytokine, Interleukine-2 Variant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Klein, I. Waldhauer, V. G. Nicolini, A. Freimoser-Grundschober, T. Nayak, D. J. Vugts, C. Dunn, M. Bolijn, J. Benz, M. Stihle, S. Lang, M. Roemmele, T. Hofer, E. Van Puijenbroek, D. Wittig, S. Moser, O. Ast P. Brunker, I. H. Gorr, S. Neumann, M. C. De Vera Mudry, H. Hinton, F. Crameri, J. Saro, S. Evers, C. Gerdes, M. Bacac, G. Van Dongen, E. Moessner, P. Umana
Cergutuzumab Amunaleukin (Cea-Il2V), A Cea-Targeted Il-2 Variant-Based Immunocytokine For Combination Cancer Immunotherapy: Overcoming Limitations Of Aldesleukin And Conventional Il-2-Based Immunocytokines.
Oncoimmunology V. 6 77306 2017
PubMed-ID: 28405498  |  Reference-DOI: 10.1080/2162402X.2016.1277306

(-) Compounds

Molecule 1 - INTERLEUKIN-2 RECEPTOR SUBUNIT BETA
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: IL2RB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-2RB,HIGH AFFINITY IL-2 RECEPTOR SUBUNIT BETA,P70-75,P75
 
Molecule 2 - CYTOKINE RECEPTOR COMMON SUBUNIT GAMMA
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: IL2RG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: INTERLEUKIN-2 RECEPTOR SUBUNIT GAMMA,IL-2RG,GAMMAC,P64
 
Molecule 3 - INTERLEUKIN-2
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : BCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1CYS1Mod. Amino AcidCYSTEINE
2FUC3Ligand/IonALPHA-L-FUCOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:42 , ARG B:43 , TRP B:44 , SER D:87binding site for residue SO4 B 310
02AC2SOFTWAREGLY B:65 , ALA B:66 , LYS B:71binding site for residue SO4 B 311
03AC3SOFTWAREHIS B:116 , GLU B:118 , ARG B:121 , ASN B:123 , CYS B:168 , NAG B:307binding site for residue CYS B 312
04AC4SOFTWAREARG B:85 , GLU C:136 , ASN C:137 , HOH C:404 , HOH C:415binding site for residue SO4 C 305
05AC5SOFTWARELYS D:49 , LYS D:54 , HIS D:55 , HOH D:327binding site for residue SO4 D 201
06AC6SOFTWAREPHE B:11 , ASN B:17 , SER B:19 , ASN B:61 , ARG B:105 , LEU B:106 , MET B:107 , GLN B:130 , PRO B:196 , HOH B:426 , HOH B:444 , HOH B:465binding site for Poly-Saccharide residues NAG B 304 through FUC B 306 bound to ASN B 17
07AC7SOFTWAREHIS B:36 , TRP B:38 , ARG B:43 , ASN B:45 , ARG B:81 , ASP D:109binding site for Poly-Saccharide residues NAG B 301 through NAG B 303 bound to ASN B 45
08AC8SOFTWAREVAL B:115 , ASN B:123 , TRP B:166 , CYS B:312 , HOH B:455binding site for Poly-Saccharide residues NAG B 307 through NAG B 308 bound to ASN B 123
09AC9SOFTWAREPHE C:43 , TYR C:47 , ASN C:49 , LEU C:84 , GLN C:94binding site for Mono-Saccharide NAG C 303 bound to ASN C 49
10AD1SOFTWAREGLU B:153 , GLU B:154 , ASN C:62 , HOH C:403binding site for Poly-Saccharide residues NAG C 301 through FUC C 302 bound to ASN C 62
11AD2SOFTWAREGLU C:136 , ASN C:137 , ASN C:153 , ARG C:155binding site for Mono-Saccharide NAG C 304 bound to ASN C 137
12AD3SOFTWAREARG B:105 , GLU B:140 , PHE B:141 , GLU B:142 , ARG B:183 , VAL B:184 , LYS B:185 , THR B:193 , SER B:195 , HOH B:408 , HOH B:466binding site for Poly-Saccharide residues TRP B 194 through MAN B 309

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1B:10 -B:20
2B:33 -B:84
3B:48 -B:60
4B:168 -B:312
5C:40 -C:50
6C:80 -C:93
7C:160 -C:209
8D:58 -D:105

(-) 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 5M5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M5E)

(-) Exons   (0, 0)

(no "Exon" information available for 5M5E)

(-) 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 B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...........eee.....eeee.......eeeeeeeeee..............eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m5e B   6 SQFTCFYNSRANISCVWSQDGALQDTSCQVHAWPDRRRWNQTCELLPVSQASWACNLILGAPDSQKLTTVDIVTLRVLCREGVRWRVMAIQDFKPFENLRLMAPISLQVVHVETHRCNISWEISQASHYFERHLEFEARTLSPGHTWEEAPLLTLKQKQEWICLETLTPDTQYEFQVRVKPLQGEFTTWSPWSQPLAFRTKPA 208
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   


Chain C from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...hhhhheeeeeeee......eeeee....eeee........eeeeeeee.................eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m5e C  33 LPLPEVQCFVFNVEYMNCTWNSSSEPQPTNLTLHYWYKNSDNDKVQKCSHYLFSEEITSGCQLQKKEIHLYQTFVVQLQDPREPRRQATQMLKLQNLVIPWAPENLTLHKLSESQLELNWNNRFLNHCLEHLVQYRTDWDHSWTEQSVDYRHKFSLPSVDGQKRYTFRVRSRFNPLCGSAQHWSEWSHPIHWG 225
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   


Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m5e D   4 SSSTKKTQLQLEHLLLDLQMILNGINNTRMLTAKFAMPKKATELKHLQCLEEELKPLEEVLNGAQSHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFAQSIISTLT 133
                                    13        23      ||39        49        59        69     || 82        92       102       112       122       132 
                                                     30|                                    75|                                                      
                                                      37                                     79
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 5M5E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M5E)

(-) Gene Ontology  (27, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL2RB_HUMAN | P14784: 1ilm 1iln 2b5i 2erj 3qaz 4gs7
        IL2RG_HUMAN | P31785: 1ill 1ilm 1iln 1ite 2b5i 2erj 3bpl 3qaz 3qb7 4gs7

(-) Related Entries Specified in the PDB File

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