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(-) Description

Title :  CRYSTAL STRUCTURE OF INSECT CELL EXPRESSED IL-22
 
Authors :  T. Xu, N. J. Logsdon, M. R. Walter
Date :  17 Jan 05  (Deposition) - 12 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Interleukin, Cytokine, Il-22, Glycosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Xu, N. J. Logsdon, M. R. Walter
Structure Of Insect-Cell-Derived Il-22.
Acta Crystallogr. , Sect. D V. 61 942 2005
PubMed-ID: 15983417  |  Reference-DOI: 10.1107/S0907444905009601

(-) Compounds

Molecule 1 - PROTEIN (INTERLEUKIN-22)
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression System CommonINSECT
    GeneIL22, ILTIF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-22, IL-10-RELATED T-CELL-DERIVED INDUCIBLE FACTOR, IL- TIF, UNQ3099/PRO10096

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:54 , MET A:58 , FUC A:1112 , NAG A:1113 , PHE B:47 , GLN B:48 , THR B:53 , PHE B:171 , ARG B:175BINDING SITE FOR RESIDUE NAG A 1111
02AC2SOFTWARETYR A:51 , ARG A:55 , NAG A:1111 , NAG A:1113BINDING SITE FOR RESIDUE FUC A 1112
03AC3SOFTWARENAG A:1111 , FUC A:1112 , GLN B:48BINDING SITE FOR RESIDUE NAG A 1113
04AC4SOFTWAREASN A:97 , SER A:126 , HIS F:39 , ARG F:41BINDING SITE FOR RESIDUE NAG A 1131
05AC5SOFTWAREASN B:97 , GLU B:101 , SER B:126BINDING SITE FOR RESIDUE NAG B 1231
06AC6SOFTWAREASN C:97 , GLU C:101 , SER C:126 , NAG C:1332BINDING SITE FOR RESIDUE NAG C 1331
07AC7SOFTWARENAG C:1331BINDING SITE FOR RESIDUE NAG C 1332
08AC8SOFTWAREPHE C:47 , PRO C:50 , THR C:53 , PHE C:171 , ARG C:175 , ASN D:54 , MET D:58 , NAG D:1412 , FUC D:1415BINDING SITE FOR RESIDUE NAG D 1411
09AC9SOFTWAREGLN C:48 , PRO C:50 , NAG D:1411 , MAN D:1413 , MAN D:1414BINDING SITE FOR RESIDUE NAG D 1412
10BC1SOFTWARENAG D:1412 , MAN D:1414BINDING SITE FOR RESIDUE MAN D 1413
11BC2SOFTWARENAG D:1412 , MAN D:1413 , ARG E:143BINDING SITE FOR RESIDUE MAN D 1414
12BC3SOFTWARETYR D:51 , ARG D:55 , NAG D:1411BINDING SITE FOR RESIDUE FUC D 1415
13BC4SOFTWAREASN D:97 , GLU D:101 , SER D:126 , NAG D:1432BINDING SITE FOR RESIDUE NAG D 1431
14BC5SOFTWARENAG D:1431BINDING SITE FOR RESIDUE NAG D 1432
15BC6SOFTWAREASN E:97 , GLU E:101 , SER E:126BINDING SITE FOR RESIDUE NAG E 1531
16BC7SOFTWAREPHE E:47 , THR E:53 , MET E:172 , ASN F:54 , ARG F:55 , MET F:58 , NAG F:1612BINDING SITE FOR RESIDUE NAG F 1611
17BC8SOFTWAREGLN E:48 , NAG F:1611BINDING SITE FOR RESIDUE NAG F 1612
18BC9SOFTWAREASN F:97 , GLU F:101 , SER F:126 , NAG F:1632BINDING SITE FOR RESIDUE NAG F 1631
19CC1SOFTWARENAG F:1631BINDING SITE FOR RESIDUE NAG F 1632

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:132
2A:89 -A:178
3B:40 -B:132
4B:89 -B:178
5C:40 -C:132
6C:89 -C:178
7D:40 -D:132
8D:89 -D:178
9E:40 -E:132
10E:89 -E:178
11F:40 -F:132
12F:89 -F:178

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gln A:112 -Pro A:113
2Gln B:112 -Pro B:113
3Gln C:112 -Pro C:113
4Gln D:112 -Pro D:113
5Gln E:112 -Pro E:113
6Gln F:112 -Pro F:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric/Biological Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013078S158GIL22_HUMANPolymorphism2227507A/B/C/D/E/FS158G

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

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTERLEUKIN_10PS00520 Interleukin-10 family signature.IL22_HUMAN84-104
 
 
 
 
 
  6A:84-104
B:84-104
C:84-104
D:84-104
E:84-104
F:84-104

(-) Exons   (5, 30)

Asymmetric/Biological Unit (5, 30)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003280871ENSE00001303127chr12:68647284-68647043242IL22_HUMAN1-62626A:39-62
B:38-62
C:38-62
D:38-62
E:38-62
F:38-62
24
25
25
25
25
25
1.2ENST000003280872ENSE00000920698chr12:68646609-6864654466IL22_HUMAN63-84226A:63-84
B:63-84
C:63-84
D:63-84
E:63-84
F:63-84
22
22
22
22
22
22
1.3ENST000003280873ENSE00000920697chr12:68646427-68646284144IL22_HUMAN85-132486A:85-132
B:85-132
C:85-132
D:85-132
E:85-132
F:85-132
48
48
48
48
48
48
1.4ENST000003280874ENSE00001100627chr12:68645358-6864529366IL22_HUMAN133-154226A:133-154
B:133-154
C:133-154
D:133-154
E:133-154
F:133-154
22
22
22
22
22
22
1.5ENST000003280875ENSE00001311233chr12:68642656-68642025632IL22_HUMAN155-179256A:155-179
B:155-179
C:155-179
D:155-179
E:155-179
F:155-179
25
25
25
25
25
25

(-) 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:141
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:141
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178 
           IL22_HUMAN    39 HCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykba_ A: Interleukin-22 (IL-22)                                                                                                             SCOP domains
               CATH domains 1ykbA00 A:39-179  [code=1.20.1250.10, no name defined]                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:39-62  Exon 1.2  PDB: A:63-84Exon 1.3  PDB: A:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: A:155-179  Transcript 1
                 1ykb A  39 HCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178 

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:142
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           IL22_HUMAN    38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykbb_ B: Interleukin-22 (IL-22)                                                                                                              SCOP domains
               CATH domains 1ykbB00 B:38-179  [code=1.20.1250.10, no name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhhhhhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:38-62   Exon 1.2  PDB: B:63-84Exon 1.3  PDB: B:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: B:155-179  Transcript 1
                 1ykb B  38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:142
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           IL22_HUMAN    38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykbc_ C: Interleukin-22 (IL-22)                                                                                                              SCOP domains
               CATH domains 1ykbC00 C:38-179  [code=1.20.1250.10, no name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:38-62   Exon 1.2  PDB: C:63-84Exon 1.3  PDB: C:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: C:155-179  Transcript 1
                 1ykb C  38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:142
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           IL22_HUMAN    38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykbd_ D: Interleukin-22 (IL-22)                                                                                                              SCOP domains
               CATH domains 1ykbD00 D:38-179  [code=1.20.1250.10, no name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:38-62   Exon 1.2  PDB: D:63-84Exon 1.3  PDB: D:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: D:155-179  Transcript 1
                 1ykb D  38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  

Chain E from PDB  Type:PROTEIN  Length:142
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:142
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           IL22_HUMAN    38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykbe_ E: Interleukin-22 (IL-22)                                                                                                              SCOP domains
               CATH domains 1ykbE00 E:38-179  [code=1.20.1250.10, no name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:38-62   Exon 1.2  PDB: E:63-84Exon 1.3  PDB: E:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: E:155-179  Transcript 1
                 1ykb E  38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  

Chain F from PDB  Type:PROTEIN  Length:142
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:142
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           IL22_HUMAN    38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d1ykbf_ F: Interleukin-22 (IL-22)                                                                                                              SCOP domains
               CATH domains 1ykbF00 F:38-179  [code=1.20.1250.10, no name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:38-62   Exon 1.2  PDB: F:63-84Exon 1.3  PDB: F:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: F:155-179  Transcript 1
                 1ykb F  38 SHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177  

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (IL22_HUMAN | Q9GZX6)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0045518    interleukin-22 receptor binding    Interacting selectively and non-covalently with the interleukin-22 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:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0046427    positive regulation of JAK-STAT cascade    Any process that activates or increases the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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        IL22_HUMAN | Q9GZX61m4r 3dgc 3dlq 3g9v 3q1s

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