3G9V - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A SOLUBLE DECOY RECEPTOR IL-22BP BOUND TO INTERLEUKIN-22

Authors :   P. R. De Moura, L. Watanabe, L. Bleicher, D. Colau, J. -C. Renauld, I. Polikarpov

Date :   14 Feb 09 (Deposition) - 14 Apr 09 (Release) - 14 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.76

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Cytokine, Cytokine Receptor, Receptor, Glycoprotein, Polymorphism, Secreted, Cytokine/Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. R. De Moura, L. Watanabe, L. Bleicher, D. Colau, L. Dumoutier, M. M. Lemaire, J. -C. Renauld, I. Polikarpov
Crystal Structure Of A Soluble Decoy Receptor Il-22Bp Bound To Interleukin-22
Febs Lett. V. 583 1072 2009
PubMed-ID: 19285080 | Reference-DOI: 10.1016/J.FEBSLET.2009.03.006
(for further references see the PDB file header)

Molecule 1 - INTERLEUKIN 22 RECEPTOR, ALPHA 2
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 21-231
	Gene	:	IL22RA2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERLEUKIN-22 BINDING PROTEIN, ISOFORM CRA_A

Molecule 2 - INTERLEUKIN-22
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 29-179
	Gene	:	IL22
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-22, IL-10-RELATED T-CELL-DERIVED-INDUCIBLE FACTOR, IL-TIF

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3G9V)

(no "Site" information available for 3G9V)

Asymmetric Unit

No.	Residues
1	A:78	-	A:86
2	B:89	-	B:178
3	C:78	-	C:86
4	D:89	-	D:178

Asymmetric Unit

No.	Residues
1	Gln B:112	-	Pro B:113
2	Gln D:112	-	Pro D:113

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013078	S	158	G	IL22_HUMAN	Polymorphism	2227507	B/D	S	158	G
2	UniProt	VAR_021494	E	190	K	I22R2_HUMAN	Polymorphism	28362173	A/C	E	158	K

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013078	S	158	G	IL22_HUMAN	Polymorphism	2227507	B	S	158	G
2	UniProt	VAR_021494	E	190	K	I22R2_HUMAN	Polymorphism	28362173	A	E	158	K

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013078	S	158	G	IL22_HUMAN	Polymorphism	2227507	D	S	158	G
2	UniProt	VAR_021494	E	190	K	I22R2_HUMAN	Polymorphism	28362173	C	E	158	K

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_10	PS00520	Interleukin-10 family signature.	IL22_HUMAN	84-104	2	B:84-104 D:84-104

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_10	PS00520	Interleukin-10 family signature.	IL22_HUMAN	84-104	1	B:84-104 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERLEUKIN_10	PS00520	Interleukin-10 family signature.	IL22_HUMAN	84-104	1	- D:84-104

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000328087	1	ENSE00001303127	chr12:68647284-68647043	242	IL22_HUMAN	1-62	62	2	B:39-62 D:41-62	24 22
1.2	ENST00000328087	2	ENSE00000920698	chr12:68646609-68646544	66	IL22_HUMAN	63-84	22	2	B:63-84 D:63-84	22 22
1.3	ENST00000328087	3	ENSE00000920697	chr12:68646427-68646284	144	IL22_HUMAN	85-132	48	2	B:85-132 D:85-130	48 46
1.4	ENST00000328087	4	ENSE00001100627	chr12:68645358-68645293	66	IL22_HUMAN	133-154	22	2	B:133-154 (gaps) D:140-154	22 15
1.5	ENST00000328087	5	ENSE00001311233	chr12:68642656-68642025	632	IL22_HUMAN	155-179	25	2	B:155-178 D:155-179	24 25

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:173
 aligned with I22R2_HUMAN | Q969J5 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:229
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248         
          I22R2_HUMAN    29 LKPQRVQFQSRNFHNILQWQPGRALTGNSSVYFVQYKIMFSCSMKSSHQKPSGCWQHISCNFPGCRTLAKYGQRQWKNKEDCWGTQELSCDLTSETSDIQEPYYGRVRAASAGSYSEWSMTPRFTPWWETKIDPPVMNITQVNGSLLVILHAPNLPYRYQKEKNVSIEDYYELLYRVFIINNSLEKEQKVYEGAHRAVEIEALTPHSSYCVVAEIYQPMLDRRSQRSEE 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee....---...eeeeeeee--------------------------------......eeeeeeeee...eee.hhhhh.....eeeeeeeee..ee...ee....hhhhhh.....eee..-----...eee...hhhhhh.....hhhhhh..eeeeee.------.eeeeee......----------.eeeeeee....ee...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g9v A  29 LKPQRVQFQSRNFHNILQWQPGRA---NSSVYFVQYKI--------------------------------YGQRQWKNKEDCWGTQELSCDLTSETSDIQEPYYGRVRAASAGSYSEWSMTPRFTPWWETKIDPPVMNIT-----LLVILHAPNLPYRYQKEKNVSIEDYYELLYRVFII------EQKVYEGAHRAVE----------CVVAEIYQPMLDRRSQRSEE 225
                                    38        48   |   |58       | -         -         -         -|       76        86        96       106       116       126       136     | 146       156       166       176      |186        |-       206       216         
                                                  52  56        66                               67                                                                  136   142                               176    183         195        206

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:140
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178
           IL22_HUMAN    39 HCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNAC 178
               SCOP domains d3g9vb_ B: Interleukin-22 (IL-22)                                                                                                            SCOP domains
               CATH domains 3g9vB00 B:39-178  [code=1.20.1250.10, no name defined]                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh....------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------G-------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------INTERLEUKIN_10       -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:39-62  Exon 1.2  PDB: B:63-84Exon 1.3  PDB: B:85-132 UniProt: 85-132         Exon 1.4              Exon 1.5  PDB: B:155-178 Transcript 1
                 3g9v B  39 HCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCH------HIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNAC 178
                                    48        58        68        78        88        98       108       118       128    |    - |     148       158       168       178
                                                                                                                        133    140

Chain C from PDB  Type:PROTEIN  Length:176
 aligned with I22R2_HUMAN | Q969J5 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:230
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
          I22R2_HUMAN    26 HESLKPQRVQFQSRNFHNILQWQPGRALTGNSSVYFVQYKIMFSCSMKSSHQKPSGCWQHISCNFPGCRTLAKYGQRQWKNKEDCWGTQELSCDLTSETSDIQEPYYGRVRAASAGSYSEWSMTPRFTPWWETKIDPPVMNITQVNGSLLVILHAPNLPYRYQKEKNVSIEDYYELLYRVFIINNSLEKEQKVYEGAHRAVEIEALTPHSSYCVVAEIYQPMLDRRSQRS 255
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..eeeeeee....---...eeeeeeee--------------------------------......eeeeeeeee...eee.hhhhh.....eeeeeeeee..ee...ee....hhhhhh.....eee...----...eee...hhhhhh.....hhhhhh..eeeeee.------.eeeeee......---------..eeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------K----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g9v C  26 HESLKPQRVQFQSRNFHNILQWQPGRA---NSSVYFVQYKI--------------------------------YGQRQWKNKEDCWGTQELSCDLTSETSDIQEPYYGRVRAASAGSYSEWSMTPRFTPWWETKIDPPVMNITQ----LLVILHAPNLPYRYQKEKNVSIEDYYELLYRVFII------EQKVYEGAHRAVE---------YCVVAEIYQPMLDRRSQRS 223
                                    35        45      |  -|       65|        -         -         -   |    73        83        93       103       113       123       133   |   143       153       163       173  |    183       193 |       - |     213       223
                                                     52  56        66                               67                                                                   137  142                               176    183         195       205

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with IL22_HUMAN | Q9GZX6 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:139
                                    50        60        70        80        90       100       110       120       130       140       150       160       170         
           IL22_HUMAN    41 RLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
               SCOP domains d3g9vd_ D: Interleukin-22 (IL-22)                                                                                                           SCOP domains
               CATH domains 3g9vD00 D:41-179  [code=1.20.1250.10, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------G--------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------INTERLEUKIN_10       --------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:41-62Exon 1.2  PDB: D:63-84Exon 1.3  PDB: D:85-130 UniProt: 85-132         Exon 1.4 [INCOMPLETE] Exon 1.5  PDB: D:155-179  Transcript 1
                 3g9v D  41 RLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNRLS---------HIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI 179
                                    50        60        70        80        90       100       110       120       130       140       150       160       170         
                                                                                                                   130       140

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: 4-helical cytokines (168)

Superfamily: 4-helical cytokines (168)

Family: Interferons/interleukin-10 (IL-10) (41)

Protein domain: Interleukin-22 (IL-22) (5)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d3g9vb_	B:
1b	d3g9vd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Growth Hormone; Chain: A; (136)

Homologous Superfamily: [code=1.20.1250.10, no name defined] (130)

Human (Homo sapiens) (110)

1a	3g9vB00	B:39-178
1b	3g9vD00	D:41-179

(no "Pfam Domain" information available for 3G9V)

Asymmetric Unit(hide GO term definitions)

Chain A,C (I22R2_HUMAN | Q969J5)

molecular function
	GO:0042017	interleukin-22 binding	Interacting selectively and non-covalently with interleukin-22.
	GO:0042018	interleukin-22 receptor activity	Combining with interleukin-22 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
biological process
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	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: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.

Chain B,D (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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3g9v)

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(no "Sites" information available for 3g9v)

	Cis Peptide Bonds
		Gln B:112 - Pro B:113	[ RasMol ]
		Gln D:112 - Pro D:113	[ RasMol ]

Biological Units
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	3g9v
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	I22R2_HUMAN \| Q969J5
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	IL22_HUMAN \| Q9GZX6
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	I22R2_HUMAN \| Q969J5
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	IL22_HUMAN \| Q9GZX6
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UniProtKB/Swiss-Prot
	IL22_HUMAN \| Q9GZX6	:	1m4r 1ykb 3dgc 3dlq 3q1s

(no "Related Entries Specified in the PDB File" available for 3G9V)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

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Exons (5, 10)

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