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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN INTERLEUKIN-17 RECEPTOR COMPLEX

Authors :   L. K. Ely, K. C. Garcia

Date :   16 Sep 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Cytokine, Interleukin, Cysteine-Knot Growth Factor, Receptor-Cytokine Complex, Disulfide Bond, Glycoprotein, Secreted, Membrane, Receptor, Transmembrane, Signaling Protein, Signaling Protein - Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. K. Ely, S. Fischer, K. C. Garcia
Structural Basis Of Receptor Sharing By Interleukin 17 Cytokines.
Nat. Immunol. V. 10 1245 2009
PubMed-ID: 19838198 | Reference-DOI: 10.1038/NI.1813

Molecule 1 - INTERLEUKIN-17F
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Gene	:	IL17F, IL24
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-17F, INTERLEUKIN-24, IL-24, CYTOKINE ML-1

Molecule 2 - INTERLEUKIN-17 RECEPTOR A
	Chains	:	C
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell	:	BACMAM 293 CELLS
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	IL17RA, IL17R
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-17 RECEPTOR, CDW217

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
3	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:53 , ARG A:73 , NAG A:202	BINDING SITE FOR RESIDUE NAG A 201
2	AC2	SOFTWARE	NAG A:201	BINDING SITE FOR RESIDUE NAG A 202
3	AC3	SOFTWARE	TRP C:193 , ASN C:194	BINDING SITE FOR RESIDUE NAG C 301
4	AC4	SOFTWARE	ASN C:36	BINDING SITE FOR RESIDUE NAG C 302
5	AC5	SOFTWARE	ASN C:18 , HIS C:212	BINDING SITE FOR RESIDUE NAG C 303
6	AC6	SOFTWARE	ARG C:187 , ARG C:232 , ASN C:234	BINDING SITE FOR RESIDUE NAG C 304
7	AC7	SOFTWARE	GLN A:81 , HIS C:7 , ASN C:23	BINDING SITE FOR RESIDUE NAG C 305
8	AC8	SOFTWARE	ASN B:43 , GLU B:45	BINDING SITE FOR RESIDUE CA B 134

Asymmetric/Biological Unit

No.	Residues
1	A:72	-	A:122
2	A:77	-	A:124
3	B:72	-	B:122
4	B:77	-	B:124
5	C:12	-	C:19
6	C:26	-	C:95
7	C:154	-	C:165
8	C:214	-	C:245
9	C:259	-	C:263

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:63	-	Pro A:64
2	Tyr B:63	-	Pro B:64
3	Leu C:133	-	Pro C:134

Asymmetric/Biological Unit (4, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_065813	S	95	L	IL17F_HUMAN	Disease (CANDF6)	748486078	A/B	S	65	L
2	UniProt	VAR_058287	E	126	G	IL17F_HUMAN	Polymorphism	2397084	A/B	E	96	G
3	UniProt	VAR_058288	V	155	I	IL17F_HUMAN	Polymorphism	11465553	A/B	V	125	I
4	UniProt	VAR_058289	H	161	R	IL17F_HUMAN	Polymorphism	763780	A	H	131	R

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

(no "PROSITE Motif" information available for 3JVF)

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000336123	1	ENSE00001424697	chr6:52109335-52109195	141	IL17F_HUMAN	1-11	11	0	-	-
1.2b	ENST00000336123	2b	ENSE00001167022	chr6:52103748-52103528	221	IL17F_HUMAN	12-85	74	2	A:24-55 B:25-55	32 31
1.3	ENST00000336123	3	ENSE00002185395	chr6:52101966-52101479	488	IL17F_HUMAN	85-163	79	2	A:55-132 (gaps) B:55-128	78 74

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:104
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:109
                                    63        73        83        93       103       113       123       133       143       153         
          IL17F_HUMAN    54 SMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPVIHHV 162
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee................hhhhhh...eeeeeee...ee..eeeeeee....ee.....ee...eeeeeeeeeeeeee..-----.eeeeeeeeeeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------L------------------------------G----------------------------I-----R- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:24-55         ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: A:55-132 (gaps) UniProt: 85-163 [INCOMPLETE]                    Transcript 1 (2)
                 3jvf A  24 SMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKH-----SFQLEKVLVTVGCTCVTPVIHHV 132
                                    33        43        53        63        73        83        93       103|     |113       123         
                                                                                                          104   110

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:104
                                    64        74        84        94       104       114       124       134       144       154    
          IL17F_HUMAN    55 MKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 158
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------IL17-3jvfB01 B:46-126                                                            -- Pfam domains (1)
           Pfam domains (2) ---------------------IL17-3jvfB02 B:46-126                                                            -- Pfam domains (2)
         Sec.struct. author .eee..............hhhhhh...eeeeeee...ee..eeeeeee...eee.....eeeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------L------------------------------G----------------------------I--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:25-55        ------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: B:55-128 UniProt: 85-163 [INCOMPLETE]                       Transcript 1 (2)
                 3jvf B  25 MKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 128
                                    34        44        54        64        74        84        94       104       114       124

Chain C from PDB  Type:PROTEIN  Length:271
 aligned with I17RA_HUMAN | Q96F46 from UniProtKB/Swiss-Prot  Length:866

    Alignment length:271
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302 
          I17RA_HUMAN    33 LRLLDHRALVCSQPGLNCTVKNSTCLDDSWIHPRNLTPSSPKDLQIQLHFAHTQQGDLFPVAHIEWTLQTDASILYLEGAELSVLQLNTNERLCVRFEFLSKLRHHHRRWRFTFSHFVVDPDQEYEVTVHHLPKPIPDGDPNHQSKNFLVPDCEHARMKVTTPCMSSGSLWDPNITVETLEAHQLRVSFTLWNESTHYQILLTSFPHMENHSCFEHMHHIPAPRPEEFHQRSNVTLTLRNLKGCCRHQVQIQPFFSSCLNDCLRHSATVSC 303
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee....................eeeeeeeeeeee.....eeeeeeeeeee..hhhhh...eeeeeeee....eeee..eee...........eeeeeeee.....eeeeeeeee............eeeee...........hhhhhh.........eee......eeeee........eeeeeeee........eeeeeee...........eeeee.........eeeeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvf C   2 LRLLDHRALVCSQPGLNCTVKNSTCLDDSWIHPRNLTPSSPkDLQIQLHFAHTQQGDLFPVAHIEWTLQTDASILYLEGAELSVLQLNTNERLCVRFEFLSKLRHHHRRWRFTFSHFVVDPDQEYEVTVHHLPKPIPDGDPNHQSKNFLVPDCEHARMKVTTPCMSSGSLWDPNITVETLEAHQLRVSFTLWNESTHYQILLTSFPHMENHSCFEHMHHIPAPRPEEFHQRSNVTLTLRNLKGCCRHQVQIQPFFSSCLNDCLRHSATVSC 272
                                    11        21        31        41 |      51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271 
                                                                    43-MLY

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 '\|'

(no "SCOP Domain" information available for 3JVF)

(no "CATH Domain" information available for 3JVF)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: IL17] (3)

Family: IL17 (3)

Homo sapiens (Human) (3)

1a	IL17-3jvfB01	B:46-126
1b	IL17-3jvfB02	B:46-126

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IL17F_HUMAN | Q96PD4)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0019955	cytokine binding	Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	GO:0005126	cytokine receptor binding	Interacting selectively and non-covalently with a cytokine 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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0042089	cytokine biosynthetic process	The chemical reactions and pathways resulting in the formation of cytokines, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	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:0042109	lymphotoxin A biosynthetic process	The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:1900017	positive regulation of cytokine production involved in inflammatory response	Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response.
	GO:2000778	positive regulation of interleukin-6 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045423	regulation of granulocyte macrophage colony-stimulating factor biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of granulocyte macrophage colony-stimulating factor.
	GO:0045076	regulation of interleukin-2 biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
	GO:0045408	regulation of interleukin-6 biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-6.
	GO:0045414	regulation of interleukin-8 biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-8.
	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway.
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.

Chain C (I17RA_HUMAN | Q96F46)

molecular function
	GO:0030368	interleukin-17 receptor activity	Combining with any member of the interleukin-17 family of cytokines and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	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).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0071345	cellular response to cytokine stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	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:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0072537	fibroblast activation	A change in the morphology or behavior of a fibroblast resulting from exposure to an activating factor such as a cellular or soluble ligand.
	GO:0071621	granulocyte chemotaxis	The movement of a granulocyte in response to an external stimulus.
	GO:1900017	positive regulation of cytokine production involved in inflammatory response	Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response.
	GO:0050729	positive regulation of inflammatory response	Any process that activates or increases the frequency, rate or extent of the inflammatory response.
	GO:2000667	positive regulation of interleukin-13 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-13 secretion.
	GO:0032747	positive regulation of interleukin-23 production	Any process that activates or increases the frequency, rate, or extent of interleukin-23 production.
	GO:2000664	positive regulation of interleukin-5 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-5 secretion.
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: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:0005887	integral component of plasma membrane	The component of the plasma 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu C:133 - Pro C:134	[ RasMol ]
		Tyr A:63 - Pro A:64	[ RasMol ]
		Tyr B:63 - Pro B:64	[ RasMol ]

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (8, 8)

SS Bonds (9, 9)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (4, 7)

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