1JPY - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF IL-17F

Authors :   S. G. Hymowitz, E. H. Filvaroff, J. Yin, J. Lee, L. Cai, P. Risser, M. Maru W. Mao, J. Foster, R. Kelley, G. Pan, A. L. Gurney, A. M. De Vos, M. A. Sta

Date :   03 Aug 01 (Deposition) - 28 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym. Unit : A,B,X,Y
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: X,Y  (1x)

Keywords :   Cystine-Knot, Cytokine, T-Cell Derived, Dimer, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Hymowitz, E. H. Filvaroff, J. P. Yin, J. Lee, L. Cai, P. Risser, M. Maruoka, W. Mao, J. Foster, R. F. Kelley, G. Pan, A. L. Gurney, A. M. De Vos, M. A. Starovasnik
Il-17S Adopt A Cystine Knot Fold: Structure And Activity Of A Novel Cytokine, Il-17F, And Implications For Receptor Binding.
Embo J. V. 20 5332 2001
PubMed-ID: 11574464 | Reference-DOI: 10.1093/EMBOJ/20.19.5332

Molecule 1 - INTERLEUKIN 17F
	Chains	:	A, B, X, Y
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Strain	:	HI5 CELLS
	Expression System Taxid	:	10469
	Expression System Vector Type	:	PLASMID
	Fragment	:	SECRETED IL-17F
	Gene	:	IL-17F
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE FIRST FOUR RESIDUES, GSHM, ARE FROM THE VECTOR
	Synonym	:	IL-17F

		1	2	3	4
Asymmetric Unit	:	A	B	X	Y
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:53 , ARG A:73	BINDING SITE FOR RESIDUE NDG A 241
2	AC2	SOFTWARE	ASN B:53 , ARG B:73 , NDG B:242	BINDING SITE FOR RESIDUE NAG B 241
3	AC3	SOFTWARE	NAG B:241	BINDING SITE FOR RESIDUE NDG B 242
4	AC4	SOFTWARE	SER X:16 , ASN X:53 , ARG X:73 , NAG X:242	BINDING SITE FOR RESIDUE NAG X 241
5	AC5	SOFTWARE	NAG X:241	BINDING SITE FOR RESIDUE NAG X 242
6	AC6	SOFTWARE	ASN Y:53 , GLN Y:71	BINDING SITE FOR RESIDUE NAG Y 241
7	AC7	SOFTWARE	SER X:41 , ARG X:42 , GLN X:105 , GLY X:106 , CYS X:107 , HOH X:244	BINDING SITE FOR RESIDUE SO4 X 243

Asymmetric Unit

No.	Residues
1	A:17	-	B:107
2	A:72	-	A:122
3	A:77	-	A:124
4	A:107	-	B:17
5	B:72	-	B:122
6	B:77	-	B:124
7	X:17	-	Y:107
8	X:72	-	X:122
9	X:77	-	X:124
10	X:107	-	Y:17
11	Y:72	-	Y:122
12	Y:77	-	Y:124

Asymmetric Unit

No.	Residues
1	Tyr A:63	-	Pro A:64
2	Tyr B:63	-	Pro B:64
3	Tyr X:63	-	Pro X:64
4	Tyr Y:63	-	Pro Y:64

Asymmetric Unit (3, 12)

								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/X/Y	S	65	L
2	UniProt	VAR_058287	E	126	G	IL17F_HUMAN	Polymorphism	2397084	A/B/X/Y	E	96	G
3	UniProt	VAR_058288	V	155	I	IL17F_HUMAN	Polymorphism	11465553	A/B/X/Y	V	125	I

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

Biological Unit 1 (3, 6)

								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

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

Biological Unit 2 (3, 6)

								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	X/Y	S	65	L
2	UniProt	VAR_058287	E	126	G	IL17F_HUMAN	Polymorphism	2397084	X/Y	E	96	G
3	UniProt	VAR_058288	V	155	I	IL17F_HUMAN	Polymorphism	11465553	X/Y	V	125	I

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

(no "PROSITE Motif" information available for 1JPY)

Asymmetric Unit (2, 8)

	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	4	A:8-55 B:8-55 X:9-55 (gaps) Y:6-55 (gaps)	48 48 47 50
1.3	ENST00000336123	3	ENSE00002185395	chr6:52101966-52101479	488	IL17F_HUMAN	85-163	79	4	A:55-128 B:55-128 X:55-128 Y:55-130	74 74 74 76

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:121
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:121
                                    47        57        67        77        87        97       107       117       127       137       147       157 
          IL17F_HUMAN    38 HTFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 158
               SCOP domains d1jpya_ A: Interleukin 17F, IL-17F                                                                                        SCOP domains
               CATH domains 1jpyA00 A:8-128 Cystine-knot cytokines                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........eeeeeeeee..........hhhhhh...eeeeeee...ee..eeeeeee....ee.....ee...eeeeeeeeeeeeeee.hhhhheeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------L------------------------------G----------------------------I--- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:8-55 UniProt: 12-85           ------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: A:55-128 UniProt: 85-163 [INCOMPLETE]                       Transcript 1 (2)
                 1jpy A   8 HTFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 128
                                    17        27        37        47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:121
                                    47        57        67        77        87        97       107       117       127       137       147       157 
          IL17F_HUMAN    38 HTFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 158
               SCOP domains d1jpyb_ B: Interleukin 17F, IL-17F                                                                                        SCOP domains
               CATH domains 1jpyB00 B:8-128 Cystine-knot cytokines                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhheeeeeeee..........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:8-55 UniProt: 12-85           ------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: B:55-128 UniProt: 85-163 [INCOMPLETE]                       Transcript 1 (2)
                 1jpy B   8 HTFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 128
                                    17        27        37        47        57        67        77        87        97       107       117       127

Chain X from PDB  Type:PROTEIN  Length:117
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:120
                                    48        58        68        78        88        98       108       118       128       138       148       158
          IL17F_HUMAN    39 TFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 158
               SCOP domains d1jpyx_ X:    Interleukin 17F, IL-17F                                                                                    SCOP domains
               CATH domains 1jpyX00 X:   9-128 Cystine-knot cytokines                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........---...eee........................eeeeeee...ee..eeeeeee....ee.....ee...eeeeeeeeeeeeeee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------L------------------------------G----------------------------I--- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: X:9-55 (gaps) UniProt: 12-85   ------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3  PDB: X:55-128 UniProt: 85-163 [INCOMPLETE]                       Transcript 1 (2)
                 1jpy X   9 TFFQKPESCP---GGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPV 128
                                    18   |    28        38        48        58        68        78        88        98       108       118       128
                                    18  22

Chain Y from PDB  Type:PROTEIN  Length:120
 aligned with IL17F_HUMAN | Q96PD4 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:125
                                    45        55        65        75        85        95       105       115       125       135       145       155     
          IL17F_HUMAN    36 VGHTFFQKPESCPPVPGGSMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPVIH 160
               SCOP domains d1jpyy_ Y: In     terleukin 17F, IL-17F                                                                                       SCOP domains
               CATH domains 1jpyY00 Y:6-1     30 Cystine-knot cytokines                                                                                   CATH domains
           Pfam domains (1) ----------------------------------------IL17-1jpyY01 Y:46-126                                                            ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------IL17-1jpyY02 Y:46-126                                                            ---- Pfam domains (2)
           Pfam domains (3) ----------------------------------------IL17-1jpyY03 Y:46-126                                                            ---- Pfam domains (3)
           Pfam domains (4) ----------------------------------------IL17-1jpyY04 Y:46-126                                                            ---- Pfam domains (4)
         Sec.struct. author .............-----.eee...............hhhhhh...eeeeeee...ee..eeeeeee....ee.....ee...eeeeeeeeeeeeeee.hhhhheeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------L------------------------------G----------------------------I----- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: Y:6-55 (gaps) UniProt: 12-85      --------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.3  PDB: Y:55-130 UniProt: 85-163 [INCOMPLETE]                         Transcript 1 (2)
                 1jpy Y   6 VGHTFFQKPESCP-----SMKLDIGIINENQRVSMSRNIESRSTSPWNYTVTWDPNRYPSEVVQAQCRNLGCINAQGKEDISMNSVPIQQETLVVRRKHQGCSVSFQLEKVLVTVGCTCVTPVIH 130
                                    15  |     25        35        45        55        65        75        85        95       105       115       125     
                                       18    24

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: Small proteins (3458)

Fold: Cystine-knot cytokines (124)

Superfamily: Cystine-knot cytokines (124)

Family: Interleukin 17F, IL-17F (1)

Protein domain: Interleukin 17F, IL-17F (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1jpya_	A:
1b	d1jpyb_	B:
1c	d1jpyx_	X:
1d	d1jpyy_	Y:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Cystine Knot Cytokines, subunit B (102)

Homologous Superfamily: Cystine-knot cytokines (102)

Human (Homo sapiens) (84)

1a	1jpyX00	X:9-128
1b	1jpyY00	Y:6-130
1c	1jpyA00	A:8-128
1d	1jpyB00	B:8-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: IL17 (3)

Homo sapiens (Human) (3)

1a	IL17-1jpyY01	Y:46-126
1b	IL17-1jpyY02	Y:46-126
1c	IL17-1jpyY03	Y:46-126
1d	IL17-1jpyY04	Y:46-126

Asymmetric Unit(hide GO term definitions)

Chain A,B,X,Y (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.

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		Tyr Y:63 - Pro Y:64	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1JPY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (12, 12)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 12)

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Exons (2, 8)

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