3WCY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   MURINE IFNAR1 IN COMPLEX WITH INTERFERON-BETA

Authors :   J. P. Vivian, N. A. De Weerd, P. J. Hertzog, J. Rossjohn

Date :   04 Jun 13 (Deposition) - 24 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,I

Keywords :   Fibronectin Type Iii, Helical Cytokine, Cytokine Receptor, Interferon, Cytokine Receptor-Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. A. De Weerd, J. P. Vivian, T. K. Nguyen, N. E. Mangan, J. A. Gould, S. J. Braniff, L. Zaker-Tabrizi, K. Y. Fung, S. C. Forster, T. Beddoe, H. H. Reid, J. Rossjohn, P. J. Hertzog
Structural Basis Of A Unique Interferon Beta Signaling Axis Mediated Via The Ifnar1 Receptor
To Be Published
PubMed: search

Molecule 1 - INTERFERON ALPHA/BETA RECEPTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	IFAR, IFNAR, IFNAR1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	IFN-R-1, IFN-ALPHA/BETA RECEPTOR 1, TYPE I INTERFERON RECEPTOR 1

Molecule 2 - INTERFERON BETA
	Chains	:	I
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	IFB, IFNB, IFNB1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	IFN-BETA

		1	2
Asymmetric/Biological Unit	:	A	I

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3WCY)

Asymmetric/Biological Unit

No.	Residues
1	A:173	-	A:194
2	A:258	-	A:266
3	A:327	-	A:332
4	A:371	-	A:393

Asymmetric/Biological Unit

No.	Residues
1	Gln A:125	-	Asp A:126
2	Ser A:249	-	Asp A:250
3	Leu A:306	-	Pro A:307
4	Ser A:330	-	Thr A:331

(no "SAP(SNP)/Variant" information available for 3WCY)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	INAR1_MOUSE	127-226 31-125 332-425	2	A:101-200 - A:306-399
2	INTERFERON_A_B_D	PS00252	Interferon alpha, beta and delta family signature.	IFNB_MOUSE	141-159	1	I:120-138

(no "Exon" information available for 3WCY)

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:318
 aligned with INAR1_MOUSE | P33896 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:392
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424  
          INAR1_MOUSE    35 IDVYIIDDNYTLKWSSHGESMGSVTFSAEYRTKDEAKWLKVPECQHTTTTKCEFSLLDTNVYIKTQFRVRAEEGNSTSSWNEVDPFIPFYTAHMSPPEVRLEAEDKAILVHISPPGQDGNMWALEKPSFSYTIRIWQKSSSDKKTINSTYYVEKIPELLPETTYCLEVKAIHPSLKKHSNYSTVQCISTTVANKMPVPGNLQVDAQGKSYVLKWDYIASADVLFRAQWLPGYSKSSSGSRSDKWKPIPTCANVQTTHCVFSQDTVYTGTFFLHVQASEGNHTSFWSEEKFIDSQKHILPPPPVITVTAMSDTLLVYVNCQDSTCDGLNYEIIFWENTSNTKISMEKDGPEFTLKNLQPLTVYCVQARVLFRALLNKTSNFSEKLCEKTRPGS 426
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.------------------------------------------................--------........hhhhhee....eeeeee....eeeeee................eeeeeeee......eeeee...eeee.......eeeeeeeee.............eeee.............eeee...eeeee...------....eeeehhhhhh........ee...........eeee.......eeeee.-------.......eeee..........eeeeee....eeeeee.........eeeeeeee......eeeee...eeee.......eeeeeeeee-----------...eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: - UniProt: 31-125                                                                -FN3  PDB: A:101-200 UniProt: 127-226                                                                ---------------------------------------------------------------------------------------------------------FN3  PDB: A:306-399 UniProt: 332-425                                                          - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcy A   9 IDVYIIDDNYTL------------------------------------------SLLDTNVYIKTQFRVR--------SWNEVDPFIPFYTAHMSPPEVRLEAEDKAILVHISPPGQDGNMWALEKPSFSYTIRIWQKSSSDKKTINSTYYVEKIPELLPETTYCLEVKAIHPSLKKHSNYSTVQCISTTVANKMPVPGNLQVDAQGKSYVLKWDY------LFRAQWLPGYSKSSSGSRSDKWKPIPTCANVQTTHCVFSQDTVYTGTFFLHV-------TSFWSEEKFIDSQKHILPPPPVITVTAMSDTLLVYVNCQDSTCDGLNYEIIFWENTSNTKISMEKDGPEFTLKNLQPLTVYCVQARVL-----------SEKLCEKTRPGS 400
                                    18 |       -         -         -         -    |   68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     |   -  |    238       248       258       268       278   |     - |     298       308       318       328       338       348       358       368        |-         -|      398  
                                      20                                         63             78       87                                                                                                                                      224    231                                                282     290                                                                                    377         389

Chain I from PDB  Type:PROTEIN  Length:160
 aligned with IFNB_MOUSE | P01575 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:160
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           IFNB_MOUSE    22 INYKQLQLQERTNIRKCQELLEQLNGKINLTYRADFKIPMEMTEKMQKSYTAFAIQEMLQNVFLVFRNNFSSTGWNETIVVRLLDELHQQTVFLKTVLEEKQEERLTWEMSSTALHLKSYYWRVQRYLKLMKYNSYAWMVVRAEIFRNFLIIRRLTRNFQ 181
               SCOP domains d3wcyi_ I: Interferon-beta                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...............hhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------INTERFERON_A_B_D   ---------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcy I   1 INYKQLQLQERTNIRKCQELLEQLNGKINLTYRADFKIPMEMTEKMQKSYTAFAIQEMLQNVFLVFRNNFSSTGWNETIVVRLLDELHQQTVFLKTVLEEKQEERLTWEMSSTALHLKSYYWRVQRYLKLMKYNSYAWMVVRAEIFRNFLIIRRLTRNFQ 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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/Biological 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: Interferon-beta (4)

Mouse (Mus musculus) [TaxId: 10090] (3)

d3wcyi_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (INAR1_MOUSE | P33896)

molecular function
	GO:0004904	interferon receptor activity	Combining with an interferon and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0019962	type I interferon binding	Interacting selectively and non-covalently with a type I interferon. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families.
	GO:0004905	type I interferon receptor activity	Combining with a type I interferon and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families.
biological process
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0035457	cellular response to interferon-alpha	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 an interferon-alpha stimulus. Interferon-alpha is a type I interferon.
	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:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0032728	positive regulation of interferon-beta production	Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0050718	positive regulation of interleukin-1 beta secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050730	regulation of peptidyl-tyrosine phosphorylation	Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0045351	type I interferon biosynthetic process	The chemical reactions and pathways resulting in the formation of any type I interferon. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0060337	type I interferon signaling pathway	A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.

Chain I (IFNB_MOUSE | P01575)

molecular function
	GO:0008811	chloramphenicol O-acetyltransferase activity	Catalysis of the reaction: chloramphenicol + acetyl-CoA = chloramphenicol 3-acetate + CoA.
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005126	cytokine receptor binding	Interacting selectively and non-covalently with a cytokine receptor.
	GO:0005132	type I interferon receptor binding	Interacting selectively and non-covalently with an interferon-type I receptor, a heterodimeric complex composed of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2).
biological process
	GO:0002312	B cell activation involved in immune response	The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0042100	B cell proliferation	The expansion of a B cell population by cell division. Follows B cell activation.
	GO:0002286	T cell activation involved in immune response	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0071549	cellular response to dexamethasone 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 dexamethasone stimulus.
	GO:0071359	cellular response to dsRNA	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 double-stranded RNA stimulus.
	GO:0035458	cellular response to interferon-beta	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 an interferon-beta stimulus. Interferon-beta is a type I interferon.
	GO:0098586	cellular response to virus	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 stimulus from a virus.
	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:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0006959	humoral immune response	An immune response mediated through a body fluid.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002323	natural killer cell activation involved in immune response	The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
	GO:0045581	negative regulation of T cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation.
	GO:2000552	negative regulation of T-helper 2 cell cytokine production	Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 2 cell cytokine production.
	GO:0045071	negative regulation of viral genome replication	Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
	GO:2001235	positive regulation of apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	Any process that activates or increases the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
	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:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
	GO:0043330	response to exogenous dsRNA	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 an exogenous double-stranded RNA stimulus.
	GO:0060337	type I interferon signaling pathway	A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
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/Biological Unit
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(no "Sites" information available for 3wcy)

	Cis Peptide Bonds
		Gln A:125 - Asp A:126	[ RasMol ]
		Leu A:306 - Pro A:307	[ RasMol ]
		Ser A:249 - Asp A:250	[ RasMol ]
		Ser A:330 - Thr A:331	[ RasMol ]

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	3wcy
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	IFNB_MOUSE \| P01575
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	INAR1_MOUSE \| P33896
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UniProtKB/Swiss-Prot
	IFNB_MOUSE \| P01575	:	1ifa 1wu3 2hif

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (4, 4)

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