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Title :   THE CRYSTAL STRUCTURE OF HUMAN INTERFERON LAMBDA 1 COMPLEXED WITH ITS HIGH AFFINITY RECEPTOR IN SPACE GROUP P212121

Authors :   Z. J. Miknis, E. Magracheva, W. Lei, A. Zdanov, S. V. Kotenko, A. Wlodawe

Date :   16 Aug 10 (Deposition) - 20 Oct 10 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Helical Bundle, Fibronectin Type Iii Domain, Beta-Sandwich, Cytokine Signaling, Membrane, Cytokine-Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. J. Miknis, E. Magracheva, W. Li, A. Zdanov, S. V. Kotenko, A. Wlodawe
Crystal Structure Of The Complex Of Human Interferon-Lambda With Its High Affinity Receptor Interferon-Lambdar1.
J. Mol. Biol. V. 404 650 2010
PubMed-ID: 20934432 | Reference-DOI: 10.1016/J.JMB.2010.09.068

Molecule 1 - INTERLEUKIN-29
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PMT/BIP/V5-HIS
	Expression System Strain	:	S2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	VIRUS
	Gene	:	IFNL1, IL29, ZCYTO21
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IL-29, INTERFERON LAMBDA-1, IFN-LAMBDA-1, CYTOKINE ZCYTO21

Molecule 2 - INTERLEUKIN 28 RECEPTOR, ALPHA (INTERFERON, LAMBDA RECEPTOR)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PMT/BIP/V5-HIS
	Expression System Strain	:	S2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	VIRUS
	Fragment	:	EXTRACELLULAR DOMAIN (UNP RESIDUE 19-226)
	Gene	:	HCG_1982865, IL28RA, RP11-10N16.1-001
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERLEUKIN 28 RECEPTOR, ALPHA (INTERFERON, LAMBDA RECEPTOR), ISOFORM CRA_E

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	GOL	4	Ligand/Ion	GLYCEROL
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:138 , LYS A:139 , LYS A:140 , GLU A:141 , HOH A:278	BINDING SITE FOR RESIDUE GOL A 182
2	AC2	SOFTWARE	LYS A:33 , ASP A:93 , VAL A:94 , HIS A:129 , SER B:171	BINDING SITE FOR RESIDUE GOL A 183
3	AC3	SOFTWARE	NAG B:302	BINDING SITE FOR RESIDUE BMA B 303
4	AC4	SOFTWARE	ASN B:122 , ALA B:123 , THR B:124 , HIS B:158 , HOH B:260 , HOH B:263 , NAG B:302	BINDING SITE FOR RESIDUE NAG B 301
5	AC5	SOFTWARE	GLY B:159 , HOH B:260 , NAG B:301 , BMA B:303	BINDING SITE FOR RESIDUE NAG B 302
6	AC6	SOFTWARE	ASN B:9	BINDING SITE FOR RESIDUE NAG B 300
7	AC7	SOFTWARE	ASN B:16 , GLN B:126	BINDING SITE FOR RESIDUE NAG B 304
8	AC8	SOFTWARE	PHE A:152 , ASN A:153 , ARG A:156 , HOH A:198 , SER B:42 , ASP B:71 , ASN B:74 , HOH B:335	BINDING SITE FOR RESIDUE GOL B 225
9	AC9	SOFTWARE	LYS B:150 , SER B:177 , PHE B:192	BINDING SITE FOR RESIDUE GOL B 226

Asymmetric/Biological Unit

No.	Residues
1	A:49	-	A:145
2	B:54	-	B:62
3	B:66	-	B:130
4	B:175	-	B:197

(no "Cis Peptide Bond" information available for 3OG6)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024506	N	188	D	IFNL1_HUMAN	Polymorphism	30461	A	N	169	D

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	INLR1_HUMAN	26-126	1	B:6-106

(no "Exon" information available for 3OG6)

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:143
 aligned with IFNL1_HUMAN | Q8IU54 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:149
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180         
          IFNL1_HUMAN    41 SLSPQELASFKKARDALEESLKLKNWSCSSPVFPGNWDLRLLQVRERPVALEAELALTLKVLEAAAGPALEDVLDQPLHTLHHILSQLQACIQPQPTAGPRPRGRLHHWLHRLQEAPKKESAGCLEASVTFNLFRLLTRDLKYVADGNL 189
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------D- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3og6 A  22 SLSPQELASFKKARDALEESLKLKNWSCSSPVFPGNWDLRLLQVRERPVALEAELALTLKVLEAAAGPALEDVLDQPLHTLHHILSQLQACIQP------RPRGRLHHWLHRLQEAPKKESAGCLEASVTFNLFRLLTRDLKYVADGNL 170
                                    31        41        51        61        71        81        91       101       111   |     -|      131       141       151       161         
                                                                                                                       115    122

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with INLR1_HUMAN | Q8IU57 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:200
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
          INLR1_HUMAN    24 LAPPQNVTLLSQNFSVYLTWLPGLGNPQDVTYFVAYQSSPTRRRWREVEECAGTKELLCSMMCLKKQDLYNKFKGRVRTVSPSSKSPWVESEYLDYLFEVEPAPPVLVLTQTEEILSANATYQLPPCMPPLDLKYEVAFWKEGAGNKTLFPVTPHGQPVQITLQPAASEHHCLSARTIYTFSVPKYSKFSKPTCFLLEVP 223
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeee.........eeeeeee.......eee.hhhh.....eee..............eeeeeee..ee...ee....hhhhhh.....eeeeeee..eeeeeee...........eeeeeeeee......ee...ee...eeeee.......eeeeeeeeeee...eee......eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FN3  PDB: B:6-106 UniProt: 26-126                                                                    ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3og6 B   4 LAPPQNVTLLSQNFSVYLTWLPGLGNPQDVTYFVAYQSSPTRRRWREVEECAGTKELLCSMMCLKKQDLYNKFKGRVRTVSPSSKSPWVESEYLDYLFEVEPAPPVLVLTQTEEILSANATYQLPPCMPPLDLKYEVAFWKEGAGNKTLFPVTPHGQPVQITLQPAASEHHCLSARTIYTFSVPKYSKFSKPTCFLLEVP 203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

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 3OG6)

(no "CATH Domain" information available for 3OG6)

(no "Pfam Domain" information available for 3OG6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IFNL1_HUMAN | Q8IU54)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0032003	interleukin-28 receptor binding	Interacting selectively and non-covalently with the interleukin-28 receptor.
	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:0007259	JAK-STAT cascade	Any process in which STAT proteins (Signal Transducers and Activators of Transcription) and JAK (Janus Activated Kinase) proteins convey a signal to trigger a change in the activity or state of a cell. The JAK-STAT cascade begins with activation of STAT proteins by members of the JAK family of tyrosine kinases, proceeds through dimerization and subsequent nuclear translocation of STAT proteins, and ends with regulation of target gene expression by STAT proteins.
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	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:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0032696	negative regulation of interleukin-13 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-13 production.
	GO:0032714	negative regulation of interleukin-5 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-5 production.
	GO:0043381	negative regulation of memory T cell differentiation	Any process that stops, prevents, or reduces the rate of memory T cell differentiation.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0002829	negative regulation of type 2 immune response	Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response.
	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:0045345	positive regulation of MHC class I biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I.
	GO:0050778	positive regulation of immune response	Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	Any process that activates or increases the frequency, rate or extent of the introduction of a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
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.
	GO:0032002	interleukin-28 receptor complex	A protein complex that binds interleukin-28 and interleukin-29. It is composed of an alpha and a beta receptor subunit (in human IFNLR1/IL28Ralpha & IL10RB) and either Interleukin-28 (IFNL2 or IFNL3) or Interleukin-29 (IFNL1).
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Chain B (INLR1_HUMAN | Q8IU57)

molecular function
	GO:0004896	cytokine receptor activity	Combining with a cytokine 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).
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:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0002385	mucosal immune response	An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0050691	regulation of defense response to virus by host	Any host process that modulates the frequency, rate, or extent of the antiviral response of a host cell or organism.
	GO:0034342	response to type III interferon	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 type III interferon stimulus. Interferon lambda is the only member of the type III interferon found so far.
cellular component
	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:0032002	interleukin-28 receptor complex	A protein complex that binds interleukin-28 and interleukin-29. It is composed of an alpha and a beta receptor subunit (in human IFNLR1/IL28Ralpha & IL10RB) and either Interleukin-28 (IFNL2 or IFNL3) or Interleukin-29 (IFNL1).
	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
(no "Cis Peptide Bonds" information available for 3og6)

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	INLR1_HUMAN \| Q8IU57
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UniProtKB/Swiss-Prot
	IFNL1_HUMAN \| Q8IU54	:	3og4
	INLR1_HUMAN \| Q8IU57	:	3og4 5ixd 5ixi 5l04 5t5w

3g9v	IL-22 BINDING PROTEIN
3hhc	INTERFERON LAMBDA 3
3og4	COMPLEX OF INTERFERON LAMBDA 1 WITH INTERFERON LAMBDA RECEPTOR 1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (32, 35)

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