2KZ1 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   INTER-MOLECULAR INTERACTIONS IN A 44 KDA INTERFERON-RECEPTOR COMPLEX DETECTED BY ASYMMETRIC BACK-PROTONATION AND 2D NOESY

Authors :   I. Nudelman, S. R. Akabayov, E. Schnur, Z. Biron, R. Levy, Y. Xu, D. Yang, J. Anglister

Date :   10 Jun 10 (Deposition) - 23 Jun 10 (Release) - 07 Jul 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)

Keywords :   Interferon, Receptor, Docking, Complex, Antiviral Defense, Cytokine, Disulfide Bond, Glycoprotein, Secreted, Antiviral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Nudelman, S. R. Akabayov, E. Schnur, Z. Biron, R. Levy, Y. Xu, D. Yang J. Anglister
Intermolecular Interactions In A 44 Kda Interferon-Receptor Complex Detected By Asymmetric Reverse-Protonation And Two-Dimensional Noesy
Biochemistry V. 49 5117 2010
PubMed-ID: 20496919 | Reference-DOI: 10.1021/BI100041F

Molecule 1 - INTERFERON ALPHA-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector	:	PTZT7U18
	Gene	:	IFNA2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IFN-ALPHA-2, INTERFERON ALPHA-A, LEIF A

Molecule 2 - SOLUBLE IFN ALPHA/BETA RECEPTOR
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector	:	PTZT7U18
	Gene	:	IFNABR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KZ1)

(no "Site" information available for 2KZ1)

NMR Structure

No.	Residues
1	A:1	-	A:98
2	A:29	-	A:138
3	B:12	-	B:95
4	B:58	-	B:66
5	B:180	-	B:200

(no "Cis Peptide Bond" information available for 2KZ1)

NMR Structure (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_004012	K	46	R	IFNA2_HUMAN	Polymorphism	1061959	A	K	23	R
2	UniProt	VAR_013001	H	57	R	IFNA2_HUMAN	Unclassified	---	A	H	34	R
3	UniProt	VAR_036329	S	177	L	IFNA2_HUMAN	Unclassified	---	A	S	154	L
4	UniProt	VAR_020523	I	196	V	INAR2_HUMAN	Polymorphism	17860223	B	I	169	V

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERFERON_A_B_D	PS00252	Interferon alpha, beta and delta family signature.	IFNA2_HUMAN	145-163	1	A:122-140

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000342136	1d	ENSE00001384199	chr21:34602279-34602521	243	INAR2_HUMAN	-	0	0	-	-
1.3a	ENST00000342136	3a	ENSE00001366893	chr21:34614145-34614282	138	INAR2_HUMAN	1-19	19	0	-	-
1.4	ENST00000342136	4	ENSE00001043262	chr21:34615978-34616019	42	INAR2_HUMAN	19-33	15	0	-	-
1.5	ENST00000342136	5	ENSE00001784597	chr21:34617256-34617379	124	INAR2_HUMAN	33-74	42	1	B:11-47	37
1.7b	ENST00000342136	7b	ENSE00001733110	chr21:34619023-34619195	173	INAR2_HUMAN	74-132	59	1	B:47-105	59
1.8a	ENST00000342136	8a	ENSE00002144798	chr21:34621014-34621159	146	INAR2_HUMAN	132-180	49	1	B:105-153	49
1.10	ENST00000342136	10	ENSE00002186976	chr21:34624967-34625135	169	INAR2_HUMAN	181-237	57	1	B:154-206	53
1.11	ENST00000342136	11	ENSE00001781920	chr21:34632902-34633032	131	INAR2_HUMAN	237-280	44	0	-	-
1.12g	ENST00000342136	12g	ENSE00001764722	chr21:34635098-34636830	1733	INAR2_HUMAN	281-515	235	0	-	-

2.1	ENST00000380206	1	ENSE00001484102	chr9:21385396-21384254	1143	IFNA2_HUMAN	1-211	211	1	A:1-165	165

NMR Structure

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:165
 aligned with IFNA2_HUMAN | P01563 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:165
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
          IFNA2_HUMAN    24 CDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE 188
               SCOP domains d2kz1a_ A: Interferon-alpha 2a                                                                                                                                        SCOP domains
               CATH domains 2kz1A00 A:1-165  [code=1.20.1250.10, no name defined]                                                                                                                 CATH domains
               Pfam domains --Interferon-2kz1A01 A:3-163                                                                                                                                       -- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...hhhhh......................hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------R----------R-----------------------------------------------------------------------------------------------------------------------L----------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------INTERFERON_A_B_D   ------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-165 UniProt: 1-211 [INCOMPLETE]                                                                                                                    Transcript 2
                 2kz1 A   1 CDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with INAR2_HUMAN | P48551 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:196
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227      
          INAR2_HUMAN    38 SCTFKISLRNFRSILSWELKNHSIVPTHYTLLYTIMSKPEDLKVVKNCANTTRSFCDLTDEWRSTHEAYVTVLEGFSGNTTLFSCSHNFWLAIDMSFEPPEFEIVGFTNHINVMVKFPSIVEEELQFDLSLVIEEQSEGIVKKHKPEIKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPPG 233
               SCOP domains d2kz1b1 B:11-109 Interferon-alpha/beta receptor beta chain                                         d2kz1b2 B:110-206 Interferon-alpha/beta receptor beta chain                                       SCOP domains
               CATH domains 2kz1B01 B:11-106 Immunoglobulins                                                                2kz1B02 B:107-206 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeee.........eeeeeee........ee..........eee..........eeeeeeeee....eeeeeeeeee..........eeeeee....eeeeee....hhhhh....eeeeeeee..eeeee..........eeeeee.......eeeeeeeee............eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:11-47 UniProt: 33-74---------------------------------------------------------Exon 1.8a  PDB: B:105-153 UniProt: 132-180       Exon 1.10  PDB: B:154-206 UniProt: 181-237            Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.7b  PDB: B:47-105 UniProt: 74-132                   ----------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2kz1 B  11 SCTFKISLRNFRSILSWELKNHSIVPTHYTLLYTIMSKPEDLKVVKNCANTTRSFCDLTDEWRSTHEAYVTVLEGFSGNTTLFSCSHNFWLAIDMSFEPPEFEIVGFTNHINVMVKFPSIVEEELQFDLSLVIEEQSEGIVKKHKPEIKGNMSGNFTYIIDKLIPNTNYCVSVYLEHSDEQAVIKSPLKCTLLPPG 206
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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 '\|'

NMR Structure

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)

2kz1A00

A:1-165

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2kz1B01	B:11-106
2b	2kz1B02	B:107-206

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 4H_Cytokine (48)

Family: Interferon (3)

Homo sapiens (Human) (1)

Interferon-2kz1A01

A:3-163

NMR Structure(hide GO term definitions)

Chain A (IFNA2_HUMAN | P01563)

molecular function
	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: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: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: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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	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: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: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: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: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: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:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:2000666	negative regulation of interleukin-13 secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-13 secretion.
	GO:2000663	negative regulation of interleukin-5 secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-5 secretion.
	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:0046597	negative regulation of viral entry into host cell	Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
	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:0042327	positive regulation of phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
	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: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.

Chain B (INAR2_HUMAN | P48551)

molecular function
	GO:0042015	interleukin-20 binding	Interacting selectively and non-covalently with interleukin-20.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	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: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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates 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:0035455	response to interferon-alpha	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 interferon-alpha stimulus. Interferon-alpha is a type I interferon.
	GO:0009615	response to virus	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 stimulus from a virus.
	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.
	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: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.
	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.

NMR Structure
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(no "Related Entries Specified in the PDB File" available for 2KZ1)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (5, 5)

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