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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF ISG15, THE INTERFERON-INDUCED UBIQUITIN CROSS REACTIVE PROTEIN

Authors :   J. Narasimhan, M. Wang, Z. Fu, J. M. Klein, A. L. Haas, J. J. Kim

Date :   08 Mar 05 (Deposition) - 24 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Isg15, Ubiquitin Cross Reactive Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Narasimhan, M. Wang, Z. Fu, J. M. Klein, A. L. Haas, J. J. Kim
Crystal Structure Of The Interferon-Induced Ubiquitin-Like Protein Isg15.
J. Biol. Chem. V. 280 27356 2005
PubMed-ID: 15917233 | Reference-DOI: 10.1074/JBC.M502814200
(for further references see the PDB file header)

Molecule 1 - INTERFERON, ALPHA-INDUCIBLE PROTEIN (CLONE IFI- 15K)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PED11D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ISG15

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	OS4	1	Ligand/Ion	OSMIUM 4+ ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:9 , GLY A:12 , ASN A:13 , HOH A:526	BINDING SITE FOR RESIDUE OS4 A 400

(no "SS Bond" information available for 1Z2M)

Asymmetric/Biological Unit

No.	Residues
1	His A:48	-	Pro A:49

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016181	S	83	N	ISG15_HUMAN	Polymorphism	1921	A	S	83	N

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	ISG15_HUMAN	3-80 82-157	2	A:3-80 A:82-154

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000379389	1	ENSE00001480807	chr1:948803-948956	154	ISG15_HUMAN	1-1	1	0	-	-
1.2	ENST00000379389	2	ENSE00001480799	chr1:949364-949920	557	ISG15_HUMAN	2-165	164	1	A:3-154	152

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
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Chain A from PDB  Type:PROTEIN  Length:152
 aligned with ISG15_HUMAN | P05161 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
          ISG15_HUMAN     3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKCDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL 154
               SCOP domains d1z2ma1 A:3-78 Interferon-induced 15 kDa protein                            d1z2ma2 A:79-154 Interferon-induced 15 kDa protein                           SCOP domains
               CATH domains 1z2mA01 A:3-77                                                             1z2mA02 A:78-154                                                              CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------ubiquitin-1z2mA01 A:87-154                                           Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------ubiquitin-1z2mA02 A:87-154                                           Pfam domains (2)
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeeee...........hhhhh.....eeeeee......eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------N----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: A:3-80 UniProt: 3-80                                        -UBIQUITIN_2  PDB: A:82-154 UniProt: 82-157                                PROSITE
               Transcript 1 Exon 1.2  PDB: A:3-154 UniProt: 2-165 [INCOMPLETE]                                                                                                       Transcript 1
                 1z2m A   3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: Interferon-induced 15 kDa protein (1)

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

1a	d1z2ma1	A:3-78
1b	d1z2ma2	A:79-154

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Human (Homo sapiens) (177)

1a	1z2mA02	A:78-154
1b	1z2mA01	A:3-77

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ubiquitin (279)

Family: ubiquitin (99)

Homo sapiens (Human) (67)

1a	ubiquitin-1z2mA01	A:87-154
1b	ubiquitin-1z2mA02	A:87-154

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ISG15_HUMAN | P05161)

molecular function
	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:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0032020	ISG15-protein conjugation	The covalent addition to a protein of ISG15, a ubiquitin-like protein.
	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:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0019941	modification-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.
	GO:0031397	negative regulation of protein ubiquitination	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:0032480	negative regulation of type I interferon production	Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	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:0045648	positive regulation of erythrocyte differentiation	Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
	GO:0032649	regulation of interferon-gamma production	Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0034340	response to type I 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 I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0019985	translesion synthesis	The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	ISG15_HUMAN \| P05161	:	2hj8 3phx 3pse 3r66 3rt3 3sdl 5tl6

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Ligands, Modified Residues, Ions (1, 1)

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