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Biological Unit 2 (Jmol Viewer)

Title :   OTU DOMAIN OF CRIMEAN CONGO HEMORRHAGIC FEVER VIRUS IN COMPLEX WITH ISG15

Authors :   M. Akutsu, Y. Ye, S. Virdee, D. Komander

Date :   04 Nov 10 (Deposition) - 02 Feb 11 (Release) - 06 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Otu Domain, De-Ubiquitinase, De-Isgylase, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Akutsu, Y. Ye, S. Virdee, J. W. Chin, D. Komander
Molecular Basis For Ubiquitin And Isg15 Cross-Reactivity In Viral Ovarian Tumor Domains.
Proc. Natl. Acad. Sci. Usa V. 108 2228 2011
PubMed-ID: 21266548 | Reference-DOI: 10.1073/PNAS.1015287108

Molecule 1 - RNA-DIRECTED RNA POLYMERASE L
	Chains	:	A
	EC Number	:	3.4.19.12, 2.7.7.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 1-183
	Gene	:	L
	Organism Common	:	CCHFV
	Organism Scientific	:	CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
	Organism Taxid	:	652961
	Strain	:	NIGERIA/IBAR10200/1970
	Synonym	:	PROTEIN L, LARGE STRUCTURAL PROTEIN, REPLICASE, TRANSCRIPTASE, UBIQUITIN THIOLESTERASE, RNA-DIRECTED RNA POLYMERASE

Molecule 2 - UBIQUITIN-LIKE PROTEIN ISG15
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 79-156
	Gene	:	ISG15, G1P2, UCRP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERFERON-INDUCED 15 KDA PROTEIN, INTERFERON-INDUCED 17 KDA PROTEIN, IP17, UBIQUITIN CROSS-REACTIVE PROTEIN, HUCRP

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	NEH	1	Ligand/Ion	ETHANAMINE
3	ZN	12	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	NEH	1	Ligand/Ion	ETHANAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	NEH	-1	Ligand/Ion	ETHANAMINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:43 , LYS A:53 , ASP A:55 , SER A:57 , TYR A:58 , HOH A:318	BINDING SITE FOR RESIDUE ZN A 184
02	AC2	SOFTWARE	SER A:6 , ASP A:8 , HIS A:56 , HIS A:59 , HOH A:255 , HOH A:268	BINDING SITE FOR RESIDUE ZN A 185
03	AC3	SOFTWARE	ASP A:8 , ASP A:96 , ACY A:193 , HOH A:262 , HOH A:266	BINDING SITE FOR RESIDUE ZN A 186
04	AC4	SOFTWARE	ASN A:24 , GLU A:126 , HOH A:320	BINDING SITE FOR RESIDUE ZN A 187
05	AC5	SOFTWARE	HIS A:151 , ASP A:153 , HOH A:258 , HOH A:259	BINDING SITE FOR RESIDUE ZN A 188
06	AC6	SOFTWARE	ASP A:88 , HOH A:234 , HOH A:330 , HOH A:331 , GLU B:127	BINDING SITE FOR RESIDUE ZN A 189
07	AC7	SOFTWARE	GLU A:47	BINDING SITE FOR RESIDUE ZN A 190
08	AC8	SOFTWARE	PRO A:35 , ASP A:37 , HIS A:43 , ACY A:193 , HOH A:254	BINDING SITE FOR RESIDUE ZN A 191
09	AC9	SOFTWARE	GLY A:-1 , ASP A:2 , ASP A:55 , HOH A:270	BINDING SITE FOR RESIDUE ZN A 192
10	BC1	SOFTWARE	ASP A:8 , ASP A:37 , ASN A:39 , HIS A:43 , HIS A:56 , TYR A:58 , ASP A:96 , ZN A:186 , ZN A:191 , HOH A:266 , HOH A:268	BINDING SITE FOR RESIDUE ACY A 193
11	BC2	SOFTWARE	ASP A:37 , CYS A:40 , TRP A:99 , THR A:150 , GLY B:156	BINDING SITE FOR RESIDUE NEH B 157
12	BC3	SOFTWARE	HIS B:106	BINDING SITE FOR RESIDUE ZN B 1
13	BC4	SOFTWARE	HIS B:106 , GLN B:109	BINDING SITE FOR RESIDUE ZN B 2
14	BC5	SOFTWARE	ACY B:4 , ASP B:119 , HOH B:240	BINDING SITE FOR RESIDUE ZN B 3
15	BC6	SOFTWARE	ZN B:3 , ASP B:119	BINDING SITE FOR RESIDUE ACY B 4

(no "SS Bond" information available for 3PHX)

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

Asymmetric 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	B	S	83	N

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

Biological Unit 1 (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	B	S	83	N

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

Biological Unit 2 (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	B	S	83	N

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

Asymmetric Unit (2, 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	1	- B:82-156
2	OTU	PS50802	OTU domain profile.	L_CCHFI	29-158	1	A:29-158

Biological Unit 1 (2, 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	1	- B:82-156
2	OTU	PS50802	OTU domain profile.	L_CCHFI	29-158	1	A:29-158

Biological Unit 2 (2, 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	1	- B:82-156
2	OTU	PS50802	OTU domain profile.	L_CCHFI	29-158	1	A:29-158

Asymmetric 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	B:80-156	77

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:162
 aligned with L_CCHFI | Q6TQR6 from UniProtKB/Swiss-Prot  Length:3945

    Alignment length:164
                              1                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    
              L_CCHFI     - --MDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------OTU-3phxA01 A:35-152                                                                                                  ---------- Pfam domains
         Sec.struct. author ...hhhhhh..eeee..eeee....hhhhheeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....eehhhhhhhhhhhh..eeeee.--.....eeeee........eeeeee...eeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------OTU  PDB: A:29-158 UniProt: 29-158                                                                                                ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phx A  -1 GPMDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTV--SDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
                                     8        18        28        38        48        58        68        78        88        98       108       118  |  | 128       138       148       158    
                                                                                                                                                    121  |                                      
                                                                                                                                                       124

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with ISG15_HUMAN | P05161 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:77
                                    89        99       109       119       129       139       149       
          ISG15_HUMAN    80 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 156
               SCOP domains d3phxb_ B: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains -------ubiquitin-3phxB01 B:87-155                                           - Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee..ee Sec.struct. author
                 SAPs(SNPs) ---N------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE U-UBIQUITIN_2  PDB: B:82-156 UniProt: 82-157                                  PROSITE
               Transcript 1 Exon 1.2  PDB: B:80-156 UniProt: 2-165 [INCOMPLETE]                           Transcript 1
                 3phx B  80 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 156
                                    89        99       109       119       129       139       149

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

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

Superfamily: Ubiquitin-like (546)

Family: automated matches (55)

Protein domain: automated matches (55)

Human (Homo sapiens) [TaxId: 9606] (39)

d3phxb_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: OTU (9)

Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970) (CCHFV) (3)

OTU-3phxA01

A:35-152

Clan: Ubiquitin (279)

Family: ubiquitin (99)

Homo sapiens (Human) (67)

ubiquitin-3phxB01

B:87-155

Asymmetric Unit(hide GO term definitions)

Chain A (L_CCHFI | Q6TQR6)

molecular function
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0036459	thiol-dependent ubiquitinyl hydrolase activity	Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0039696	RNA-templated viral transcription	A transcription process that uses viral RNA as a template.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039648	modulation by virus of host protein ubiquitination	Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
	GO:0039689	negative stranded viral RNA replication	A viral genome replication process where the template genome is negative stranded, single stranded RNA ((-)ssRNA).
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0039579	suppression by virus of host ISG15 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
	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.

Chain B (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.

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	ISG15_HUMAN \| P05161	:	1z2m 2hj8 3pse 3r66 3rt3 3sdl 5tl6
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (0, 0)

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