3PRP - JenaLib

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Title :   STRUCTURAL ANALYSIS OF A VIRAL OTU DOMAIN PROTEASE FROM THE CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS IN COMPLEX WITH HUMAN UBIQUITIN

Authors :   G. C. Capodagli, M. A. Mckercher, E. A. Baker, E. M. Masters, J. S. Brunze S. D. Pegan

Date :   30 Nov 10 (Deposition) - 26 Jan 11 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Ubiquitin Hydrolase, Deubiquitinase, Hydrolase, Cysteine Protease, Viral Protein, Hydrolase-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. C. Capodagli, M. A. Mckercher, E. A. Baker, E. M. Masters, J. S. Brunzelle, S. D. Pegan
Structural Analysis Of A Viral Ovarian Tumor Domain Proteas From The Crimean-Congo Hemorrhagic Fever Virus In Complex With Covalently Bonded Ubiquitin.
J. Virol. V. 85 3621 2011
PubMed-ID: 21228232 | Reference-DOI: 10.1128/JVI.02496-10

Molecule 1 - L PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
	Organism Taxid	:	11593
	Strain	:	IBAR10200

Molecule 2 - UBIQUITIN
	Chains	:	B, D
	EC Number	:	3.4.19.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB2
	Expression System Strain	:	BL21 CODONPLUS
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	UBC
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	3CN	2	Ligand/Ion	3-AMINOPROPANE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3CN	1	Ligand/Ion	3-AMINOPROPANE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	3CN	1	Ligand/Ion	3-AMINOPROPANE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:38 , CYS A:40 , TRP A:99 , THR A:150 , HIS A:151 , GLY B:75 , ASP D:39	BINDING SITE FOR RESIDUE 3CN B 76
2	AC2	SOFTWARE	ASP B:39 , GLY C:36 , GLY C:38 , CYS C:40 , TRP C:99 , THR C:150 , HIS C:151 , GLY D:75	BINDING SITE FOR RESIDUE 3CN D 76

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

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

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

(no "PROSITE Motif" information available for 3PRP)

(no "Exon" information available for 3PRP)

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:161
 aligned with Q6TFZ7_9VIRU | Q6TFZ7 from UniProtKB/TrEMBL  Length:3945

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
         Q6TFZ7_9VIRU     2 DFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee..eeee....hhhhheeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....eehhhhhhhhhhhh..eeeeee.....eeeeeee........eeeeee...eeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prp A   2 DFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with Q9PT09_ONCMY | Q9PT09 from UniProtKB/TrEMBL  Length:128

    Alignment length:75
                                    10        20        30        40        50        60        70     
         Q9PT09_ONCMY     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
               SCOP domains d3prpb_ B: Ubiquitin                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3prp B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                                    10        20        30        40        50        60        70

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with Q6TFZ7_9VIRU | Q6TFZ7 from UniProtKB/TrEMBL  Length:3945

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
         Q6TFZ7_9VIRU     2 DFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------OTU-3prpC01 C:35-152                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) ---------------------------------OTU-3prpC02 C:35-152                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author ........eeee..eeee....hhhhheeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....eehhhhhhhhhhhh..eeeeee.....eeeeeee........eeeeee...eeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prp C   2 DFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFE 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:75
 aligned with Q9PT09_ONCMY | Q9PT09 from UniProtKB/TrEMBL  Length:128

    Alignment length:75
                                    10        20        30        40        50        60        70     
         Q9PT09_ONCMY     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
               SCOP domains d3prpd_ D: Ubiquitin                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----ubiquitin-3prpD01 D:6-74                                             - Pfam domains (1)
           Pfam domains (2) -----ubiquitin-3prpD02 D:6-74                                             - Pfam domains (2)
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 3prp D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  75
                                    10        20        30        40        50        60        70

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: Ubiquitin-related (337)

Protein domain: Ubiquitin (162)

Human (Homo sapiens) [TaxId: 9606] (121)

1a	d3prpb_	B:
1b	d3prpd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: OTU (9)

Crimean-Congo hemorrhagic fever virus (4)

1a	OTU-3prpC01	C:35-152
1b	OTU-3prpC02	C:35-152

Clan: Ubiquitin (279)

Family: ubiquitin (99)

Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) (1)

2a	ubiquitin-3prpD01	D:6-74
2b	ubiquitin-3prpD02	D:6-74

Asymmetric Unit(hide GO term definitions)

Chain A,C (Q6TFZ7_9VIRU | Q6TFZ7)

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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	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.

Chain B,D (Q9PT09_ONCMY | Q9PT09)

molecular function
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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Description

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