5G52 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF FULL PARTICLE OF DEFORMED WING VIRUS

Authors :   K. Skubnik, J. Novacek, T. Fuzik, A. Pridal, R. Paxton, P. Plevka

Date :   18 May 16 (Deposition) - 22 Mar 17 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (60x)

Keywords :   Virus, Picornavirales, Iflaviridae, Iflavirus, Dwv Capsid, P Jellyroll, Catalytic Site Protease, Lipase Esterase Recepto (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Skubnik, J. Novacek, T. Fuzik, A. Pridal, R. J. Paxton, P. Plevka
Structure Of Deformed Wing Virus, A Major Honey Bee Pathogen.
Proc. Natl. Acad. Sci. V. 114 3210 2017 U. S. A.
PubMed-ID: 28270616 | Reference-DOI: 10.1073/PNAS.1615695114

Molecule 1 - VP1
	Chains	:	A
	Organism Scientific	:	DEFORMED WING VIRUS
	Organism Taxid	:	198112

Molecule 2 - VP2
	Chains	:	B
	Organism Scientific	:	DEFORMED WING VIRUS
	Organism Taxid	:	198112

Molecule 3 - VP3
	Chains	:	C
	Organism Scientific	:	DEFORMED WING VIRUS
	Organism Taxid	:	198112

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (60x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	U5P	1	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

Biological Unit 1 (1, 60)

No.	Name	Count	Type	Full Name
1	U5P	60	Ligand/Ion	URIDINE-5'-MONOPHOSPHATE

(no "Site" information available for 5G52)

(no "SS Bond" information available for 5G52)

Asymmetric Unit

No.	Residues
1	Leu A:16	-	Gln A:17
2	Gln A:17	-	Ser A:18
3	Glu A:28	-	Ala A:29
4	Arg A:38	-	Arg A:39
5	Asn A:117	-	Ser A:118
6	Ser A:134	-	Ala A:135
7	Thr A:146	-	Gly A:147
8	Gln A:148	-	Gly A:149
9	Arg A:163	-	Val A:164
10	Ala A:191	-	Ala A:192
11	Val A:197	-	Ser A:198
12	Ser A:198	-	Leu A:199
13	Leu A:248	-	Pro A:249
14	Lys B:18	-	Asp B:19
15	Pro B:86	-	Arg B:87
16	Ser B:171	-	Asn B:172
17	His C:18	-	Ser C:19
18	Ala C:21	-	Leu C:22
19	Glu C:51	-	Asp C:52
20	Gly C:95	-	Thr C:96
21	Val C:110	-	Ser C:111
22	Gly C:193	-	Asn C:194
23	Arg C:257	-	Asn C:258
24	Asn C:258	-	Asp C:259
25	Ala C:269	-	Pro C:270

(no "SAP(SNP)/Variant" information available for 5G52)

(no "PROSITE Motif" information available for 5G52)

(no "Exon" information available for 5G52)

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:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee..............................eeeeeee.............eeee..........................hhhhhh.....ee..eeeee.........eeee.................................eeee.........eee............................eeeee....eeeeeeee....ee...........hhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g52 A   1 GEESRNTTVLDTTTTLQSSGFGRAFFGEAFNDLKTLMRRYQLYGQLLLSVTTDKDIDHCMFTFPCLPQGLALDIGSAGSPHEIFNRCRDGIIPLIASGYRFYRGDLRYKIVFPSNVNSNIWVQHRPDRRLEGWSAAKIVNCDAVSTGQGVYNHGYASHIQITRVNNVIELEVPFYNATCYNYLQAFNASSAASSYAVSLGEISVGFVNKPVTIYYSIGDGMQFSQWVGYQPMMILDQLPAPVV 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     ||220       230       240       250   
                                                                                                                                                                                                                                       206|                                    
                                                                                                                                                                                                                                        217

Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee........ee...............hhhhhh......hhhhhh..eeeeee..................hhhhhhhhh...hhhhh..hhhhhhh.ee....eeeeee........eeeeeee.............hhhhhhh..eeeee.....eee...........ee...............eeeeeeee.............eeeeee..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g52 B   1 MDNPNPGPDGEGEVELEKDSNVVLTTQRDPSTSIPAPVSVKWSRWTSNDVVDDYATITSRWYQIAEFVWSKDDPFDKELARLILPRALLSSIEANSDAICDVPNTIPFKVHAYWRGDMEVRVQINSNKFQVGQLQATWYYSDHENLNISSKRSVYGFSQMDHALISASASNEAKLVIPFKHVYPFLPTRIVPDWTTGILDMGALNIRVIAPLRMSATGPTTCNVVVFIKLNNSEFTGTSSGKFYASQIRA 251
                                    10        20        30        40   ||   51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
                                                                      44|                                                                                                                                                                                                             
                                                                       46

Chain C from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................ee.....................hhhhhh...eeeeeeee..................................hhhhhh..........eeeeeee.......eeeeeeeee...hhhhh..hhhhhh..eeeeeee.....eeeee.........................eeee..eee...........eeeeeeeee.......................................eee....hhhhh..eee...................eeeeeee.hhhhh........eeeeee.....eeeeee.hhhhhhhhhhhhh......hhhhhh....hhhh...........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g52 C   2 NPSYQQSPRHFVPTGMHSLALGTNLVEPLHALRLDAAGTTQHPVGCAPDEDMTVSSIASRYGLIRRVQWKKDHAKGSLLLQLDADPFVEQRIEGTNPISLYWFAPVGVVSSMFMQWRGSLEYRFDIIASQFHTGRLIVGYVPGLTASLQLQMDYMKLKSSSYVVFDLQESNSFTFEVPYVSYRPWWVRKYGGNYLPSSTDAPSTLFMYVQVPLIPMEAVSDTIDINVYVRGGSSFEVCVPVQPSLGLNWNTDFILRNDEEYRAKTGYAPYYAGVWHSFNNSNSLVFRWGSASDQIAQWPTISVPRGELAFLRIKDGKQAAVGTQPWRTMVVWPSGHGYNIGIPTYNAERARQLAQHLYGGGSLTDEKAKQLFVPANQQGPGKVSNGNPVWEVMRAPL 398
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391

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 5G52)

(no "CATH Domain" information available for 5G52)

(no "Pfam Domain" information available for 5G52)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		U5P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 5g52)

	Cis Peptide Bonds
		Ala A:191 - Ala A:192	[ RasMol ]
		Ala C:21 - Leu C:22	[ RasMol ]
		Ala C:269 - Pro C:270	[ RasMol ]
		Arg A:163 - Val A:164	[ RasMol ]
		Arg A:38 - Arg A:39	[ RasMol ]
		Arg C:257 - Asn C:258	[ RasMol ]
		Asn A:117 - Ser A:118	[ RasMol ]
		Asn C:258 - Asp C:259	[ RasMol ]
		Gln A:148 - Gly A:149	[ RasMol ]
		Gln A:17 - Ser A:18	[ RasMol ]
		Glu A:28 - Ala A:29	[ RasMol ]
		Glu C:51 - Asp C:52	[ RasMol ]
		Gly C:193 - Asn C:194	[ RasMol ]
		Gly C:95 - Thr C:96	[ RasMol ]
		His C:18 - Ser C:19	[ RasMol ]
		Leu A:16 - Gln A:17	[ RasMol ]
		Leu A:248 - Pro A:249	[ RasMol ]
		Lys B:18 - Asp B:19	[ RasMol ]
		Pro B:86 - Arg B:87	[ RasMol ]
		Ser A:134 - Ala A:135	[ RasMol ]
		Ser A:198 - Leu A:199	[ RasMol ]
		Ser B:171 - Asn B:172	[ RasMol ]
		Thr A:146 - Gly A:147	[ RasMol ]
		Val A:197 - Ser A:198	[ RasMol ]
		Val C:110 - Ser C:111	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	Q8B3M2_9VIRU \| Q8B3M2	:	5g51 5l7q 5l8q

5g51	HIGH RESOLUTION STRUCTURE OF THE PART OF VP3 PROTEIN OF DEFORMED WING VIRUS FORMING P-DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (25, 25)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (20, 20)

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