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Title :   CRYSTAL STRUCTURE OF FLOCK HOUSE VIRUS CALCIUM MUTANT

Authors :   J. E. Johnson, M. Banerjee, J. A. Speir, R. Huang

Date :   03 Feb 10 (Deposition) - 21 Apr 10 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.60

Chains :   Asym. Unit : A,B,C,D,E,F,R
Biol. Unit 1: A,B,C,D,E,F,R  (60x)

Keywords :   Virus, Flock House Virus, Rna, Beta-Barrel, Jellyroll, Aspartyl Protease, Capsid Protein, Hydrolase, Protease, Virion, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Banerjee, J. A. Speir, M. H. Kwan, R. Huang, P. P. Aryanpur, B. Bothner, J. E. Johnson
Structure And Function Of A Genetically Engineered Mimic Of A Nonenveloped Virus Entry Intermediate.
J. Virol. V. 84 4737 2010
PubMed-ID: 20164221 | Reference-DOI: 10.1128/JVI.02670-09

Molecule 1 - COAT PROTEIN BETA
	Chains	:	A, B, C
	EC Number	:	3.4.23.44
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PBACPAK9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	ALPHA, FLOCK HOUSE VIRUS COAT PROTEIN ALPHA
	Mutation	:	YES
	Organism Common	:	FHV
	Organism Scientific	:	FLOCK HOUSE VIRUS
	Organism Taxid	:	12287
	Synonym	:	COAT PROTEIN BETA, NODAVIRUS ENDOPEPTIDASE, COAT PROTEIN GAMMA

Molecule 2 - COAT PROTEIN GAMMA
	Chains	:	D, E, F
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PBACPAK9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	ALPHA, FLOCK HOUSE VIRUS COAT PROTEIN ALPHA
	Organism Common	:	FHV
	Organism Scientific	:	FLOCK HOUSE VIRUS
	Organism Taxid	:	12287
	Synonym	:	COAT PROTEIN BETA, NODAVIRUS ENDOPEPTIDASE, COAT PROTEIN GAMMA

*Molecule 3 - RNA (5'-R(UPUPUAPUPCPUP(P))-3')*
	Chains	:	R
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Organism Scientific	:	SPODOPTERA FRUGIPERDA
	Organism Taxid	:	7108

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	R
Biological Unit 1 (60x)	:	A	B	C	D	E	F	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 300)

No.	Name	Count	Type	Full Name
1	SO4	300	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:258 , GLN A:260 , THR A:261 , ALA A:265 , GLN C:201 , PRO C:203	BINDING SITE FOR RESIDUE SO4 A 364
2	AC2	SOFTWARE	ARG B:87 , ARG C:87 , ASN C:249	BINDING SITE FOR RESIDUE SO4 C 364
3	AC3	SOFTWARE	GLN A:201 , PRO A:203 , GLY B:258 , GLN B:260 , THR B:261 , PRO B:264 , ALA B:265	BINDING SITE FOR RESIDUE SO4 B 364
4	AC4	SOFTWARE	GLN B:201 , PRO B:203 , GLY C:258 , GLN C:260 , THR C:261 , ALA C:265	BINDING SITE FOR RESIDUE SO4 C 400
5	AC5	SOFTWARE	HIS B:215	BINDING SITE FOR RESIDUE SO4 B 500

Asymmetric Unit

No.	Residues
1	A:69	-	A:318
2	B:69	-	B:318
3	C:69	-	C:318

Asymmetric Unit

No.	Residues
1	Asp A:207	-	Pro A:208
2	Leu A:262	-	Pro A:263
3	Asp B:207	-	Pro B:208
4	Leu B:262	-	Pro B:263
5	Asp C:207	-	Pro C:208
6	Leu C:262	-	Pro C:263

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

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

(no "Exon" information available for 3LOB)

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:312
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:340
                                    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
            CAPSD_FHV    22 TAPVPQQNVPRNGRRRRNRTRRNRRRVRGMNMAALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAA 361
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----------------------------...hhhhhhhhhhhhh..................eeeeeeeeee..ee....eeeeeee........eeeeee.........ee......hhhhhhh.hhhhhh..eeeeee..eeeeeee.........eeeeeee..eeeeee...........eeeeee.hhhhh......eeee.hhheeeee.........ee.............hhhhhh...ee.................eeeeeee.......eeeeeeeeeeeeee....hhhhh.ee....hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lob A  22 TAPVPQQ----------------------------TRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSNQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLNGVLAVGPDNFSESFIKGVFSQSACNEPNFQFNDILQGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAA 361
                                  |  -         -         -     |  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
                                 28                           57

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:306
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      
            CAPSD_FHV    57 TRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQ 362
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..................eeee..eeeeeeee....eeeeeee.....eeeeeeeee.........eeeeee..........hhhhh...eeeeee..eeeeeee.........eeeeeee..eeeeee...........eeeeeehhhhhh......eeee....eeeee.........ee......ee.....hhhhhh...eee................eeeeee........eeeeeeee.eeeee..........ee....hhhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lob B  57 TRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSNQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLNGVLAVGPDNFSESFIKGVFSQSACNEPNFQFNDILQGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQ 362
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356

Chain C from PDB  Type:PROTEIN  Length:309
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:309
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         
            CAPSD_FHV    55 ALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN 363
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh....................eeeeeeeeeeee....eeeeeee.....eeeeeeeee.........eeeeee..hhhhhhh....hhhhheeeeee..eeeeeee.........eeeeeee..eeeeee...........eeeeee.hhhhh......eeee....eeeee.........ee......ee..............eee................eeeeeee.......eeeeeeeeeeeeee...hhhhhhh......hhhhhhhhhhhhhhh...ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lob C  55 ALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSNQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLNGVLAVGPDNFSESFIKGVFSQSACNEPNFQFNDILQGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN 363
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354

Chain D from PDB  Type:PROTEIN  Length:4
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:4
            CAPSD_FHV   370 VKSI 373
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3lob D 370 VKSI 373

Chain E from PDB  Type:PROTEIN  Length:4
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:4
            CAPSD_FHV   368 ERVK 371
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3lob E 368 ERVK 371

Chain F from PDB  Type:PROTEIN  Length:18
 aligned with CAPSD_FHV | P12870 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:18
                                   373        
            CAPSD_FHV   364 ASMWERVKSIIKSSLAAA 381
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
           Pfam domains (1) Peptidase_A6-3lobF Pfam domains (1)
           Pfam domains (2) Peptidase_A6-3lobF Pfam domains (2)
           Pfam domains (3) Peptidase_A6-3lobF Pfam domains (3)
           Pfam domains (4) Peptidase_A6-3lobF Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3lob F 364 ASMWERVKSIIKSSLAAA 381
                                   373

Chain R from PDB  Type:RNA  Length:7
                                       
                 3lob R   3 UUUAUCU  10
                              ||   
                              5|   
                               7

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 3LOB)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Peptidase_A6 (1)

Flock house virus (FHV) (1)

1a	Peptidase_A6-3lobF01	F:364-381
1b	Peptidase_A6-3lobF02	F:364-381
1c	Peptidase_A6-3lobF03	F:364-381
1d	Peptidase_A6-3lobF04	F:364-381

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (CAPSD_FHV | P12870)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0039665	permeabilization of host organelle membrane involved in viral entry into host cell	Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
	GO:0039617	T=3 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:207 - Pro A:208	[ RasMol ]
		Asp B:207 - Pro B:208	[ RasMol ]
		Asp C:207 - Pro C:208	[ RasMol ]
		Leu A:262 - Pro A:263	[ RasMol ]
		Leu B:262 - Pro B:263	[ RasMol ]
		Leu C:262 - Pro C:263	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3lob
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	CAPSD_FHV \| P12870
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	3.4.23.44
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	CAPSD_FHV \| P12870	:	4fsj 4ftb 4fte 4fts

1f8v	THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA
1nov	NODAMURA VIRUS
2q23	CRYSTAL STRUCTURE OF FLOCK HOUSE N363T MUTANT
2q25	FLOCK HOUSE VIRUS COAT PROTEIN D75N MUTANT
2q26	FHV VIRUS LIKE PARTICLE
2z2q	CRYSTAL STRUCTURE OF FLOCK HOUSE VIRUS

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (3, 3)

Cis Peptide Bonds (6, 6)

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