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Title :   STRUCTURE OF ROTAVIRUS OUTER CAPSID PROTEIN VP7 TRIMER IN COMPLEX WITH A NEUTRALIZING FAB

Authors :   S. T. Aoki, E. C. Settembre, S. D. Trask, H. B. Greenberg, S. C. Harrison, P. R. Dormitzer

Date :   22 Dec 08 (Deposition) - 23 Jun 09 (Release) - 02 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

Chains :   Asym. Unit : A,H,L
Biol. Unit 1: A,H,L  (3x)

Keywords :   Antibody-Antigen Complex, Calcium Dependent Trimer, Antiparallel Beta-Sandwich, Jelly Roll, Alpha-Beta-Alpha Sandwich, Rossmann Fold, Capsid Protein, Endoplasmic Reticulum, Glycoprotein, Membrane, Transmembrane, Virion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. T. Aoki, E. C. Settembre, S. D. Trask, H. B. Greenberg, S. C. Harrison, P. R. Dormitzer
Structure Of Rotavirus Outer-Layer Protein Vp7 Bound With A Neutralizing Fab.
Science V. 324 1444 2009
PubMed-ID: 19520960 | Reference-DOI: 10.1126/SCIENCE.1170481

Molecule 1 - FAB OF NEUTRALIZING ANTIBODY 4F8, LIGHT CHAIN
	Chains	:	L
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

Molecule 2 - FAB OF NEUTRALIZING ANTIBODY 4F8, HEAVY CHAIN
	Chains	:	H
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

Molecule 3 - GLYCOPROTEIN VP7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Fragment	:	TRIMER SUBUNIT
	Gene	:	S9, VP7
	Organism Scientific	:	SIMIAN ROTAVIRUS
	Organism Taxid	:	10922
	Strain	:	RRV
	Synonym	:	SEROTYPE-SPECIFIC ANTIGEN, OUTER CAPSID GLYCOPROTEIN

		1	2	3
Asymmetric Unit	:	A	H	L
Biological Unit 1 (3x)	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:177 , LYS A:183 , ASP A:228 , VAL A:229 , ASP A:231 , ASP A:301	BINDING SITE FOR RESIDUE CA A 327
2	AC2	SOFTWARE	ASP A:95 , GLY A:206 , THR A:214 , GLU A:216	BINDING SITE FOR RESIDUE CA A 328

Asymmetric Unit

No.	Residues
1	A:82	-	A:135
2	A:165	-	A:249
3	A:191	-	A:244
4	A:196	-	A:207
5	H:22	-	H:98
6	H:152	-	H:218
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Pro L:94	-	Pro L:95
3	Phe H:158	-	Pro H:159
4	Glu H:160	-	Pro H:161
5	Arg H:210	-	Pro H:212

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_VP7_ROTRH_002 *	A	171	T	VP7_ROTRH	---	---	A	T	171	T
	* ID not provided by source

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

Biological Unit 1 (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_VP7_ROTRH_002 *	A	171	T	VP7_ROTRH	---	---	A	T	171	T
	* ID not provided by source

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

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

(no "Exon" information available for 3FMG)

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:235
 aligned with VP7_ROTRH | P12476 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:235
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     
            VP7_ROTRH    78 TSTLCLYYPTEAATEINDNSWKDTLSQLFLTKGWPTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDIALYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDTATFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSK 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhh....hhhhhhhhhhhh......eeeeee..hhhhhh.......eeeeeee..hhh...hhhhhhhhheeeeeee..............eeeeeee...eeeeee..................eeee....eeee......eeeeee....eeeeeeeeeee...eeeeee....................eeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmg A  78 TSTLCLYYPTEAATEINDNSWKDTLSQLFLTKGWPTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDTATFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSK 312
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fmgH01 H:1-123 Immunoglobulins                                                                                          3fmgH02 H:124-237 Immunoglobulins                                                                  - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh..eeeeee......eeeeeee...eeeee....hhheeeeee...eeeeeee........eeeeeee.........eeee...eeeee.........eeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmg H   1 QVQLQQSGAELMKPGALVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGSINYNEKFKGKATFTADTSSNTAYMQLNSLTSEDSAVYYCARNHGSPDFHVMDYWGQGTSITVSSAKTTAPPVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR 238
                                    10        20        30        40        50  ||    61        71        81     || 92       102       112       122       132       144       154       164|||    179|      190|      202   ||||215       225       237 
                                                                               53|                              87|                                                140|                  164|||    179|      190|          206|||                  233|  
                                                                                55                               89                                                 143                   166||     181       193           209||                   236  
                                                                                                                                                                                           167|                              210|                        
                                                                                                                                                                                            172                               212

Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3fmgL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.......................eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fmg L   1 DIQMTQSPASLSASVGETVTITCRPSENIYSYLAWYQQKQGKSPQLLVYKAKTLPEGVPSRFSGSGSGTHFSLKISSVQPEDFGTYYCQHHNGPPLTFGAGTKLELKRADAAPTVSIFPPSSKQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 3FMG)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mus musculus. Organism_taxid: 10090. (3)

1a	3fmgL02	L:109-211
1b	3fmgH01	H:1-123
1c	3fmgH02	H:124-237

(no "Pfam Domain" information available for 3FMG)

Asymmetric Unit(hide GO term definitions)

Chain A (VP7_ROTRH | P12476)

biological process
	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:0039621	T=13 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=13 symmetry. The T=13 capsid is composed of 12 pentameric and 120 hexameric capsomeres.
	GO:0044165	host cell endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0044166	host cell endoplasmic reticulum lumen	The volume enclosed by the membranes of the host cell endoplasmic reticulum.
	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:0039624	viral outer capsid	The outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg H:210 - Pro H:212	[ RasMol ]
		Glu H:160 - Pro H:161	[ RasMol ]
		Phe H:158 - Pro H:159	[ RasMol ]
		Pro L:94 - Pro L:95	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (5, 5)

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