3MIW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ROTAVIRUS NSP4

Authors :   A. R. Chacko, R. J. Read, E. J. Dodson, D. C. Rao, K. Suguna

Date :   12 Apr 10 (Deposition) - 25 May 11 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: B,C,E,G,I  (1x)
Biol. Unit 2: A,D,F,H,J  (1x)

Keywords :   Rotavirus Enterotoxin, Non Structural Protein, Nsp4, Pentameric Coiled Coil, Virulence, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Chacko, J. Jeyakanthan, G. Ueno, K. Sekar, C. D. Rao, E. J. Dodson, K. Suguna, R. J. Read
A New Pentameric Structure Of Rotavirus Nsp4 Revealed By Molecular Replacement.
Acta Crystallogr. , Sect. D V. 68 57 2012
PubMed-ID: 22194333 | Reference-DOI: 10.1107/S0907444911049705

Molecule 1 - NON-STRUCTURAL GLYCOPROTEIN 4
	Chains	:	B, C, E, G, I, A, D, F, H, J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B+
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DIARRHEA-INDUCING DOMAIN (UNP RESIDUES 95-146)
	Gene	:	G10
	Organism Common	:	RV-A
	Organism Scientific	:	HUMAN ROTAVIRUS G4
	Organism Taxid	:	10960
	Strain	:	STRAIN ST. THOMAS 3
	Synonym	:	NSP4, NCVP5, NS28

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:		B	C		E		G		I
Biological Unit 2 (1x)	:	A			D		F		H		J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 27)

No.	Name	Count	Type	Full Name
1	EDO	27	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 14)

No.	Name	Count	Type	Full Name
1	EDO	14	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 13)

No.	Name	Count	Type	Full Name
1	EDO	13	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	EDO B:39 , ARG B:101 , ARG C:107	BINDING SITE FOR RESIDUE EDO B 18
02	AC2	SOFTWARE	MET B:94 , ASN B:133 , MET D:94 , GLU F:96	BINDING SITE FOR RESIDUE EDO B 20
03	AC3	SOFTWARE	EDO B:18 , THR B:136 , ARG B:137	BINDING SITE FOR RESIDUE EDO B 39
04	AC4	SOFTWARE	ARG F:119	BINDING SITE FOR RESIDUE EDO B 40
05	AC5	SOFTWARE	HOH B:261	BINDING SITE FOR RESIDUE EDO B 41
06	AC6	SOFTWARE	ARG C:129	BINDING SITE FOR RESIDUE EDO C 1
07	AC7	SOFTWARE	EDO C:24 , ARG C:119	BINDING SITE FOR RESIDUE EDO C 21
08	AC8	SOFTWARE	EDO C:21 , EDO C:37	BINDING SITE FOR RESIDUE EDO C 24
09	AC9	SOFTWARE	EDO C:24 , GLU C:111	BINDING SITE FOR RESIDUE EDO C 37
10	BC1	SOFTWARE	GLU G:111 , ASP G:114	BINDING SITE FOR RESIDUE EDO G 42
11	BC2	SOFTWARE	ILE J:135	BINDING SITE FOR RESIDUE EDO I 30
12	BC3	SOFTWARE	ARG A:108 , GLU A:111 , MET A:112	BINDING SITE FOR RESIDUE EDO A 16
13	BC4	SOFTWARE	GLU A:122 , GLU A:125 , LEU A:126 , HOH D:16 , LYS D:128 , LYS E:104	BINDING SITE FOR RESIDUE EDO A 23
14	BC5	SOFTWARE	ARG A:129 , ASN A:133 , GLN C:98 , HIS D:131	BINDING SITE FOR RESIDUE EDO A 28
15	BC6	SOFTWARE	EDO D:32	BINDING SITE FOR RESIDUE EDO D 27
16	BC7	SOFTWARE	EDO D:27 , ARG D:101	BINDING SITE FOR RESIDUE EDO D 32
17	BC8	SOFTWARE	ARG F:107	BINDING SITE FOR RESIDUE EDO F 8
18	BC9	SOFTWARE	LEU H:134	BINDING SITE FOR RESIDUE EDO H 35
19	CC1	SOFTWARE	GLU J:111	BINDING SITE FOR RESIDUE EDO J 36
20	CC2	SOFTWARE	ASP J:132	BINDING SITE FOR RESIDUE EDO J 38

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

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

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

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

(no "Exon" information available for 3MIW)

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:43
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:43
                                   103       113       123       133   
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLIT 136
               SCOP domains d3miwa_ A: automated matches                SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 3miw A  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLIT 136
                                   103       113       123       133

Chain B from PDB  Type:PROTEIN  Length:44
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:44
                                   103       113       123       133    
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
               SCOP domains d3miwb_ B: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 3miw B  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
                                   103       113       123       133

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:46
                                   103       113       123       133      
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITRPV 139
               SCOP domains d3miwc_ C: automated matches                   SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 3miw C  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITRPV 139
                                   103       113       123       133

Chain D from PDB  Type:PROTEIN  Length:45
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:45
                                   103       113       123       133     
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITRP 138
               SCOP domains d3miwd_ D: automated matches                  SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 3miw D  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITRP 138
                                   103       113       123       133

Chain E from PDB  Type:PROTEIN  Length:44
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:44
                                   103       113       123       133    
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
               SCOP domains d3miwe_ E: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 3miw E  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
                                   103       113       123       133

Chain F from PDB  Type:PROTEIN  Length:44
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:44
                                   103       113       123       133    
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
               SCOP domains d3miwf_ F: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 3miw F  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLITR 137
                                   103       113       123       133

Chain G from PDB  Type:PROTEIN  Length:41
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:41
                                   103       113       123       133 
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNL 134
               SCOP domains d3miwg_ G: automated matches              SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3miw G  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNL 134
                                   103       113       123       133

Chain H from PDB  Type:PROTEIN  Length:40
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:40
                                   104       114       124       134
           NSP4_ROTHT    95 IEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNL 134
               SCOP domains d3miwh_ H: automated matches             SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3miw H  95 IEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNL 134
                                   104       114       124       134

Chain I from PDB  Type:PROTEIN  Length:43
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:43
                                   103       113       123       133   
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLIT 136
               SCOP domains d3miwi_ I: automated matches                SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 3miw I  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLIT 136
                                   103       113       123       133

Chain J from PDB  Type:PROTEIN  Length:42
 aligned with NSP4_ROTHT | Q82035 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:42
                                   103       113       123       133  
           NSP4_ROTHT    94 EIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLI 135
               SCOP domains d3miwj_ J: automated matches               SCOP domains
               CATH domains ------------------------------------------ CATH domains
           Pfam domains (1) -Rota_NSP4-3miwJ01 J:95-135                Pfam domains (1)
           Pfam domains (2) -Rota_NSP4-3miwJ02 J:95-135                Pfam domains (2)
           Pfam domains (3) -Rota_NSP4-3miwJ03 J:95-135                Pfam domains (3)
           Pfam domains (4) -Rota_NSP4-3miwJ04 J:95-135                Pfam domains (4)
           Pfam domains (5) -Rota_NSP4-3miwJ05 J:95-135                Pfam domains (5)
           Pfam domains (6) -Rota_NSP4-3miwJ06 J:95-135                Pfam domains (6)
           Pfam domains (7) -Rota_NSP4-3miwJ07 J:95-135                Pfam domains (7)
           Pfam domains (8) -Rota_NSP4-3miwJ08 J:95-135                Pfam domains (8)
           Pfam domains (9) -Rota_NSP4-3miwJ09 J:95-135                Pfam domains (9)
          Pfam domains (10) -Rota_NSP4-3miwJ10 J:95-135                Pfam domains (10)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 3miw J  94 MIEQQMDRIVKEMRRQLEMIDKLTTREIEQIELLKRIHDNLI 135
                                   103       113       123       133

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: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: Rotavirus nonstructural proteins (6)

Family: NSP4 oligomerization domain (5)

Protein domain: automated matches (3)

Human rotavirus g4 [TaxId: 10960] (1)

1a	d3miwa_	A:
1b	d3miwb_	B:
1c	d3miwc_	C:
1d	d3miwd_	D:
1e	d3miwe_	E:
1f	d3miwf_	F:
1g	d3miwg_	G:
1h	d3miwh_	H:
1i	d3miwi_	I:
1j	d3miwj_	J:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Rota_NSP4] (3)

Family: Rota_NSP4 (3)

Rotavirus A (strain Human/United Kingdom/ST3/1975 G4-P2A[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1) (RV-A) (Rota (1)

1a	Rota_NSP4-3miwJ01	J:95-135
1b	Rota_NSP4-3miwJ02	J:95-135
1c	Rota_NSP4-3miwJ03	J:95-135
1d	Rota_NSP4-3miwJ04	J:95-135
1e	Rota_NSP4-3miwJ05	J:95-135
1f	Rota_NSP4-3miwJ06	J:95-135
1g	Rota_NSP4-3miwJ07	J:95-135
1h	Rota_NSP4-3miwJ08	J:95-135
1i	Rota_NSP4-3miwJ09	J:95-135
1j	Rota_NSP4-3miwJ10	J:95-135

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H,I,J (NSP4_ROTHT | Q82035)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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: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:0044155	host caveola	A small pit, depression, or invagination, such as any of the minute pits or incuppings of the host cell membrane formed during pinocytosis, that communicates with the outside of a host cell and extends inward, indenting the host cytoplasm and the host cell membrane. Such caveolae may be pinched off to form free vesicles within the host cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	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:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0044169	host cell rough endoplasmic reticulum membrane	The lipid bilayer surrounding the host cell rough endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 27)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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