4YG6 - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURAL BASIS OF GLYCAN RECOGNITION IN NEONATE-SPECIFIC ROTAVIRUSES

Authors :   L. Hu, B. V. V. Prasad

Date :   25 Feb 15 (Deposition) - 30 Sep 15 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Rotavirus, Structural Biology, Glycan, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Hu, S. Ramani, R. Czako, B. Sankaran, Y. Yu, D. F. Smith, R. D. Cummings, M. K. Estes, B. V. Venkataram Prasad
Structural Basis Of Glycan Specificity In Neonate-Specific Bovine-Human Reassortant Rotavirus.
Nat Commun V. 6 8346 2015
PubMed-ID: 26420502 | Reference-DOI: 10.1038/NCOMMS9346

Molecule 1 - OUTER CAPSID PROTEIN VP8*
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 65-225
	Organism Common	:	RV-A
	Organism Scientific	:	ROTAVIRUS A
	Organism Taxid	:	10930
	Strain	:	ISOLATE COW/UNITED STATES/B223/1983 G10-P8[11]-I2-RX-CX-MX- A13-NX-TX-E2-HX
	Synonym	:	HEMAGGLUTININ

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	BGC	3	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	7	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (4, 5)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	BGC	-1	Ligand/Ion	BETA-D-GLUCOSE
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:85 , HIS A:161 , ARG A:162 , PRO A:196 , HOH A:1101 , HOH A:1105 , HOH A:1108 , HOH A:1131 , HOH A:1193	binding site for residue PO4 A 1005
2	AC2	SOFTWARE	ASN B:85 , HIS B:161 , ARG B:162 , ASP B:171 , HOH B:1142 , HOH B:1203 , HOH B:1210	binding site for residue PO4 B 1005
3	AC3	SOFTWARE	ASN C:85 , HIS C:161 , ARG C:162 , PRO C:196 , HOH C:1102 , HOH C:1107 , HOH C:1126 , HOH C:1138 , HOH C:1169 , HOH C:1366	binding site for residue PO4 C 1005
4	AC4	SOFTWARE	ASN D:85 , HIS D:161 , ARG D:162 , HOH D:1106 , HOH D:1117 , HOH D:1138 , HOH D:1149	binding site for residue PO4 D 1003
5	AC5	SOFTWARE	ASN A:155 , TYR A:156 , TRP A:178 , GLY A:179 , ALA A:180 , ASP A:185 , ARG A:187 , HOH A:1110 , HOH A:1149 , HOH A:1152 , HOH A:1155 , HOH A:1167 , HOH A:1181 , HOH A:1192 , HOH A:1218 , HOH A:1238 , HOH A:1372 , HOH A:1373 , HOH A:1478 , HOH A:1483 , ASN D:120 , ASN D:123 , THR D:125 , HOH D:1300	binding site for Poly-Saccharide residues GAL A 1001 through BGC A 1004
6	AC6	SOFTWARE	SER A:64 , ASN A:155 , TYR A:156 , TRP A:178 , GLY A:179 , ALA A:180 , ASP A:185 , ARG A:187 , GLN A:213 , HOH A:1110 , HOH A:1149 , HOH A:1152 , HOH A:1155 , HOH A:1167 , HOH A:1181 , HOH A:1192 , HOH A:1218 , HOH A:1238 , HOH A:1372 , HOH A:1373 , HOH A:1478 , HOH A:1483 , ASN B:155 , TYR B:156 , TRP B:178 , ASP B:185 , ARG B:187 , HOH B:1103 , HOH B:1105 , HOH B:1115 , HOH B:1160 , HOH B:1165 , HOH B:1173 , HOH B:1174 , HOH B:1176 , HOH B:1198 , HOH B:1213 , HOH B:1217 , HOH B:1328 , HOH B:1371 , GLY D:63 , ASN D:120 , ASN D:123 , THR D:125 , GLN D:213 , THR D:216 , GLU D:219 , TYR D:220 , HOH D:1136 , HOH D:1160 , HOH D:1300	binding site for Poly-Saccharide residues GAL B 1001 through BGC B 1004
7	AC7	SOFTWARE	SER A:64 , GLN A:213 , ASN B:120 , ASN B:123 , THR B:125 , ASN B:155 , TYR B:156 , TRP B:178 , ASP B:185 , ARG B:187 , HOH B:1103 , HOH B:1105 , HOH B:1115 , HOH B:1146 , HOH B:1160 , HOH B:1165 , HOH B:1173 , HOH B:1174 , HOH B:1176 , HOH B:1198 , HOH B:1213 , HOH B:1217 , HOH B:1328 , HOH B:1371 , ASN C:155 , TYR C:156 , TRP C:178 , GLY C:179 , ALA C:180 , ASP C:185 , ARG C:187 , HOH C:1129 , HOH C:1133 , HOH C:1141 , HOH C:1142 , HOH C:1147 , HOH C:1156 , HOH C:1185 , HOH C:1193 , HOH C:1198 , HOH C:1221 , HOH C:1249 , HOH C:1332 , HOH C:1435 , HOH C:1455 , HOH C:1486 , GLY D:63 , GLN D:213 , THR D:216 , GLU D:219 , TYR D:220 , HOH D:1136 , HOH D:1160	binding site for Poly-Saccharide residues GAL C 1001 through BGC C 1004
8	AC8	SOFTWARE	GLY B:63 , ASN B:120 , ASN B:123 , THR B:125 , GLN B:213 , THR B:216 , GLU B:219 , TYR B:220 , HOH B:1146 , HOH B:1306 , ASN C:155 , TYR C:156 , TRP C:178 , GLY C:179 , ALA C:180 , ASP C:185 , ARG C:187 , HOH C:1129 , HOH C:1133 , HOH C:1141 , HOH C:1142 , HOH C:1147 , HOH C:1156 , HOH C:1185 , HOH C:1193 , HOH C:1198 , HOH C:1221 , HOH C:1249 , HOH C:1332 , HOH C:1435 , HOH C:1455 , HOH C:1486 , ASN D:85 , ASN D:155 , TYR D:156 , HIS D:161 , ARG D:162 , ASP D:185 , ARG D:187 , HOH D:1106 , HOH D:1117 , HOH D:1138 , HOH D:1149 , HOH D:1345 , HOH D:1366 , HOH D:1368 , HOH D:1379 , HOH D:1440	binding site for Poly-Saccharide residues GAL D 1001 through NAG D 1002

(no "SS Bond" information available for 4YG6)

Asymmetric Unit

No.	Residues
1	Gly A:67	-	Pro A:68
2	Gly B:67	-	Pro B:68
3	Gly C:67	-	Pro C:68
4	Gly D:67	-	Pro D:68

(no "SAP(SNP)/Variant" information available for 4YG6)

(no "PROSITE Motif" information available for 4YG6)

(no "Exon" information available for 4YG6)

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:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeee........eeee.........eee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yg6 A  64 SLDGPYAPDSSNLPSNCWYLVNPSNDGVVFSVTDNSTFWMFTYLVLPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYIKTSSTQAYGSRNYLNTAHRLQAYRRDGDGNISNYWGADTQGDLRVGTYSNPVPNAVINLNADFYVIPDSQQETCTEYIRGGL 225
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeee........eeee.........eee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yg6 B  63 GSLDGPYAPDSSNLPSNCWYLVNPSNDGVVFSVTDNSTFWMFTYLVLPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYIKTSSTQAYGSRNYLNTAHRLQAYRRDGDGNISNYWGADTQGDLRVGTYSNPVPNAVINLNADFYVIPDSQQETCTEYIRGGL 225
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain C from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeee........eeee.........eee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yg6 C  63 GSLDGPYAPDSSNLPSNCWYLVNPSNDGVVFSVTDNSTFWMFTYLVLPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYIKTSSTQAYGSRNYLNTAHRLQAYRRDGDGNISNYWGADTQGDLRVGTYSNPVPNAVINLNADFYVIPDSQQETCTEYIRGGL 225
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain D from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeee........eeee.........eee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yg6 D  63 GSLDGPYAPDSSNLPSNCWYLVNPSNDGVVFSVTDNSTFWMFTYLVLPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYIKTSSTQAYGSRNYLNTAHRLQAYRRDGDGNISNYWGADTQGDLRVGTYSNPVPNAVINLNADFYVIPDSQQETCTEYIRGGL 225
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Legend:		→ Mismatch	(orange background)
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	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 4YG6)

(no "CATH Domain" information available for 4YG6)

(no "Pfam Domain" information available for 4YG6)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:67 - Pro A:68	[ RasMol ]
		Gly B:67 - Pro B:68	[ RasMol ]
		Gly C:67 - Pro C:68	[ RasMol ]
		Gly D:67 - Pro D:68	[ RasMol ]

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	4yg6
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	VP4_ROTBB \| P35746	:	4yg3

4ye2
4yfw
4yfz
4yg0
4yg3	4YG3 CONTAINS THE SAME PROTEIN IN THE ABSENCE OF LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (10, 10)

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