4RM0 - JenaLib

Title :   CRYSTAL STRUCTURE OF NOROVIRUS OIF P DOMAIN IN COMPLEX WITH LEWIS A TRISACCHARIDE

Authors :   W. Liu, Y. Chen, M. Tan, M. Xia, X. Li, X. Jiang, Z. Rao

Date :   18 Oct 14 (Deposition) - 24 Jun 15 (Release) - 04 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Mixed Alpha/Beta, Receptor Binding, Hbga, Virus Caspid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Liu, Y. Chen, X. Jiang, M. Xia, Y. Yang, M. Tan, X. Li, Z. Rao
A Unique Human Norovirus Lineage With A Distinct Hbga Binding Interface.
Plos Pathog. V. 11 05025 2015
PubMed-ID: 26147716 | Reference-DOI: 10.1371/JOURNAL.PPAT.1005025

Compounds

Molecule 1 - CAPSID PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PROTRUSION DOMAIN (UNP RESIDUES 220-527)
	Mutation	:	YES
	Organism Scientific	:	NOROVIRUS
	Organism Taxid	:	286545
	Strain	:	OIF

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:295 , TRP A:296 , SER A:354 , THR A:356 , SER A:357 , GLU A:358 , ASN A:392 , ASN A:394 , THR A:395 , ASP A:478 , HOH A:750 , HOH A:841 , ASP B:254 , ARG B:398	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 601 TO 603
2	AC2	SOFTWARE	GLN A:466 , HOH A:946 , TRP B:296 , SER B:354 , THR B:356 , SER B:357 , ASN B:392 , ASN B:394 , THR B:395 , HOH B:767 , HOH B:877	BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 601 TO 603

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeeee..........................hhhhh..eeeee..........eeeeee........................eeeeeee.............eeeeee......hhhh.eeeeeeee.......eeeeeeeeee...................................eeeeeeeeee.eee....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rm0 A 221 KTKPFTLPILTIGELTNSRFPAPIDQLYTSPNADVVVQPQNGRCSLDGELQGTTQLLTTAICSYRGMTSNPTRDYWDGHLLHLVHPNGATYDPTEDVPAPFGTQDFRGILYGVLTQNPRASGDEAANSQGVYISSTSEKFTPKLGTIGLHQVQGNIASNQQSKFTPVGIAVNGNTPFRQWELPNYSGALTLNTNLAPAVGPNFPGEQILFFRSNVPSVQGGQPIEIDCLIPQEWVSHFYQESAPSQSDVALVRYVNPDTGRTIFEAKLHRQGFITIAATGSNPVVVPPNGYFRFDSWVNQFYALAPM 527
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520

Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh..........eeeee..........................hhhhh..eeeee..........eeeeee........................eeeeeee.............eeeeee......hhhh.eeeeeeee.......eeeeeeeeee...................................eeeeeeeeee.eee....eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rm0 B 222 TKPFTLPILTIGELTNSRFPAPIDQLYTSPNADVVVQPQNGRCSLDGELQGTTQLLTTAICSYRGMTSNPTRDYWDGHLLHLVHPNGATYDPTEDVPAPFGTQDFRGILYGVLTQNPRASGDEAANSQGVYISSTSEKFTPKLGTIGLHQVQGNIASNQQSKFTPVGIAVNGNTPFRQWELPNYSGALTLNTNLAPAVGPNFPGEQILFFRSNVPSVQGGQPIEIDCLIPQEWVSHFYQESAPSQSDVALVRYVNPDTGRTIFEAKLHRQGFITIAATGSNPVVVPPNGYFRFDSWVNQFYALAPM 527
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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Description