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Asym./Biol. Unit (Jmol Viewer)

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Title :   NEWCASTLE DISEASE VIRUS HEMAGGLUTININ-NEURAMINIDASE: EVIDENCE FOR A SECOND SIALIC ACID BINDING SITE AND IMPLICATIONS FOR FUSION

Authors :   V. Zaitsev, M. Von Itzstein, D. Groves, M. Kiefel, T. Takimoto, A. Portner, G. Taylor

Date :   28 Nov 03 (Deposition) - 02 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Hydrolase, Sialidase, Neuraminidase, Hemagglutinin-Neuraminidase, Hemagglutinin, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Zaitsev, M. Von Itzstein, D. Groves, M. Kiefel, T. Takimoto, A. Portner, G. Taylor
Second Sialic Acid Binding Site In Newcastle Disease Virus Hemagglutinin-Neuraminidase: Implications For Fusion
J. Virol. V. 78 3733 2004
PubMed-ID: 15016893 | Reference-DOI: 10.1128/JVI.78.7.3733-3741.2004
(for further references see the PDB file header)

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE GLYCOPROTEIN
	Chains	:	A, B
	EC Number	:	3.2.1.18
	Fragment	:	HEAD DOMAIN, RESIDUES 124-577
	Organism Scientific	:	NEWCASTLE DISEASE VIRUS
	Organism Taxid	:	11176
	Strain	:	KANSAS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 9)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	DAN	2	Ligand/Ion	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SIA	2	Ligand/Ion	O-SIALIC ACID
5	WIA	1	Ligand/Ion	METHYL(6S)-1-THIO-L-MANNO-HEXODIALDO-6,2-PYRANOSIDE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:155 , PHE A:156 , THR A:515 , ARG A:516 , VAL A:517 , SER A:518 , SER A:519 , WIA A:1578 , HOH A:2039 , HOH A:2437 , HOH A:2439 , HOH A:2440 , HOH A:2441 , THR B:168 , GLY B:169 , ARG B:353	BINDING SITE FOR RESIDUE SIA A1571
2	AC2	SOFTWARE	GLY A:169 , ALA B:155 , PHE B:156 , THR B:515 , ARG B:516 , VAL B:517 , SER B:518 , SER B:519 , HOH B:2420 , HOH B:2463 , HOH B:2464 , HOH B:2465	BINDING SITE FOR RESIDUE SIA B1572
3	AC3	SOFTWARE	TYR A:479 , ASN A:481 , THR A:483 , HOH A:2362 , HOH A:2447 , HOH A:2448 , HOH A:2449 , HOH A:2450 , HOH A:2451 , THR B:232 , GLN B:233	BINDING SITE FOR RESIDUE NDG A1573
4	AC4	SOFTWARE	TYR B:479 , ASN B:481 , THR B:483	BINDING SITE FOR RESIDUE NDG B1571
5	AC5	SOFTWARE	ASP A:261 , SER A:264 , VAL A:266 , VAL A:296	BINDING SITE FOR RESIDUE CA A1574
6	AC6	SOFTWARE	ASP B:261 , SER B:264 , VAL B:266 , VAL B:296 , HOH B:2153	BINDING SITE FOR RESIDUE CA B1573
7	AC7	SOFTWARE	ARG A:174 , GLU A:258 , TYR A:299 , TYR A:317 , ARG A:363 , GLU A:401 , ARG A:416 , ARG A:498 , TYR A:526 , HOH A:2203 , HOH A:2262 , HOH A:2307 , HOH A:2443 , HOH A:2444 , HOH A:2445 , HOH A:2446	BINDING SITE FOR RESIDUE DAN A1572
8	AC8	SOFTWARE	SIA A:1571 , HOH A:2452 , HOH A:2453 , HOH A:2454 , ARG B:353	BINDING SITE FOR RESIDUE WIA A1578
9	AC9	SOFTWARE	ARG B:174 , GLU B:258 , TYR B:299 , TYR B:317 , GLU B:401 , ARG B:416 , ARG B:498 , TYR B:526 , HOH B:2222 , HOH B:2459 , HOH B:2460 , HOH B:2461 , HOH B:2462	BINDING SITE FOR RESIDUE DAN B1570

Asymmetric/Biological Unit

No.	Residues
1	A:172	-	A:196
2	A:186	-	A:247
3	A:238	-	A:251
4	A:344	-	A:461
5	A:455	-	A:465
6	A:531	-	A:542
7	B:172	-	B:196
8	B:186	-	B:247
9	B:344	-	B:461
10	B:455	-	B:465
11	B:531	-	B:542

Asymmetric/Biological Unit

No.	Residues
1	Ile A:453	-	Pro A:454
2	Ile B:453	-	Pro B:454

(no "SAP(SNP)/Variant" information available for 1USR)

(no "PROSITE Motif" information available for 1USR)

(no "Exon" information available for 1USR)

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:448
 aligned with HN_NDVB | P32884 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:448
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563        
              HN_NDVB   124 GAPIHDPDFIGGIGKELIVDDASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPTSAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDGV 571
               SCOP domains d1usra_ A: Paramyxovirus hemagglutinin-neuraminidase head domain                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1usrA00 A:124-571  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......ee....hhh.eee..................eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh....eeeeeee.....eeeee.hhhhhh..eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhhh.hhhhh..eeeeeeeeee.........eee............eeeeee..eeeeee........eeeeeeeee..eeee...eee............................eeeeee.....eeeeeeeee........eeeeee........ee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usr A 124 GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDGV 571
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563

Chain B from PDB  Type:PROTEIN  Length:447
 aligned with HN_NDVB | P32884 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:447
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       
              HN_NDVB   124 GAPIHDPDFIGGIGKELIVDDASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPTSAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDG 570
               SCOP domains d1usrb_ B: Paramyxovirus hemagglutinin-neuraminidase head domain                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1usrB00 B:124-570  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......ee....hhh.eee..................eeeeeeeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeee.hhhhhh..eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhh..hhhhh..eeeeeeeeee.........eee............eeeeee..eeeeee........eeeeeeeee..eeee...eee............................eeeeee.....eeeeeeeee........eeeeee........ee.......eeeeeeeeeee....eeeeeeeeeee......eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usr B 124 GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDG 570
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: Sialidases (neuraminidases) (178)

Protein domain: Paramyxovirus hemagglutinin-neuraminidase head domain (5)

Newcastle disease virus [TaxId: 11176] (5)

1a	d1usra_	A:
1b	d1usrb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 6 Propellor (215)

Topology: Neuraminidase (215)

Homologous Superfamily: [code=2.120.10.10, no name defined] (150)

Newcastle disease virus. Organism_taxid: 11176. Strain: kansas (5)

1a	1usrB00	B:124-570
1b	1usrA00	A:124-571

(no "Pfam Domain" information available for 1USR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HN_NDVB | P32884)

molecular function
	GO:0052794	exo-alpha-(2->3)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052795	exo-alpha-(2->6)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052796	exo-alpha-(2->8)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0004308	exo-alpha-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
	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.
biological process
	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.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	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:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	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.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric/Biological Unit
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		Ile A:453 - Pro A:454	[ RasMol ]
		Ile B:453 - Pro B:454	[ RasMol ]

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	HN_NDVB \| P32884	:	1usx

1usx	CRYSTAL STRUCTURE OF THE NEWCASTLE DISEASE VIRUS HEMAGGLUTININ-NEURAMINIDASE COMPLEXED WITH THIOSIALOSIDE

Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

SS Bonds (11, 11)

Cis Peptide Bonds (2, 2)

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