1E8U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE MULTIFUNCTIONAL PARAMYXOVIRUS HEMAGGLUTININ-NEURAMINIDASE

Authors :   S. Crennell, T. Takimoto, A. Portner, G. Taylor

Date :   01 Oct 00 (Deposition) - 03 Apr 01 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   S. Crennell, T. Takimoto, A. Portner, G. Taylor
Crystal Structure Of The Multifunctional Paramyxovirus Hemagglutinin-Neuraminidase
Nat. Struct. Biol. V. 7 1068 2000
PubMed-ID: 11062565 | Reference-DOI: 10.1038/81002
(for further references see the PDB file header)

Molecule 1 - HEMAGGLUTININ-NEURAMINIDASE
	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
	Synonym	:	HN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SLB	2	Ligand/Ion	5-N-ACETYL-BETA-D-NEURAMINIC ACID

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:236 , GLU A:258 , TYR A:299 , TYR A:317 , ARG A:363 , PHE A:364 , GLU A:401 , ARG A:416 , ARG A:498 , TYR A:526 , HOH A:2085 , HOH A:2232	BINDING SITE FOR RESIDUE SLB A1570
2	AC2	SOFTWARE	TYR A:340 , ASN A:341	BINDING SITE FOR RESIDUE NAG A1571
3	AC3	SOFTWARE	NAG A:1572	BINDING SITE FOR RESIDUE NAG A1573
4	AC4	SOFTWARE	LYS B:236 , GLU B:258 , TYR B:299 , TYR B:317 , GLU B:401 , ARG B:416 , VAL B:466 , ARG B:498 , TYR B:526 , HOH B:2064 , HOH B:2094 , HOH B:2138	BINDING SITE FOR RESIDUE SLB B1573
5	AC5	SOFTWARE	NAG B:1574	BINDING SITE FOR RESIDUE NAG B1575
6	AC6	SOFTWARE	ASP A:261 , SER A:264 , VAL A:266 , VAL A:296	BINDING SITE FOR RESIDUE CA A1002
7	AC7	SOFTWARE	ASP B:261 , SER B:264 , VAL B:266 , VAL B:296	BINDING SITE FOR RESIDUE CA B1003
8	AC8	SOFTWARE	ASN A:481 , THR A:483 , NAG A:1573	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 481 RESIDUES 1572 TO 1572
9	AC9	SOFTWARE	TYR B:479 , ASN B:481 , THR B:483 , NAG B:1575	BINDING SITE FOR MONO-SACCHARIDE NAG B1574 BOUND TO ASN B 481

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:238	-	B:251
10	B:344	-	B:461
11	B:455	-	B:465
12	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 1E8U)

(no "PROSITE Motif" information available for 1E8U)

(no "Exon" information available for 1E8U)

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:447
 aligned with HN_NDVK | Q9Q2W5 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_NDVK   124 GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDG 570
               SCOP domains d1e8ua_ A: Paramyxovirus hemagglutinin-neuraminidase head domain                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1e8uA00 A:124-569  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                        - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhh.eee..................eee..eeee....eeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.........eeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeee.hhhhhh..eeeeee.....eee..eeeeeeeeee...hhhhhhhh...............hhhhhhhhhhhhhhhhhhh..eeeeeeeeee.........eee............eeeeee..eeeeee........eeeeeeeee..eeee...eee............................eeeee........eeeeeee........eeeeee................eeeeeeeeeeee....eeeeeeeeeeehhhhh..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e8u A 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

Chain B from PDB  Type:PROTEIN  Length:450
 aligned with HN_NDVK | Q9Q2W5 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:450
                                   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       573
              HN_NDVK   124 GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDGVRE 573
               SCOP domains d1e8ub_ B: Paramyxovirus hemagglutinin-neuraminidase head domain                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1e8uB00 B:124-572  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.............hhh.eee..................eee..eeee....eeeeeeee..........eeeeeeeeeee.....eeeeeeeeeee.........eeeee..eeeeeeee...hhhhhhhh....eeeeeeee....eeeee.hhhhhh..eeeeee.....eee..eeeeeeeeee...hhhhhh.................hhhhhhhhhhhhhhhhhhh...eeeeeeeee.........eee............eeeeee..eeeeee........eeeeeeeee..eeee...eee............................eeeee........eeeeeee........eeeeee................eeeeeeeeeeee....eeeeeeeeeee.......eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e8u B 124 GAPIHDPDFIGGIGKELIVDNASDVTSFYPSAFQEHLNFIPAPTTGSGCTRIPSFDMSATHYCYTHNVILSGCRDHSHSHQYLALGVLRTTATGRIFFSTLRSISLDDTQNRKSCSVSATPLGCDMLCSKVTETEEEDYNSAVPTLMAHGRLGFDGQYHEKDLDVTTLFEDWVANYPGVGGGSFIDGRVWFSVYGGLKPNSPSDTVQEGKYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRFGGKRIQQAILSIKVSTSLGEDPVLTVPPNTVTLMGAEGRILTVGTSHFLYQRGSSYFSPALLYPMTVSNKTATLHSPYTFNAFTRPGSIPCQASARCPNSCVTGVYTDPYPLIFYRNHTLRGVFGTMLDSEQARLNPASAVFDSTSRSRITRVSSSSTKAAYTTSTCFKVVKTNKTYCLSIAEISNTLFGEFRIVPLLVEILKNDGVRE 573
                                   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       573

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	d1e8ua_	A:
1b	d1e8ub_	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	1e8uA00	A:124-569
1b	1e8uB00	B:124-572

(no "Pfam Domain" information available for 1E8U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HN_NDVK | Q9Q2W5)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SLB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:453 - Pro A:454	[ RasMol ]
		Ile B:453 - Pro B:454	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1e8u
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HN_NDVK \| Q9Q2W5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.18
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HN_NDVK \| Q9Q2W5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HN_NDVK \| Q9Q2W5	:	1e8t 1e8v

1e8t	STRUCTURE OF THE MULTIFUNCTIONAL PARAMYXOVIRUS HEMAGGLUTININ-NEURAMINIDASE
1e8v	STRUCTURE OF THE MULTIFUNCTIONAL PARAMYXOVIRUS HEMAGGLUTININ-NEURAMINIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (12, 12)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File