1TI8 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   H7 HAEMAGGLUTININ

Authors :   R. J. Russell, S. J. Gamblin, L. F. Haire, D. J. Stevens, B. Xaio, Y. Ha, J.

Date :   02 Jun 04 (Deposition) - 21 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   H7, Haemagglutinin, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Russell, S. J. Gamblin, L. F. Haire, D. J. Stevens, B. Xiao, Y. Ha, J. J. Skehel
H1 And H7 Influenza Haemagglutinin Structures Extend A Structural Classification Of Haemagglutinin Subtypes.
Virology V. 325 287 2004
PubMed-ID: 15246268 | Reference-DOI: 10.1016/J.VIROL.2004.04.040

Molecule 1 - HEMAGGLUTININ
	Chains	:	A
	Fragment	:	RESIDUES 21-334
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	11320
	Other Details	:	BROMELAIN CLEAVED
	Strain	:	A-TURKEY-ITALY-02

Molecule 2 - HEMAGGLUTININ
	Chains	:	B
	Fragment	:	RESIDUES 340-511
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	11320
	Other Details	:	BROMELAIN CLEAVED
	Strain	:	A-TURKEY-ITALY-02

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MAN	5	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	MAN	15	Ligand/Ion	ALPHA-D-MANNOSE
2	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	3	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	NDG A:340 , GLU B:72 , LYS B:75 , ASN B:82	BINDING SITE FOR RESIDUE NAG B 339
2	AC2	SOFTWARE	ASN A:298 , SER A:299 , ARG A:300 , MAN A:341 , NAG B:339	BINDING SITE FOR RESIDUE NDG A 340
3	AC3	SOFTWARE	NDG A:340 , MAN A:342 , MAN A:343 , MAN A:345	BINDING SITE FOR RESIDUE MAN A 341
4	AC4	SOFTWARE	MAN A:341 , MAN A:343	BINDING SITE FOR RESIDUE MAN A 342
5	AC5	SOFTWARE	ARG A:91 , MAN A:341 , MAN A:342 , MAN A:344	BINDING SITE FOR RESIDUE MAN A 343
6	AC6	SOFTWARE	MAN A:343	BINDING SITE FOR RESIDUE MAN A 344
7	AC7	SOFTWARE	MAN A:341 , HOH A:416	BINDING SITE FOR RESIDUE MAN A 345
8	AC8	SOFTWARE	ASN A:38	BINDING SITE FOR RESIDUE NAG A 349

Asymmetric Unit

No.	Residues
1	A:14	-	B:137
2	A:52	-	A:277
3	A:64	-	A:76
4	A:97	-	A:139
5	A:281	-	A:305
6	B:144	-	B:148

(no "Cis Peptide Bond" information available for 1TI8)

(no "SAP(SNP)/Variant" information available for 1TI8)

(no "PROSITE Motif" information available for 1TI8)

(no "Exon" information available for 1TI8)

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:314
 aligned with Q6GYW3_9INFA | Q6GYW3 from UniProtKB/TrEMBL  Length:560

    Alignment length:314
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330    
        Q6GYW3_9INFA     21 ICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNVPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKDPALIIWGIHHSGSTTEQTKLYGSGNKLITVGSSNYQQSFVPSPGARPQVNGQSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSSVQVDANCEGDCYHSGGTIISNLPFQNINSRAVGKCPRYVKQESLMLATGMKNVPE  334
               SCOP domains d1ti8a1 A:13-325 Hemagglutinin                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ti8A01 A:13-56,A:273-325                   1ti8A02 A:57-272  [code=3.90.209.20, no name defined]                                                                                                                                                                   1ti8A01 A:13-56,A:273-325                              CATH domains
               Pfam domains Hemagglutinin-1ti8A01 A:13-325                                                                                                                                                                                                                                                                                             Pfam domains
         Sec.struct. author .eeee......eeee....eeeee..ee..ee......ee.....eee......hhhhhhhhhhhhhh.....eeee..............hhhhhhhhhh....eeeee.......ee....hhhhh.........ee..ee..........eeeee......eeeeeeeee..hhhhhhhhh.......eeee..ee...........hhhhh..eeeeeeeee....eeeee....eeee.eeeee....eeee....ee......eee..ee......ee......ee...ee.......ee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ti8 A   13 ICLGHHAVSNGTKVNTLTERGVEVVNATETVERTNVPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGSDVCYPGKFVNEEALRQILRESGGIDKETMGFTYSGIRTNGATSACRRSGSSFYAEMKWLLSNTDNAAFPQMTKSYKNTRKDPALIIWGIHHSGSTTEQTKLYGSGNKLITVGSSNYQQSFVPSPGARPQVNGQSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGIQSSVQVDANCEGDCYHSGGTIISNLPFQNINSRAVGKCPRYVKQESLMLATGMKNVPE  325
                                    22        32        42        52        62        72        82        92       102       112       122       132       142|      153     ||161       171       181       191       201       211       221       231       241       251       261|      272    |  281       291       301       311       321    
                                                                                                                                                           142|           158A|                                                                                                    261|          276A                                                 
                                                                                                                                                            144            158B                                                                                                     263

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q701T7_9INFA | Q701T7 from UniProtKB/TrEMBL  Length:560

    Alignment length:166
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499      
        Q701T7_9INFA    340 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFTEVEKQIGNVINWTRDSMTEVWSYNAELLVAMENQHTIDLADSEMNKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSRYREEA  505
               SCOP domains d1ti8b1 B:1-166 Influenza hemagglutinin (stalk)                                                                                                                        SCOP domains
               CATH domains 1ti8B00 B:1-166  [code=3.90.20.10, no name defined]                                                                                                                    CATH domains
               Pfam domains Hemagglutinin-1ti8B01 B:1-166                                                                                                                                          Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee....hhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ti8 B    1 GLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLNRLIEKTNQQFELIDNEFTEVEKQIGNVINWTRDSMTEVWSYNAELLVAMENQHTIDLTDSEMNKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSRYREEA  166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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(hide GO term definitions)

Chain A (Q6GYW3_9INFA | Q6GYW3)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	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: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.

Chain B (Q701T7_9INFA | Q701T7)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0019065	receptor-mediated endocytosis of virus by host cell	Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
	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: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 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
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ti8)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	1ti8
		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
	Q6GYW3_9INFA \| Q6GYW3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	Q701T7_9INFA \| Q701T7
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		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
	Q6GYW3_9INFA \| Q6GYW3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q701T7_9INFA \| Q701T7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q6GYW3_9INFA \| Q6GYW3	:	4bsg 4bsh 5jw3

(no "Related Entries Specified in the PDB File" available for 1TI8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (17, 34)

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