4BGX - JenaLib

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Title :   H5 (VN1194) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN

Authors :   X. Xiong, P. Coombs, S. R Martin, J. Liu, H. Xiao, J. W. Mccauley, K. Loch P. A. Walker, P. J. Collins, Y. Kawaoka, J. J. Skehel, S. J. Gamblin

Date :   29 Mar 13 (Deposition) - 24 Apr 13 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.48

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

Keywords :   Viral Protein, N-Glycosylation, Virus Receptor, Bird Flu (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xiong, P. Coombs, S. R Martin, J. Liu, H. Xiao, J. W. Mccauley, K. Locher, P. A. Walker, P. J. Collins, Y. Kawaoka, J. J. Skehel, S. J. Gamblin
Receptor Binding By A Ferret-Transmissible H5 Avian Influenza Virus.
Nature V. 497 392 2013
PubMed-ID: 23615615 | Reference-DOI: 10.1038/NATURE12144

Molecule 1 - HEMAGGLUTININ
	Chains	:	A
	Fragment	:	HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340
	Organism Scientific	:	INFLUENZA VIRUS
	Organism Taxid	:	644788
	Other Details	:	THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
	Strain	:	A/VIETNAM/1194/2004(H5N1)
	Synonym	:	HAEMAGGLUTININ HA1
	Variant	:	A/VN/1194/04/NIBRG14 VACCINE STRAIN

Molecule 2 - HEMAGGLUTININ
	Chains	:	B
	Fragment	:	HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
	Organism Scientific	:	INFLUENZA VIRUS
	Organism Taxid	:	644788
	Other Details	:	THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC)
	Strain	:	A/VIETNAM/1194/2004(H5N1)
	Synonym	:	HAEMAGGLUTININ HA2
	Variant	:	A/VN/1194/04/NIBRG14 VACCINE STRAIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	EPE	3	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
3	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SIA	3	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:14 , HIS B:25 , TYR B:34 , ASN B:135 , CYS B:137	BINDING SITE FOR RESIDUE EPE B1163
2	AC2	SOFTWARE	ASN A:23	BINDING SITE FOR MONO-SACCHARIDE NAG A1023 BOUND TO ASN A 23
3	AC3	SOFTWARE	ASN A:165 , ASN A:236 , HOH A:2121	BINDING SITE FOR MONO-SACCHARIDE NAG A1165 BOUND TO ASN A 165
4	AC4	SOFTWARE	GLU B:147 , GLU B:150 , ASN B:154	BINDING SITE FOR MONO-SACCHARIDE NAG B1154 BOUND TO ASN B 154
5	AC5	SOFTWARE	TYR A:91 , LEU A:129 , VAL A:131 , SER A:132 , SER A:133 , HIS A:179 , ASN A:182 , GLU A:186 , LEU A:190 , GLY A:221 , GLN A:222 , HOH A:2065 , HOH A:2122	BINDING SITE FOR POLY-SACCHARIDE RESIDUES SIA A1322 THROUGH GAL A1323

Asymmetric Unit

No.	Residues
1	A:4	-	B:137
2	A:42	-	A:274
3	A:55	-	A:67
4	A:90	-	A:135
5	A:278	-	A:302
6	B:144	-	B:148

(no "Cis Peptide Bond" information available for 4BGX)

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

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

(no "Exon" information available for 4BGX)

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:321
 aligned with Q6DQ34_9INFA | Q6DQ34 from UniProtKB/TrEMBL  Length:565

    Alignment length:321
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336 
         Q6DQ34_9INFA    17 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP 337
               SCOP domains d4bgxa_ A: automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...........eee.hhhhhhhhhh.eeeeeeee................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeeee....eee....eeeeee.eee..ee......ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgx A   1 DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP 321
                                    10        20        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

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q6DQ34_9INFA | Q6DQ34 from UniProtKB/TrEMBL  Length:565

    Alignment length:162
                                   356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506  
         Q6DQ34_9INFA   347 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQY 508
               SCOP domains d4bgxb_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bgx B   1 GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQY 162
                                    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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q6DQ34_9INFA | Q6DQ34)

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
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bgx)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4bgx
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UniProtKB/Swiss-Prot
	Q6DQ34_9INFA \| Q6DQ34	:	2ibx
UniProtKB/TrEMBL
	Q6DQ34_9INFA \| Q6DQ34	:	3znk 3znl 3znm 3zp0 3zp1 3zp2 3zp3 3zp6 3zpa 3zpb 4bgw 4bgy 4cqp 4cqq 4cqr 4cqs 4cqu 4cqz 4cr0 5ajm 5jw4

4bgw	STRUCTURE OF H5 (VN1194) INFLUENZA HAEMAGGLUTININ
4bgy	H5 (VN1194) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
4bgz	CRYSTAL STRUCTURE OF H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ
4bh0	H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bh1	H5 (TYTY) INFLUENZA VIRUS HAEMAGGLUTININ IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
4bh2	CRYSTAL STRUCTURE OF THE HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS
4bh3	HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS IN COMPLEX WITH HUMAN RECEPTOR ANALOGUE 6'-SLN
4bh4	HAEMAGGLUTININ FROM A TRANSMISSIBLE MUTANT H5 INFLUENZA VIRUS IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (5, 5)

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

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Related Entries

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