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Title :   CRYSTAL STRUCTURE OF INFLUENZA B VIRUS HEMAGGLUTININ IN COMPLEX WITH LSTC RECEPTOR ANALOG

Authors :   Q. Wang, X. Tian, X. Chen, J. Ma

Date :   01 Oct 07 (Deposition) - 05 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Influenza, Receptor Specificity, Human Receptor Analog, Envelope Protein, Fusion Protein, Hemagglutinin, Membrane, Transmembrane, Virion, Glycoprotein, Lipoprotein, Palmitate, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Wang, X. Tian, X. Chen, J. Ma
Structural Basis For Receptor Specificity Of Influenza B Virus Hemagglutinin.
Proc. Natl. Acad. Sci. Usa V. 104 16874 2007
PubMed-ID: 17942670 | Reference-DOI: 10.1073/PNAS.0708363104

Molecule 1 - INFLUENZA B HEMAGGLUTININ (HA)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	INFLUENZA B VIRUS
	Expression System Taxid	:	11520
	Gene	:	HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73)
	Organism Taxid	:	11531
	Strain	:	B/HONGKONG/8/73

Molecule 2 - INFLUENZA B HEMAGGLUTININ (HA)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	INFLUENZA B VIRUS
	Expression System Taxid	:	11520
	Gene	:	HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73)
	Organism Taxid	:	11531
	Strain	:	B/HONGKONG/8/73

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (3, 42)

No.	Name	Count	Type	Full Name
1	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	36	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SIA	3	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:12 , PRO A:13 , ASN A:25 , TYR A:334 , NAG A:344	BINDING SITE FOR RESIDUE NAG A 343
02	AC2	SOFTWARE	NAG A:343	BINDING SITE FOR RESIDUE NAG A 344
03	AC3	SOFTWARE	ASN A:123 , ALA A:127 , VAL A:137 , GLN A:268 , NAG A:346	BINDING SITE FOR RESIDUE NAG A 345
04	AC4	SOFTWARE	NAG A:345	BINDING SITE FOR RESIDUE NAG A 346
05	AC5	SOFTWARE	ASN A:145 , GLY A:149 , ASN A:150	BINDING SITE FOR RESIDUE NAG A 347
06	AC6	SOFTWARE	GLU A:289 , ASN A:301 , NAG A:350	BINDING SITE FOR RESIDUE NAG A 349
07	AC7	SOFTWARE	NAG A:349	BINDING SITE FOR RESIDUE NAG A 350
08	AC9	SOFTWARE	ASN A:163	BINDING SITE FOR RESIDUE NAG A 348
09	AD1	SOFTWARE	ASN A:330 , NAG A:352 , TRP B:21 , ILE B:45 , THR B:49	BINDING SITE FOR RESIDUE NAG A 351
10	BC1	SOFTWARE	NAG A:351	BINDING SITE FOR RESIDUE NAG A 352
11	BC2	SOFTWARE	ASN B:145 , THR B:147	BINDING SITE FOR RESIDUE NAG B 170
12	BC3	SOFTWARE	THR A:139 , SER A:140 , GLY A:141 , VAL A:160 , ASP A:193 , GLN A:197 , LEU A:201 , PRO A:238 , SER A:240 , GAL A:802 , NAG A:803	BINDING SITE FOR RESIDUE SIA A 801
13	BC4	SOFTWARE	SIA A:801 , GAL A:802	BINDING SITE FOR RESIDUE NAG A 803
14	BC5	SOFTWARE	PRO A:238 , SIA A:801 , NAG A:803	BINDING SITE FOR RESIDUE GAL A 802

Asymmetric Unit

No.	Residues
1	A:4	-	B:137
2	A:54	-	A:57
3	A:60	-	A:72
4	A:94	-	A:143
5	A:178	-	A:272
6	A:292	-	A:318
7	B:144	-	B:148

(no "Cis Peptide Bond" information available for 2RFU)

(no "SAP(SNP)/Variant" information available for 2RFU)

(no "PROSITE Motif" information available for 2RFU)

(no "Exon" information available for 2RFU)

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:342
 aligned with HEMA_INBHK | P03462 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:342
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348  
           HEMA_INBHK     9 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGNIPSAKASILHEVKPGTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRRKVIEGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 350
               SCOP domains d2rfua_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eee..............hhhhhhhhhhhhhhhheeeee................eeee.................eeeeee........eee..........eeeeeeeeee.hhhhhhhhh......eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeeeee.eee........ee.eee...eee.....ee......eee...ee.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rfu A   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 342
                                    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       330       340

Chain A from PDB  Type:PROTEIN  Length:342
 aligned with Q84097_9INFB | Q84097 from UniProtKB/TrEMBL  Length:582

    Alignment length:342
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355  
         Q84097_9INFB    16 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 357
               SCOP domains d2rfua_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeee.....eeee..eee...........ee....ee..........hhhhhhhh............eee..............hhhhhhhhhhhhhhhheeeee................eeee.................eeeeee........eee..........eeeeeeeeee.hhhhhhhhh......eeeeee..eeeeee...................eeeeeeeee.....eeeee...eeee...eeeeee.eee........ee.eee...eee.....ee......eee...ee.....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rfu A   1 DRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTQTRGKLCPNCLNCTDLDVALGRPKCMGTIPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSARNVTNAETAPGGPYIVGTSGSCPNVTNGNGFFATMAWAVPKNKTATNPLTVEVPYICTKGEDQITVWGFHSDDETQMVKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQAEDEGLPQSGRIVVDYMVQKPGKTGTIAYQRGVLLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLK 342
                                    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       330       340

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with HEMA_INBHK | P03462 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:169
                                   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512         
           HEMA_INBHK   353 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLFSLSELEVKNLHRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 521
               SCOP domains d2rfub_ B: Influenza hemagglutinin (stalk)                                                                                                                                SCOP domains
               CATH domains 2rfuB00 B:1-169  [code=3.90.20.10, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) Hemagglutinin-2rfuB01 B:1-169                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Hemagglutinin-2rfuB02 B:1-169                                                                                                                                             Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfu B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with Q84097_9INFB | Q84097 from UniProtKB/TrEMBL  Length:582

    Alignment length:169
                                   369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519         
         Q84097_9INFB   360 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 528
               SCOP domains d2rfub_ B: Influenza hemagglutinin (stalk)                                                                                                                                SCOP domains
               CATH domains 2rfuB00 B:1-169  [code=3.90.20.10, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) Hemagglutinin-2rfuB01 B:1-169                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Hemagglutinin-2rfuB02 B:1-169                                                                                                                                             Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....hhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rfu B   1 GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVDIGNGCFETKHKCNQTCLDRIAAGTFNAGEFSLPTFDS 169
                                    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

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Hemagglutinin Ectodomain; Chain B (70)

Homologous Superfamily: [code=3.90.20.10, no name defined] (69)

Influenza b virus (strain b/hong kong/8/73). Organism_taxid: 11531. Strain: b/hongkong/8/73. (2)

2rfuB00

B:1-169

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Hemagglutinin] (58)

Family: Hemagglutinin (58)

Influenza B virus (2)

1a	Hemagglutinin-2rfuB01	B:1-169
1b	Hemagglutinin-2rfuB02	B:1-169

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEMA_INBHK | P03462)

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: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: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 A,B (Q84097_9INFB | Q84097)

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: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: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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	2rfu
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	Q84097_9INFB \| Q84097
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UniProtKB/Swiss-Prot
	HEMA_INBHK \| P03462	:	2rft 3bt6
	Q84097_9INFB \| Q84097	:	2rft 3bt6

2rft	2RFT IS THE SAME PROTEIN IN COMPLEX WITH LSTA RECEPTOR ANALOG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (7, 7)

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 (1, 1)

Pfam Domains (1, 2)

Gene Ontology (14, 28)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File