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Title :   STRUCTURES OF MONOMERIC HEMAGGLUTININ AND ITS COMPLEX WITH AN FAB FRAGMENT OF A NEUTRALIZING ANTIBODY THAT BINDS TO H1 SUBTYPE INFLUENZA VIRUSES: MOLECULAR BASIS OF INFECTIVITY OF 2009 PANDEMIC H1N1 INFLUENZA A VIRUSES

Authors :   K. H. Kim, K. J. Cho, J. H. Lee, Y. H. Park, T. G. Khan, J. Y. Lee, S. H. Kang, I

Date :   27 Mar 12 (Deposition) - 22 May 13 (Release) - 12 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Influenza Virus, Haemagglutinin, Conformation, Antibody, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. J. Cho, J. H. Lee, K. W. Hong, S. H. Kim, Y. Park, J. Y. Lee, S. Kang, S. Kim, J. H. Yang, E. K. Kim, J. H. Seok, S. Unzai, S. Y. Park, X. Saelens, C. J. Kim, J. Y. Lee, C. Kang, H. B. Oh, M. S. Chung, K. H. Kim
Insight Into Structural Diversity Of Influenza Virus Haemagglutinin
J. Gen. Virol. V. 94 1712 2013
PubMed-ID: 23636824 | Reference-DOI: 10.1099/VIR.0.051136-0

Molecule 1 - HEMAGGLUTININ
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HI5
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	HA1 SUBUNIT, UNP RESIDUES 18-344
	Gene	:	HA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	644289
	Strain	:	A/KOREA/01/2009 H1N1

Molecule 2 - HEMAGGLUTININ
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HI5
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	HA2 SUBUNIT, UNP RESIDUES 345-520
	Gene	:	HA
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	644289
	Strain	:	A/KOREA/01/2009 H1N1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:64 , GLU A:66 , ASP A:86 , ASN A:87 , CYS A:90 , ARG A:221	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 87 RESIDUES 401 TO 402
2	AC2	SOFTWARE	ARG A:45 , ASN A:276	BINDING SITE FOR MONO-SACCHARIDE NAG A 403 BOUND TO ASN A 276
3	AC3	SOFTWARE	ASN A:287	BINDING SITE FOR MONO-SACCHARIDE NAG A 404 BOUND TO ASN A 287
4	AC4	SOFTWARE	ASN C:64 , ASP C:86 , ASN C:87 , CYS C:90 , ARG C:221 , HOH C:514	BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 87 RESIDUES 401 TO 402
5	AC5	SOFTWARE	ARG C:45 , GLY C:46 , ASN C:276	BINDING SITE FOR MONO-SACCHARIDE NAG C 403 BOUND TO ASN C 276
6	AC6	SOFTWARE	ASN C:287	BINDING SITE FOR MONO-SACCHARIDE NAG C 404 BOUND TO ASN C 287

Asymmetric Unit

No.	Residues
1	A:4	-	B:137
2	A:42	-	A:275
3	A:55	-	A:67
4	A:90	-	A:136
5	A:279	-	A:303
6	B:144	-	B:148
7	C:42	-	C:275
8	C:55	-	C:67
9	C:90	-	C:136
10	C:279	-	C:303
11	D:144	-	D:148

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

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

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

(no "Exon" information available for 4EDA)

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
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4edaa_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee......................ee.........eeee.....eee...hhhhhhhhhhhhh..........eee...............hhhhhhhhh..eeeeeeee..........ee.....eeeeee..eee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.ee....ee.....ee......ee...ee......ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eda A   1 DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNV 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:148
                                                                                                                                                                                    
               SCOP domains d4edab_ B: Influenza hemagglutinin (stalk)                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..............hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee.......hhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eda B  10 IEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEID 174
                                    19        29        39        49        59     || 86        96       106       116       126       136       146       156       166        
                                                                                  65|                                                                                           
                                                                                   83

Chain C from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4edac_ C: Hemagglutinin                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee......eeee.....ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhh..eeeeeeee..hhhhhh..ee.....eeeee....ee....eee.ee.......eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeeee.ee....ee.....ee......ee...ee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eda C  11 NSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNV 321
                                    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 D from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..............hhhhh.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4eda D  10 IEGGWTGMVDAADLKSTQNAIDEITNKVNSVIEKMNTKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLNAKEIGNGCCDNTCMESVKNGYPKYSEEAKLNRE 171
                                    19|       44        54      ||85        95       105       115       125||     137|      153 ||    166     
                                    19|                        61|                                        126|     137|        155|            
                                     35                         83                                         129      144         159

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4EDA)

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (6, 6)

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

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