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Title :   CRYSTAL STRUCTURE OF FAB 3.1 IN COMPLEX WITH THE 1918 INFLUENZA VIRUS HEMAGGLUTININ

Authors :   C. Dreyfus

Date :   26 Mar 14 (Deposition) - 21 May 14 (Release) - 04 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.91

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

Keywords :   Hemagglutinin Glycoproteins, Immunoglobulin Fab Fragment, Membrane Fusion, Neutralizing Antibodies, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Wyrzucki, C. Dreyfus, I. Kohler, M. Steck, I. A. Wilson, L. Hangartner
Alternative Recognition Of The Conserved Stem Epitope In Influenza A Virus Hemagglutinin By A Vh3-30-Encoded Heterosubtypic Antibody.
J. Virol. V. 88 7083 2014
PubMed-ID: 24719426 | Reference-DOI: 10.1128/JVI.00178-14

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	PLASMID
	Fragment	:	RECEPTOR BINDING SUBUNIT (UNP RESIDUES 18-344)
	Gene	:	HA, HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	59375
	Strain	:	A/SOUTH CAROLINA/1/1918(H1N1)

Molecule 2 - HEMAGGLUTININ HA2 CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	PLASMID
	Fragment	:	MEMBRANE FUSION SUBUNIT (UNP RESIDUES 345-520)
	Gene	:	HA, HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	59375
	Strain	:	A/SOUTH CAROLINA/1/1918(H1N1)

Molecule 3 - ANTIBODY 3.1 HEAVY CHAIN
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - ANTIBODY 3.1 LIGHT CHAIN
	Chains	:	J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	I	J
Biological Unit 1 (3x)	:	A	B	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MLI	2	Ligand/Ion	MALONATE ION
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	MLI	6	Ligand/Ion	MALONATE ION
2	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:38 , ARG I:106 , ILE I:108 , TRP J:32 , ALA J:50 , ALA J:91	BINDING SITE FOR RESIDUE MLI I 301
2	AC2	SOFTWARE	ARG I:106 , ALA J:91 , PHE J:94	BINDING SITE FOR RESIDUE MLI J 301
3	AC3	SOFTWARE	ASN A:33	BINDING SITE FOR MONO-SACCHARIDE NAG A 401 BOUND TO ASN A 33
4	AC4	SOFTWARE	ASN A:74 , GLU A:96 , ASN A:97 , CYS A:100 , ARG A:231	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 97 RESIDUES 402 TO 403
5	AC5	SOFTWARE	ASN A:286 , ASN A:297	BINDING SITE FOR MONO-SACCHARIDE NAG A 404 BOUND TO ASN A 297

Asymmetric Unit

No.	Residues
1	A:14	-	B:137
2	A:52	-	A:285
3	A:65	-	A:77
4	A:100	-	A:146
5	A:289	-	A:313
6	B:144	-	B:148
7	I:22	-	I:96
8	J:23	-	J:88
9	J:134	-	J:194

Asymmetric Unit

No.	Residues
1	Ala A:7	-	Asp A:8
2	Lys A:140	-	Gly A:141
3	Gly A:141	-	Val A:142
4	Gly A:195	-	Thr A:196
5	Ser A:273	-	Gly A:274
6	Asn I:57	-	Lys I:58
7	Gly I:102	-	Tyr I:103
8	Phe I:151	-	Pro I:152
9	Ser J:7	-	Pro J:8
10	Phe J:94	-	Pro J:95
11	Tyr J:140	-	Pro J:141
12	Ala J:144	-	Lys J:145

(no "SAP(SNP)/Variant" information available for 4PY8)

(no "PROSITE Motif" information available for 4PY8)

(no "Exon" information available for 4PY8)

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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.......ee.......ee...eee.ee......eee......ee....hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee..hhhhhh.........eeeeee..eee....eee..........eeeeee......eeeeeeeee....hhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..eee..ee......ee......ee...ee......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py8 A   7 ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSI 334
                                    16        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

Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee....eeeeehhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py8 B   1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI 173
                                    10        20        30        40        50        60 ||     72        82        92       102       112       122       132       142       152       162       172 
                                                                                        62|                                                                                                            
                                                                                         65

Chain I from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.....eeeeeee.hhhhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee........eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee...........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py8 I   1 QVQLVQSGGGVVQPGRSLRLSCAASEFTFRMYATHWVRQAPGKGLEWVALISYDGSNKYYADSVKGRFTISRDNSMNTVYLQMNTLRPEDTAVYYCARDLGGYFIRGIMDVWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain J from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee......eeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4py8 J   1 ELQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 "SCOP Domain" information available for 4PY8)

(no "CATH Domain" information available for 4PY8)

(no "Pfam Domain" information available for 4PY8)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		MLI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ 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 ]

	Cis Peptide Bonds
		Ala A:7 - Asp A:8	[ RasMol ]
		Ala J:144 - Lys J:145	[ RasMol ]
		Asn I:57 - Lys I:58	[ RasMol ]
		Gly A:141 - Val A:142	[ RasMol ]
		Gly A:195 - Thr A:196	[ RasMol ]
		Gly I:102 - Tyr I:103	[ RasMol ]
		Lys A:140 - Gly A:141	[ RasMol ]
		Phe I:151 - Pro I:152	[ RasMol ]
		Phe J:94 - Pro J:95	[ RasMol ]
		Ser A:273 - Gly A:274	[ RasMol ]
		Ser J:7 - Pro J:8	[ RasMol ]
		Tyr J:140 - Pro J:141	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	HEMA_I18A0 \| Q9WFX3	:	1rd8 1ruz 2wrg 3gbn 3lzf 3r2x 4eef 4gxu 4gxx 4jug 4juh 4juj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (5, 5)

SS Bonds (9, 9)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (17, 17)

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