3ZTN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF INFLUENZA A NEUTRALIZING ANTIBODY SELECTED FROM CULTURES OF SINGLE HUMAN PLASMA CELLS IN COMPLEX WITH HUMAN H1 INFLUENZA HAEMAGGLUTININ.

Authors :   P. A. Hubbard, A. J. Ritchie, D. Corti, J. E. Voss, S. J. Gamblin, G. Codon A. Macagno, D. Jarrossay, D. Pinna, A. Minola, F. Vanzetta, C. Silacci B. M. Fernandez-Rodriguez, G. Agatic, I. Giacchetto-Sasselli, S. G. F. Sallusto, P. J. Collins, L. F. Haire, N. Temperton, J. P. M. Langedij J. J. Skehel, A. Lanzavecchia

Date :   12 Jul 11 (Deposition) - 10 Aug 11 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,H,L

Keywords :   Viral Protein-Immune System Complex, Monoclonal Antibody. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Corti, J. E. Voss, S. J. Gamblin, G. Codoni, A. Macagno, D. Jarrossay S. G. Vachieri, D. Pinna, A. Minola, F. Vanzetta, C. Silacci, B. M. Fernandez-Rodriguez, G. Agatic, S. Bianchi, I. Giacchetto-Sasselli, L. Calder, F. Sallusto, P. J. Collins, L. F. Haire, N. Temperton, J. P. M. Langedijk, J. J. Skehel, A. Lanzavecchia
A Neutralizing Antibody Selected From Plasma Cells That Binds To Group 1 And Group 2 Influenza A Hemagglutinins.
Science V. 333 850 2011
PubMed-ID: 21798894 | Reference-DOI: 10.1126/SCIENCE.1205669

Molecule 1 - HAEMAGGLUTININ
	Chains	:	A
	Fragment	:	HA1, RESIDUES 18-344
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	641501
	Strain	:	A/CALIFORNIA/04/2009(H1N1)

Molecule 2 - HAEMAGGLUTININ
	Chains	:	B
	Fragment	:	HA2, RESIDUES 345-520
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	641501
	Strain	:	A/CALIFORNIA/04/2009(H1N1)

Molecule 3 - FI6V3 ANTIBODY LIGHT CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - FI6V3 ANTIBODY LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 15)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:11 , GOL A:414 , VAL B:18	BINDING SITE FOR RESIDUE NAG A 610
02	AC2	SOFTWARE	HIS A:37 , LYS A:283	BINDING SITE FOR RESIDUE SO4 A1328
03	AC3	SOFTWARE	LYS A:311 , ARG A:313	BINDING SITE FOR RESIDUE SO4 A1329
04	AC4	SOFTWARE	LEU B:38 , ARG L:93	BINDING SITE FOR RESIDUE SO4 L1179
05	AC5	SOFTWARE	ASN A:31 , ARG A:313	BINDING SITE FOR RESIDUE SO4 A1330
06	AC6	SOFTWARE	THR A:133 , ALA A:134 , GLN A:223	BINDING SITE FOR RESIDUE SO4 A1331
07	AC7	SOFTWARE	HIS A:8 , ASN A:10 , ASN A:11 , HIS A:28 , NAG A:403	BINDING SITE FOR RESIDUE GOL A1332
08	AC8	SOFTWARE	ASN A:23	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 23 RESIDUES 630 TO 631
09	AC9	SOFTWARE	ASN A:276	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 276 RESIDUES 640 TO 640
10	BC1	SOFTWARE	ASN A:64 , GLU A:66 , ASP A:86 , ASN A:87	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 600 TO 601
11	BC2	SOFTWARE	ASN A:38 , ASN A:287 , ASP H:53 , ARG H:71 , ASP H:72 , ASN H:73 , SER H:74	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 620 TO 622
12	BC3	SOFTWARE	ASN A:38 , ASN A:287 , BMA A:406 , ASP H:53 , ARG H:71 , ASP H:72 , ASN H:73 , SER H:74	BINDING SITE FOR CHAIN A OF DI-SACCHARIDE NAG A 620 AND NAG A 621

Asymmetric/Biological 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	H:22	-	H:92
8	L:23	-	L:88

Asymmetric/Biological Unit

No.	Residues
1	Phe H:142	-	Pro H:143
2	Glu H:144	-	Pro H:145
3	Ser L:7	-	Pro L:8
4	Thr L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141

(no "SAP(SNP)/Variant" information available for 3ZTN)

(no "PROSITE Motif" information available for 3ZTN)

(no "Exon" information available for 3ZTN)

Asymmetric/Biological 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:327
 aligned with C3W5S1_I09A0 | C3W5S1 from UniProtKB/TrEMBL  Length:566

    Alignment length:327
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       
        C3W5S1_I09A0     18 DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPSIQSR  344
               SCOP domains d3ztna_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eee.......eee..eee.ee......eee......ee....hhhhhhhhhhhhh..........eee...............hhhhhhhhhh.eeeeeeee..........ee....................ee..ee..........eee.....eeeeeeeeee..hhhhhhhhhh.....eeeee...eeee...............eeeeeeeee....eee......eeee.eeeeeee.....eee....eeeee..ee....ee.....ee......ee...ee......eee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ztn A    1 DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPSIQSR  327
                                    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:173
 aligned with C3W5S1_I09A0 | C3W5S1 from UniProtKB/TrEMBL  Length:566

    Alignment length:173
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514   
        C3W5S1_I09A0    345 GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEI  517
               SCOP domains d3ztnb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeee....hhhhhhhhh....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ztn B    1 GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEI  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain H from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhh.eeeeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee.............eeee...eeeee............eee...............ee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ztn H    1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSTYAMHWVRQAPGKGLEWVAVISYDANYKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDSQLRSLLYFEWLSQGYFDYWGQGTLVTVSSASTKGPSCLVKDYFPEPTFPAVLQSSGLYSLSSVVNHKPSNTKV  203
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||| 104       114     ||139     ||164       174  ||   200   
                                                                              52A                            82A||               100A|||||100J||                 120|      145|             177|         
                                                                                                              82B|                100B|||||100K|                  136       161              194         
                                                                                                               82C                 100C|||||100L                                                         
                                                                                                                                    100D|||||                                                            
                                                                                                                                     100E||||                                                            
                                                                                                                                      100F|||                                                            
                                                                                                                                       100G||                                                            
                                                                                                                                        100H|                                                            
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                       
               SCOP domains d3ztnl1 L:1-106 automated matches                                                                             ---------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeeee.....ee..ee.eeeeee......eeee..............eeeee..eeeeee.........eeeeee......ee..................eeee....................eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ztn L    1 DIVMTQSPDSLAVSLGERATINCKSSQSVTFNYKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQHYRTPPTFGQGTKVEIKRTVAAPSVLLNNFYPQSGNSQESVTEQDSKDSTYSLSST  178
                                    10        20       27C|       36        46        56        66        76        86        96       106       135     ||158       168       178
                                                     27A|||                                                                                     115|   141|                       
                                                      27B||                                                                                      135    155                       
                                                       27C|                                                                                                                       
                                                        27D

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 3ZTN)

(no "Pfam Domain" information available for 3ZTN)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (C3W5S1_I09A0 | C3W5S1)

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/Biological Unit
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	Cis Peptide Bonds
		Glu H:144 - Pro H:145	[ RasMol ]
		Phe H:142 - Pro H:143	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr L:94 - Pro L:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	3ztn
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(no "Related Entries Specified in the PDB File" available for 3ZTN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (12, 12)

SS Bonds (8, 8)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

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Gene Ontology (17, 17)

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