3LZF - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FAB 2D1 IN COMPLEX WITH THE 1918 INFLUENZA VIRUS HEMAGGLUTININ

Authors :   D. C. Ekiert, I. A. Wilson

Date :   01 Mar 10 (Deposition) - 07 Apr 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: A,B,H,L  (3x)
Biol. Unit 2: A,B  (3x)
Biol. Unit 3: H,L  (1x)

Keywords :   Hemagglutinin, Fab, Neutralizing Antibodies, Antibody, Pandemic Flu, Swine Flu, Envelope Protein, Fusion Protein, Glycoprotein, Antigen, Virion, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Xu, D. C. Ekiert, J. C. Krause, R. Hai, J. E. Crowe, I. A. Wilson
Structural Basis Of Preexisting Immunity To The 2009 H1N1 Pandemic Influenza Virus.
Science V. 328 357 2010
PubMed-ID: 20339031 | Reference-DOI: 10.1126/SCIENCE.1186430

Molecule 1 - HEMAGGLUTININ, HA1 SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Strain	:	BTI-TN-5B1-4
	Expression System Taxid	:	7111
	Expression System Vector Type	:	AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
	Fragment	:	ECTODOMAIN HA1, RESIDUES 18-344
	Gene	:	HA, HEMAGGLUTININ
	Organism Common	:	INFLUENZA A VIRUS
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	59375
	Strain	:	A/SOUTH CAROLINA/1/1918(H1N1)
	Synonym	:	HEMAGGLUTININ HA1 CHAIN, HEMAGGLUTININ HA2 CHAIN

Molecule 2 - HEMAGGLUTININ, HA2 SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Strain	:	BTI-TN-5B1-4
	Expression System Taxid	:	7111
	Expression System Vector Type	:	AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
	Fragment	:	ECTODOMAIN HA2, RESIDUES 345-520
	Gene	:	HA, HEMAGGLUTININ
	Organism Common	:	INFLUENZA A VIRUS
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	59375
	Strain	:	A/SOUTH CAROLINA/1/1918(H1N1)
	Synonym	:	HEMAGGLUTININ HA1 CHAIN, HEMAGGLUTININ HA2 CHAIN

Molecule 3 - 2D1 FAB, HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293F
	Expression System Common	:	HUMAN
	Expression System Organ	:	KIDNEY
	Expression System Plasmid	:	PEE6.4
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	IMMUNOGLOBULIN, GAMMA CHAIN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - 2D1 FAB, LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293F
	Expression System Common	:	HUMAN
	Expression System Organ	:	KIDNEY
	Expression System Plasmid	:	PEE12.4
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	IMMUNOGLOBULIN, LAMBDA CHAIN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (3x)	:	A	B	H	L
Biological Unit 2 (3x)	:	A	B
Biological Unit 3 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 27)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	21	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 27)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	21	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:21	BINDING SITE FOR RESIDUE NAG A 401
2	AC2	SOFTWARE	ASN A:33 , NAG A:502	BINDING SITE FOR RESIDUE NAG A 501
3	AC3	SOFTWARE	NAG A:501	BINDING SITE FOR RESIDUE NAG A 502
4	AC4	SOFTWARE	ASN A:73 , GLU A:75 , GLU A:94 , ASN A:95 , CYS A:97 , ARG A:224 , NAG A:602	BINDING SITE FOR RESIDUE NAG A 601
5	AC5	SOFTWARE	NAG A:601 , BMA A:603	BINDING SITE FOR RESIDUE NAG A 602
6	AC6	SOFTWARE	NAG A:602 , MAN A:604	BINDING SITE FOR RESIDUE BMA A 603
7	AC7	SOFTWARE	ARG A:224 , BMA A:603	BINDING SITE FOR RESIDUE MAN A 604
8	AC8	SOFTWARE	ASN A:289 , NAG A:702	BINDING SITE FOR RESIDUE NAG A 701
9	AC9	SOFTWARE	NAG A:701	BINDING SITE FOR RESIDUE NAG A 702

Asymmetric Unit

No.	Residues
1	A:14	-	B:137
2	A:52	-	A:277
3	A:64	-	A:76
4	A:97	-	A:139
5	A:281	-	A:305
6	B:144	-	B:148
7	H:22	-	H:92
8	H:142	-	H:208
9	L:23	-	L:88
10	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Phe H:148	-	Pro H:149
2	Glu H:150	-	Pro H:151
3	Tyr L:140	-	Pro L:141

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

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

(no "Exon" information available for 3LZF)

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:323
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:323
                                    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   
          HEMA_I18A0     18 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPS  340
               SCOP domains d3lzfa_ A: Hemagglutinin                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eee.......eee..eee.ee......eeee.....ee....hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee.................eeeeee......ee..eeeee..hhhhhhhhhh.....eeee....eeee...............eeeee..ee....eeeeee...ee...eeeeeee.....eee....eeeeee.eee..ee......ee......ee...ee......eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lzf A   11 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPS  325
                                    20        30        40        50    |   59        69        79    |   88       |97       107       117      125B|     133A       143       153       163       173       183       193       203       213       223       233       243       253       263 |     272       282       292       302       312       322   
                                                                      54A                           83A          95A                           125A||     133A                                                                                                                                264A                                                             
                                                                                                                                                125B|                                                                                                                                                                                                          
                                                                                                                                                 125C

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:173
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514   
          HEMA_I18A0    345 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  517
               SCOP domains d3lzfb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Hemagglutinin-3lzfB01 B:1-173                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) Hemagglutinin-3lzfB02 B:1-173                                                                                                                                                 Pfam domains (2)
         Sec.struct. author .....................eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhh........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lzf B    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEI  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:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeeeee......eeeeeee.....eee.........eeeeee....eeeeee...hhhhheeeeeeeeee...............eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3lzf H    2 VQLVESGPALVKPTQTLTLTCSFSGFSLSTSGMSVSWIRQPPGKALEWLALIDWDDDTYYITYSSSLKTRLTISKDTSKSQVVLTMTNMDPVDTATYYCARTLRVSGDYVRDFDLWGRGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV  223
                                    11        21        31    ||  39        49   |    58    ||  66        76      ||83        93      100C|||    107       117       137       147      |162      |173      |184       194     ||207       217      
                                                            35A|               52A        62A|                  82A||               100A|||||                       126|              154|||    169|      180|               200||                  
                                                             35B                           62B                   82B|                100B||||                        137               156||     171       182                203|                  
                                                                                                                  82C                 100C|||                                           157|                                   205                  
                                                                                                                                       100D||                                            162                                                        
                                                                                                                                        100E|                                                                                                       
                                                                                                                                         100F

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d3lzfl1 L:2-107 automated matches                                                                              d3lzfl2 L:108-211 automated matches                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee.....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeee....ee...eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lzf L    2 PVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVSWYQQVPGTAPKLLIYGNNERPSGVPDRFSGSKSATSASLAISGLQSEDEADYYCAAWDDSLNGFWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAP  211
                                   |12        22     || 30        40        50        60        70        80        90     |||97      106A       116       126       136       146       156       166 ||    177       187       197  ||   209  
                                   9|              27A|                                                                  95A||        106A                                                           168|                           200|        
                                   11               27B                                                                   95B|                                                                        170                            203        
                                                                                                                           95C

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 3LZF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEMA_I18A0 | Q9WFX3)

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
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	3lzf
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	HEMA_I18A0 \| Q9WFX3	:	1rd8 1ruz 2wrg 3gbn 3r2x 4eef 4gxu 4gxx 4jug 4juh 4juj 4py8

3lzg	CRYSTAL STRUCTURE OF A 2009 H1N1 INFLUENZA VIRUS HEMAGGLUTININ

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (10, 10)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

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Pfam Domains (1, 2)

Gene Ontology (17, 17)

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