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Title :   CRYSTAL STRUCTURE OF THE DE NOVO DESIGNED BINDING PROTEIN HB36.3 IN COMPLEX THE THE 1918 INFLUENZA VIRUS HEMAGGLUTININ

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

Date :   14 Mar 11 (Deposition) - 11 May 11 (Release) - 25 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Hemagglutinin, Glycoprotein, Viral Protein-De Novo Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Fleishman, T. A. Whitehead, D. C. Ekiert, C. Dreyfus, J. E. Corn, E. M. Strauch, I. A. Wilson, D. Baker
Computational Design Of Proteins Targeting The Conserved Stem Region Of Influenza Hemagglutinin.
Science V. 332 816 2011
PubMed-ID: 21566186 | Reference-DOI: 10.1126/SCIENCE.1202617

Molecule 1 - HEMAGGLUTININ
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Strain	:	HIGH FIVE
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	HA1 CHAIN (UNP RESIDUES 18-344)
	Gene	:	HA, HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	88776
	Strain	:	A/SOUTH CAROLINA/1/1918 (H1N1)
	Synonym	:	1918 HEMAGGLUTININ RECEPTOR BINDING DOMAIN

Molecule 2 - HEMAGGLUTININ
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Strain	:	HIGH FIVE
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	HA2 CHAIN (UNP RESIDUES 345-520)
	Gene	:	HA, HEMAGGLUTININ
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	88776
	Strain	:	A/SOUTH CAROLINA/1/1918 (H1N1)
	Synonym	:	1918 HEMAGGLUTININ FUSION SUBUNIT

Molecule 3 - HB36.3, DESIGNED HEMAGGLUTININ BINDING PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA 2 (BL21/DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARTIFICIAL GENE
	Organism Taxid	:	32630

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

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

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:33	BINDING SITE FOR RESIDUE NAG A 501
2	AC2	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
3	AC3	SOFTWARE	ARG A:224 , NAG A:601 , BMA A:603	BINDING SITE FOR RESIDUE NAG A 602
4	AC4	SOFTWARE	NAG A:602 , MAN A:604	BINDING SITE FOR RESIDUE BMA A 603
5	AC5	SOFTWARE	BMA A:603	BINDING SITE FOR RESIDUE MAN A 604

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

(no "Cis Peptide Bond" information available for 3R2X)

(no "SAP(SNP)/Variant" information available for 3R2X)

(no "PROSITE Motif" information available for 3R2X)

(no "Exon" information available for 3R2X)

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:322
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:322
                                    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 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP  339
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......ee.......ee...eee.ee......eee......eeee..hhhhhhhhhhhhhhhh.......eee...............hhhhhhhhhh.eeeeeeee.................eeeeee..eee....eee..........eeeeee......eeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee.eeeeeee.....eee....eeeee..ee....ee.....ee......ee...ee......eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r2x A   11 DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIP  324
                                    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:171
 aligned with HEMA_I18A0 | Q9WFX3 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:171
                                   354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514 
          HEMA_I18A0    345 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNRE  515
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Hemagglutinin-3r2xB01 B:1-171                                                                                                                                               Pfam domains (1)
           Pfam domains (2) Hemagglutinin-3r2xB02 B:1-171                                                                                                                                               Pfam domains (2)
         Sec.struct. author .....................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r2x B    1 GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNRE  171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:82
                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3r2x C    6 DGQQLNRLLLEWIGAWDPFGLGKDAYDVEAEAVLQAVYETESAFDLAMRIMWIYVFAFNRPIPFPHAQKLARRLLELKQAAS   87
                                    15        25        35        45        55        65        75        85

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 3R2X)

(no "CATH Domain" information available for 3R2X)

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

(no "Related Entries Specified in the PDB File" available for 3R2X)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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