4B7M - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   H1N1 2009 PANDEMIC INFLUENZA VIRUS: RESISTANCE OF THE I223R NEURAMINIDASE MUTANT EXPLAINED BY KINETIC AND STRUCTURAL ANALYSIS

Authors :   E. Van Der Vries, S. G. Vachieri, X. Xiong, J. Liu, P. J. Collins, P. A. W L. F. Haire, A. J. Hay, M. Schutten, A. D. M. E. Osterhaus, S. R. Martin, C. A. B. Boucher, J. J. Skehel, S. J. Gamblin

Date :   21 Aug 12 (Deposition) - 03 Oct 12 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Hydrolase, Antiviral Resistance, Immunocompromised (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Van Der Vries, P. J. Collins, S. G. Vachieri, X. Xiong, J. Liu, P. A. Walker, L. F. Haire, A. J. Hay, M. Schutten, A. D. M. E. Osterhaus, S. R. Martin, C. A. B. Boucher, J. J. Skehel, S. J. Gamblin
H1N1 2009 Pandemic Influenza Virus: Resistance Of The I223R Neuraminidase Mutant Explained By Kinetic And Structural Analysis
Plos Pathog. V. 8 2914 2012
PubMed-ID: 23028314 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002914

Molecule 1 - NEURAMINIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	GALLUS GALLUS
	Expression System Common	:	CHICKEN
	Expression System Plasmid	:	PHW2000
	Expression System Taxid	:	9031
	Expression System Vector Type	:	RECOMBINANT INFLUENZA VIRUS
	Organism Scientific	:	INFLUENZA A VIRUS (A/NETHERLANDS/2631/2010(H1N1))
	Organism Taxid	:	1027873
	Other Details	:	APO STRUCTURE
	Other Details - Source	:	PATIENT ISOLATE
	Variant	:	H1N1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 26)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PO4	8	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:150 , PRO A:198 , ASP A:199 , HOH A:2035 , HOH A:2057 , TRP B:455	BINDING SITE FOR RESIDUE PO4 A1469
02	AC2	SOFTWARE	ARG A:293 , ARG A:368 , TYR A:402	BINDING SITE FOR RESIDUE PO4 A1470
03	AC3	SOFTWARE	ASP A:294 , GLY A:298 , ASP A:324 , GLY A:342 , ASN A:344 , HOH A:2090	BINDING SITE FOR RESIDUE CA A1471
04	AC4	SOFTWARE	TRP A:455 , LYS B:150 , PRO B:198 , ASP B:199	BINDING SITE FOR RESIDUE PO4 B1469
05	AC5	SOFTWARE	ARG B:118 , ARG B:293 , ARG B:368 , TYR B:402	BINDING SITE FOR RESIDUE PO4 B1470
06	AC6	SOFTWARE	ASP B:294 , GLY B:298 , ASP B:324 , GLY B:342 , ASN B:344	BINDING SITE FOR RESIDUE CA B1471
07	AC7	SOFTWARE	ASN A:88	BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 88
08	AC8	SOFTWARE	ASN A:146 , THR A:148	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 146 RESIDUES 511 TO 512
09	AC9	SOFTWARE	LYS A:84 , ASN A:235 , GLN A:308	BINDING SITE FOR MONO-SACCHARIDE NAG A 521 BOUND TO ASN A 235
10	BC1	SOFTWARE	ASN B:88	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 88 RESIDUES 501 TO 502
11	BC2	SOFTWARE	ASN B:146 , THR B:148	BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 146 RESIDUES 511 TO 512
12	BC3	SOFTWARE	LYS B:84 , ASN B:235 , GLN B:308	BINDING SITE FOR MONO-SACCHARIDE NAG B 521 BOUND TO ASN B 235

Asymmetric Unit

No.	Residues
1	A:92	-	A:417
2	A:124	-	A:129
3	A:184	-	A:231
4	A:233	-	A:238
5	A:279	-	A:292
6	A:281	-	A:290
7	A:318	-	A:335
8	B:92	-	B:417
9	B:124	-	B:129
10	B:184	-	B:231
11	B:233	-	B:238
12	B:279	-	B:292
13	B:281	-	B:290
14	B:318	-	B:335
15	B:421	-	B:446

Asymmetric Unit

No.	Residues
1	Asn A:325	-	Pro A:326
2	Arg A:430	-	Pro A:431
3	Leu A:463	-	Pro A:464
4	Asn B:325	-	Pro B:326
5	Arg B:430	-	Pro B:431
6	Leu B:463	-	Pro B:464

(no "SAP(SNP)/Variant" information available for 4B7M)

(no "PROSITE Motif" information available for 4B7M)

(no "Exon" information available for 4B7M)

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:386
 aligned with F8UU09_9INFA | F8UU09 from UniProtKB/TrEMBL  Length:469

    Alignment length:386
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462      
         F8UU09_9INFA    83 VKLAGNSSLCPVSGWAIYSKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNRLRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNDFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID 468
               SCOP domains d4b7ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhh....eeeeeeeeee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeee.....eeeee................................eeeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b7m A  83 VKLAGNSSLCPVSGWAIYSKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNRLRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNDFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID 468
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462

Chain B from PDB  Type:PROTEIN  Length:386
 aligned with F8UU09_9INFA | F8UU09 from UniProtKB/TrEMBL  Length:469

    Alignment length:386
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462      
         F8UU09_9INFA    83 VKLAGNSSLCPVSGWAIYSKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNRLRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNDFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID 468
               SCOP domains d4b7mb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhh.....eeee...eee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee...........eeeee..eeeee..........eeeee.....eeeee................................eeeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b7m B  83 VKLAGNSSLCPVSGWAIYSKDNSIRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNRLRTQESECACVNGSCFTVMTDGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNDFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTID 468
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 6-bladed beta-propeller (327)

Superfamily: Sialidases (238)

Family: automated matches (54)

Protein domain: automated matches (54)

Influenza a virus (a/netherlands/2631/2010(h1n1)) [TaxId: 1027873] (2)

1a	d4b7ma_	A:
1b	d4b7mb_	B:

(no "CATH Domain" information available for 4B7M)

(no "Pfam Domain" information available for 4B7M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (F8UU09_9INFA | F8UU09)

molecular function
	GO:0052794	exo-alpha-(2->3)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052795	exo-alpha-(2->6)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0052796	exo-alpha-(2->8)-sialidase activity	Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
	GO:0004308	exo-alpha-sialidase activity	Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:430 - Pro A:431	[ RasMol ]
		Arg B:430 - Pro B:431	[ RasMol ]
		Asn A:325 - Pro A:326	[ RasMol ]
		Asn B:325 - Pro B:326	[ RasMol ]
		Leu A:463 - Pro A:464	[ RasMol ]
		Leu B:463 - Pro B:464	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	4b7m
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		Orientation in Membranes	:	OPM
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	F8UU09_9INFA \| F8UU09
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		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/TrEMBL
	F8UU09_9INFA \| F8UU09	:	4b7j 4b7n

4b7j	H1N1 2009 PANDEMIC INFLUENZA VIRUS: RESISTANCE OF THE I223R NEURAMINIDASE MUTANT EXPLAINED BY KINETIC AND STRUCTURAL ANALYSIS
4b7n	H1N1 2009 PANDEMIC INFLUENZA VIRUS: RESISTANCE OF THE I223R NEURAMINIDASE MUTANT EXPLAINED BY KINETIC AND STRUCTURAL ANALYSIS
4b7q	H1N1 2009 PANDEMIC INFLUENZA VIRUS: RESISTANCE OF THE I223R NEURAMINIDASE MUTANT EXPLAINED BY KINETIC AND STRUCTURAL ANALYSIS
4b7r	H1N1 2009 PANDEMIC INFLUENZA VIRUS: RESISTANCE OF THE I223R NEURAMINIDASE MUTANT EXPLAINED BY KINETIC AND STRUCTURAL ANALYSIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (12, 12)

SS Bonds (15, 15)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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