1WYY - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   POST-FUSION HAIRPIN CONFORMATION OF THE SARS CORONAVIRUS SPIKE GLYCOPROTEIN

Authors :   S. Duquerroy, A. Vigouroux, P. J. M. Rottier, F. A. Rey, B. J. Bosch

Date :   18 Feb 05 (Deposition) - 17 May 05 (Release) - 23 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Membrane Fusion, Severe Acute Respiratory Syndrome, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Duquerroy, A. Vigouroux, P. J. M. Rottier, F. A. Rey, B. J. Bosch
Central Ions And Lateral Asparagine/Glutamine Zippers Stabilize The Post-Fusion Hairpin Conformation Of The Sars Coronavirus Spike Glycoprotein
Virology V. 335 276 2005
PubMed-ID: 15840526 | Reference-DOI: 10.1016/J.VIROL.2005.02.022

Molecule 1 - E2 GLYCOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 885-1189
	Gene	:	S
	Organism Scientific	:	SARS CORONAVIRUS
	Organism Taxid	:	227859

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:902	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	HOH A:11	BINDING SITE FOR RESIDUE CL A 2
3	AC3	SOFTWARE	HOH B:40	BINDING SITE FOR RESIDUE CL B 3
4	AC4	SOFTWARE	GLN B:902	BINDING SITE FOR RESIDUE CL B 4

(no "SS Bond" information available for 1WYY)

(no "Cis Peptide Bond" information available for 1WYY)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_038 *	T	894	A	SPIKE_CVHSA	---	---	A/B	T	894	A
2	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	A/B	L	1147	F
3	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	A/B	K	1162	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_038 *	T	894	A	SPIKE_CVHSA	---	---	A	T	894	A
2	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	A	L	1147	F
3	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	A	K	1162	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_038 *	T	894	A	SPIKE_CVHSA	---	---	B	T	894	A
2	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	B	L	1147	F
3	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	B	K	1162	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (3, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_038 *	T	894	A	SPIKE_CVHSA	---	---	B	T	894	A
2	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	B	L	1147	F
3	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	B	K	1162	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1WYY)

(no "Exon" information available for 1WYY)

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:126
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:300
                                   899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189
         SPIKE_CVHSA    890 GIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE 1189
               SCOP domains d1wyya1 A:890-973,A:1147-1188 E2 spike glycoprotein                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------d1wyya1 A:890-973,A:1147-1188              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.............hhhhhhhhhhhhhhhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ----A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F--------------E-------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1wyy A  890 GIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEV------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE 1188
                                   899       909       919       929       939       949       959       969   |     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -      1148      1158      1168      1178      1188
                                                                                                             973                                                                                                                                                                           1147

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:298
                                   901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181        
         SPIKE_CVHSA    892 GVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE 1189
               SCOP domains d1wyyb1 B:892-973,B:1147-1188 E2 spike glycoprotein                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------d1wyyb1 B:892-973,B:1147-1188              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Corona_S2-1wyyB01 B:892-1188                                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) Corona_S2-1wyyB02 B:892-1188                                                                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.............hhhhhhhhhhhhhhhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F--------------E-------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wyy B  892 GVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEV------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE 1188
                                   901       911       921       931       941       951       961       971 |       -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -      1150      1160      1170      1180        
                                                                                                           973                                                                                                                                                                           1147

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: Coiled coil proteins (689)

Fold: Stalk segment of viral fusion proteins (231)

Superfamily: Coronavirus S2 glycoprotein (11)

Family: Coronavirus S2 glycoprotein (11)

Protein domain: E2 spike glycoprotein (11)

Human coronavirus (strain SARS) [TaxId: 227859] (9)

1a	d1wyya1	A:890-973,A:1147-1188
1b	d1wyyb1	B:892-973,B:1147-1188

(no "CATH Domain" information available for 1WYY)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Corona_S2] (8)

Family: Corona_S2 (8)

Human SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus) (6)

1a	Corona_S2-1wyyB01	B:892-1188
1b	Corona_S2-1wyyB02	B:892-1188

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPIKE_CVHSA | P59594)

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: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:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0046813	receptor-mediated virion attachment to host cell	The process by which a virion attaches to a host cell by binding to a receptor on the host cell surface.
	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:0044173	host cell endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the host cell ER-Golgi intermediate compartment system.
	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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Biological Units
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	1wyy
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (17, 17)

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