2BEQ - JenaLib

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Title :   STRUCTURE OF A PROTEOLYTICALLY RESISTANT CORE FROM THE SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS S2 FUSION PROTEIN

Authors :   V. M. Supekar, C. Bruckmann, P. Ingallinella, E. Bianchi, A. Pessi, A. C

Date :   29 Nov 04 (Deposition) - 22 Dec 04 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)

Keywords :   Viral Protein, Coiled Coil, Membrane Fusion, Sars, Viral Entry, Envelope Protein, Glycoprotein, Transmembrane, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. M. Supekar, C. Bruckmann, P. Ingallinella, E. Bianchi, A. Pessi, A. Carfi
Structure Of A Proteolytically Resistant Core From The Severe Acute Respiratory Syndrome Coronavirus S2 Fusion Protein
Proc. Natl. Acad. Sci. Usa V. 101 17958 2004
PubMed-ID: 15604146 | Reference-DOI: 10.1073/PNAS.0406128102

Molecule 1 - E2 GLYCOPROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Fragment	:	RESIDUES 914-949
	Organism Common	:	HCOV-SARS
	Organism Scientific	:	SARS CORONAVIRUS PUMC03
	Organism Taxid	:	253435
	Other Details	:	N-TERMINAL CAPPED WITH ACETYL GROUP BUT ONLY VISIBLE DENSITY ON B, C, D AND F. C-TERMINAL A, B, C, D, E, F CAPPED WITH AMINE GROUP
	Synonym	:	SARS CORONAVIRUS S2 FRAGMENT, SPIKE GLYCOPROTEIN, PEPLOMER PROTEIN
	Synthetic	:	YES

Molecule 2 - E2 GLYCOPROTEIN
	Chains	:	D, E, F
	Engineered	:	YES
	Fragment	:	RESIDUES 1148-1193
	Organism Common	:	HCOV-SARS
	Organism Scientific	:	SARS CORONAVIRUS PUMC03
	Organism Taxid	:	253435
	Other Details	:	N-TERMINAL CAPPED WITH ACETYL GROUP BUT ONLY VISIBLE DENSITY ON B, C, D AND F. C-TERMINAL A, B, C, D, E, F CAPPED WITH AMINE GROUP
	Synonym	:	SARS CORONAVIRUS S2 FRAGMENT, SPIKE GLYCOPROTEIN, PEPLOMER PROTEIN
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	NH2	6	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (2, 20)

No.	Name	Count	Type	Full Name
1	ACE	8	Mod. Amino Acid	ACETYL GROUP
2	NH2	12	Mod. Amino Acid	AMINO GROUP

(no "Site" information available for 2BEQ)

(no "SS Bond" information available for 2BEQ)

(no "Cis Peptide Bond" information available for 2BEQ)

Asymmetric Unit (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	D/E/F	L	1148	F
2	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	D/E/F	K	1163	E
	* ID not provided by source

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

Biological Unit 1 (2, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_042 *	L	1148	F	SPIKE_CVHSA	---	---	D/E/F	L	1148	F
2	UniProt	VAR_SPIKE_CVHSA_043 *	K	1163	E	SPIKE_CVHSA	---	---	D/E/F	K	1163	E
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2BEQ)

(no "Exon" information available for 2BEQ)

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:37
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:37
                                   923       933       943       
         SPIKE_CVHSA    914 SQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSS  950
               SCOP domains d2beq.1 A:,D: E2 spike glycoprotein   SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                2beq A  914 SQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSx  950
                                   923       933       943      |
                                                              950-NH2

Chain B from PDB  Type:PROTEIN  Length:38
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:38
                                   922       932       942        
         SPIKE_CVHSA    913 ISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSS  950
               SCOP domains d2beq.2 B:,E: E2 spike glycoprotein    SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                2beq B  913 xSQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSx  950
                            |      922       932       942       |
                            |                                  950-NH2
                          913-ACE

Chain C from PDB  Type:PROTEIN  Length:38
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:38
                                   922       932       942        
         SPIKE_CVHSA    913 ISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSS  950
               SCOP domains d2beq.3 C:,F: E2 spike glycoprotein    SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                2beq C  913 xSQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSx  950
                            |      922       932       942       |
                            |                                  950-NH2
                          913-ACE

Chain D from PDB  Type:PROTEIN  Length:48
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:48
                                  1156      1166      1176      1186        
         SPIKE_CVHSA   1147 DLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKW 1194
               SCOP domains d2beq.1 A:,D: E2 spike glycoprotein              SCOP domains
               CATH domains -2beqD00 D:1148-1193 Single helix bin          - CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhh....ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -F--------------E------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                2beq D 1147 xLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKx 1194
                            |     1156      1166      1176      1186       |
                            |                                           1194-NH2
                         1147-ACE

Chain E from PDB  Type:PROTEIN  Length:47
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:47
                                  1157      1167      1177      1187       
         SPIKE_CVHSA   1148 LGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKW 1194
               SCOP domains d2beq.2 B:,E: E2 spike glycoprotein             SCOP domains
               CATH domains 2beqE00 E:1148-1193 Single helix bin          - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh....eee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) F--------------E------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                2beq E 1148 LGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKx 1194
                                  1157      1167      1177      1187      |
                                                                       1194-NH2

Chain F from PDB  Type:PROTEIN  Length:48
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:48
                                  1156      1166      1176      1186        
         SPIKE_CVHSA   1147 DLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKW 1194
               SCOP domains d2beq.3 C:,F: E2 spike glycoprotein              SCOP domains
               CATH domains -2beqF00 F:1148-1193 Single helix bin          - CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhh....eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -F--------------E------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                2beq F 1147 xLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKx 1194
                            |     1156      1166      1176      1186       |
                            |                                           1194-NH2
                         1147-ACE

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	d2beq.1	A:,D:
1b	d2beq.2	B:,E:
1c	d2beq.3	C:,F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: Single helix bin (1)

[unclassified] (1)

1a	2beqD00	D:1148-1193
1b	2beqE00	E:1148-1193
1c	2beqF00	F:1148-1193

(no "Pfam Domain" information available for 2BEQ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (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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(no "Cis Peptide Bonds" information available for 2beq)

Biological Unit
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1q4z	S1 SUBUNIT MODEL OF SARS CORONAVIRUS S PROTEIN
1wnc	CRYSTAL STRUCTURE OF THE SARS-COV SPIKE PROTEIN FUSION CORE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 6)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 3)

CATH Domains (1, 3)

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Gene Ontology (17, 17)

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