2GHV - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SARS SPIKE PROTEIN RECEPTOR BINDING DOMAIN

Authors :   W. C. Hwang, Y. Lin, E. Santelli, J. Sui, L. Jaroszewski, B. Stec, M. Farz W. A. Marasco, R. C. Liddington

Date :   27 Mar 06 (Deposition) - 19 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : C,E

Keywords :   Sars, S Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. C. Hwang, Y. Lin, E. Santelli, J. Sui, L. Jaroszewski, B. Stec, M. Farzan, W. A. Marasco, R. C. Liddington
Structural Basis Of Neutralization By A Human Anti-Severe Acute Respiratory Syndrome Spike Protein Antibody, 80R.
J. Biol. Chem. V. 281 34610 2006
PubMed-ID: 16954221 | Reference-DOI: 10.1074/JBC.M603275200

Molecule 1 - SPIKE GLYCOPROTEIN
	Chains	:	E, C
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Fragment	:	RBD OF SPIKE PROTEIN S1 (318-510)
	Gene	:	S
	Organism Scientific	:	SARS CORONAVIRUS
	Organism Taxid	:	227859
	Synonym	:	PEPLOMER PROTEIN, E2, RBD

		1	2
Asymmetric/Biological Unit	:	C	E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2GHV)

(no "Site" information available for 2GHV)

Asymmetric/Biological Unit

No.	Residues
1	C:366	-	C:419
2	C:467	-	C:474
3	E:323	-	E:348
4	E:366	-	E:419
5	E:467	-	E:474

Asymmetric/Biological Unit

No.	Residues
1	Pro E:469	-	Pro E:470
2	Pro C:469	-	Pro C:470

Asymmetric/Biological Unit (9, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	C/E	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	C/E	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	C/E	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	C/E	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	C/E	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	C/E	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	C/E	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	C/E	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	C/E	F	501	Y
	* ID not provided by source

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

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

(no "Exon" information available for 2GHV)

Asymmetric/Biological 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 C from PDB  Type:PROTEIN  Length:183
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:183
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499   
          SPIKE_CVHSA   320 TNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE 502
               SCOP domains d2ghvc1 C:320-502 Spike protein S1                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.....hhhhheeeee.....hhhhh.......eeeee..hhhhhhhhhh..eeeeeeeee.hhhhhh.....hhhhhhh........eeeeeeehhhhhh........eee....................................eee.......hhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ghv C 320 TNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE 502
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499

Chain E from PDB  Type:PROTEIN  Length:183
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:183
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499   
          SPIKE_CVHSA   320 TNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE 502
               SCOP domains d2ghve_ E: Spike protein S1                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....hhhhheeeee.....hhhhh.......eeeee..hhhhhhhhhh..eeeeeeeee.hhhhhh.....hhhhhhh........eeeeeeehhhhhh........eee....................................eee.......hhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ghv E 320 TNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE 502
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: SARS receptor-binding domain-like (12)

Superfamily: SARS receptor-binding domain-like (12)

Family: SARS receptor-binding domain-like (12)

Protein domain: Spike protein S1 (8)

SARS coronavirus [TaxId: 227859] (8)

1a	d2ghvc1	C:320-502
1b	d2ghve_	E:

(no "CATH Domain" information available for 2GHV)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain C,E (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/Biological Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2ghv)

	Sites
(no "Sites" information available for 2ghv)

	Cis Peptide Bonds
		Pro C:469 - Pro C:470	[ RasMol ]
		Pro E:469 - Pro E:470	[ RasMol ]

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Access by PDB/NDB ID
	2ghv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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Access by UniProt ID/Accession number
	SPIKE_CVHSA \| P59594
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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2ajf	CRYSTAL STRUCTURE OF S1 RBD IN COMPLEX WITH ITS RECEPTOR
2ghw	CRYSTAL STRUCTURE OF S1 RBD IN COMPLEX WITH A NEUTRALIZING ANTIBODY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 18)

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 (17, 17)

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Related Entries

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