2C36 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR-MEDIATED ACTIVATION OF VIRUS ENTRY

Authors :   C. Krummenacher, V. M. Supekar, J. C. Whitbeck, E. Lazear, S. A. Connolly, R. J. Eisenberg, G. H. Cohen, D. C. Wiley, A. Carfi

Date :   04 Oct 05 (Deposition) - 23 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

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

Keywords :   Virus, Viral Protein, Herpes, Immunoglobulin-Like, Glycoprotein, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Krummenacher, V. M. Supekar, J. C. Whitbeck, E. Lazear, S. A. Connolly, R. J. Eisenberg, G. H. Cohen, D. C. Wiley, A. Carfi
Structure Of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation Of Virus Entry
Embo J. V. 24 4144 2005
PubMed-ID: 16292345 | Reference-DOI: 10.1038/SJ.EMBOJ.7600875

Molecule 1 - GLYCOPROTEIN D HSV-1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Plasmid	:	PRSVNT
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Mutation	:	YES
	Organism Common	:	HERPES SIMPLEX VIRUS (HSV-1, HUMAN)
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10298
	Other Details	:	N-ACETYL-GLUCOSAMINE LINKED TO ASN121 AND ASN94 IN BOTH SUBUNITS (CHAIN A, B)
	Strain	:	PATTON

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 13)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:41 , ASN A:94 , NAG A:1309 , HOH A:2271 , HOH A:2272 , HOH A:2273	BINDING SITE FOR RESIDUE NAG A1308
02	AC2	SOFTWARE	TYR A:306 , NAG A:1308 , MAN A:1310	BINDING SITE FOR RESIDUE NAG A1309
03	AC3	SOFTWARE	NAG A:1309	BINDING SITE FOR RESIDUE MAN A1310
04	AC4	SOFTWARE	GLN B:41 , GLN B:91 , ASN B:94 , TYR B:306 , NAG B:1309 , HOH B:2236	BINDING SITE FOR RESIDUE NAG B1308
05	AC5	SOFTWARE	NAG B:1308 , BMA B:1310	BINDING SITE FOR RESIDUE NAG B1309
06	AC6	SOFTWARE	NAG B:1309	BINDING SITE FOR RESIDUE BMA B1310
07	AC7	SOFTWARE	NDG B:1312	BINDING SITE FOR RESIDUE MAN B1313
08	AC8	SOFTWARE	NDG B:1311 , MAN B:1313	BINDING SITE FOR RESIDUE NDG B1312
09	AC9	SOFTWARE	SER B:119 , ASN B:121 , NDG B:1312	BINDING SITE FOR RESIDUE NDG B1311
10	BC1	SOFTWARE	HIS A:39 , ASP A:215 , HIS B:39 , ASP B:215	BINDING SITE FOR RESIDUE ZN A1311
11	BC2	SOFTWARE	GLN A:27 , PHE A:223 , ILE A:224 , ASN A:227	BINDING SITE FOR RESIDUE CL A1312
12	BC3	SOFTWARE	LYS A:245 , LYS B:245	BINDING SITE FOR RESIDUE CL A1313
13	BC4	SOFTWARE	GLN B:27 , PHE B:223 , ILE B:224 , ASN B:227	BINDING SITE FOR RESIDUE CL B1314

Asymmetric Unit

No.	Residues
1	A:66	-	A:189
2	A:106	-	A:202
3	A:118	-	A:127
4	A:307	-	B:307
5	B:66	-	B:189
6	B:106	-	B:202
7	B:118	-	B:127

Asymmetric Unit

No.	Residues
1	Gly A:243	-	Pro A:244
2	Gly B:243	-	Pro B:244
3	Gly B:284	-	Thr B:285

(no "SAP(SNP)/Variant" information available for 2C36)

(no "PROSITE Motif" information available for 2C36)

(no "Exon" information available for 2C36)

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:274
 aligned with GD_HHV1P | P57083 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:285
                                    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     
             GD_HHV1P    48 PVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPYH 332
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c36A00 A:23-307  [code=2.70.230.10, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee...................eeeeee.....eeee....hhhhhhhh.hhhhhh..eeeeeeeeeee..eeeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhhh........ee..hhhhhhhhhhhhhhhhh................-----------....hhhhhh.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c36 A  23 PVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPE-----------LAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPYC 307
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   |     -     | 272       282       292       302     
                                                                                                                                                                                                                                                                   256         268

Chain B from PDB  Type:PROTEIN  Length:274
 aligned with GD_HHV1P | P57083 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:285
                                    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     
             GD_HHV1P    48 PVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPYH 332
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c36B00 B:23-307  [code=2.70.230.10, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..................eeeeeee.....eeee....hhhhhhhh...hhhhh.eeeeeeeeeee..eeeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhhh........ee..hhhhhhhhhhhhhhhhh.......ee.......-----------....hhhhhh.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c36 B  23 PVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPE-----------LAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPYC 307
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   |     -     | 272       282       292       302     
                                                                                                                                                                                                                                                                   256         268

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 2C36)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Glycoprotein D; Chain: A; (4)

Homologous Superfamily: [code=2.70.230.10, no name defined] (4)

Herpes simplex virus (hsv-1, human) (Human herpesvirus 1) (1)

1a	2c36A00	A:23-307
1b	2c36B00	B:23-307

(no "Pfam Domain" information available for 2C36)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GD_HHV1P | P57083)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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: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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:243 - Pro A:244	[ RasMol ]
		Gly B:243 - Pro B:244	[ RasMol ]
		Gly B:284 - Thr B:285	[ RasMol ]

Biological Units
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	2c36
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	GD_HHV1P \| P57083	:	1jma 1l2g 2c3a

1jma	CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIND BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
1l2g	STRUCTURE OF A C-TERMINALLY TRUNCATED FORM OF GLYCOPROTEIND FROM HSV-1
2c3a	STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR-MEDIATED ACTIVATION OF VIRUS ENTRY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 13)

Sites (13, 13)

SS Bonds (7, 7)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (1, 2)

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Gene Ontology (9, 9)

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