4L1R - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   GLYCOPROTEIN B FROM HERPES SIMPLEX VIRUS TYPE 1, A549T RATE-OF-ENTRY MUTANT, LOW-PH

Authors :   S. D. Stampfer, E. E. Heldwein

Date :   03 Jun 13 (Deposition) - 26 Jun 13 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.03

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

Keywords :   Coiled-Coil, Envelope Glycoprotein, Membrane Fusion, Viral Protein, Rate Of Entry, Entry Rate, Pleckstrin Homology Domain, Viral Entry, Heparan Sulfate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :

PubMed: search

Molecule 1 - ENVELOPE GLYCOPROTEIN B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PVT-BAC
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	ECTODOMAIN (UNP RESIDUES 30 TO 730)
	Gene	:	GB, UL27
	Mutation	:	YES
	Organism Common	:	HHV-1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10306
	Strain	:	KOS
	Synonym	:	GB, GB-1, GB1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:139 , GLN A:140 , ASN A:141	BINDING SITE FOR RESIDUE NAG A 1141
02	AC2	SOFTWARE	ASN A:398 , LEU A:443 , ASN A:445 , NAG A:1399	BINDING SITE FOR RESIDUE NAG A 1398
03	AC3	SOFTWARE	NAG A:1398	BINDING SITE FOR RESIDUE NAG A 1399
04	AC4	SOFTWARE	ALA A:426 , ARG A:427 , ASN A:430 , NAG A:1431	BINDING SITE FOR RESIDUE NAG A 1430
05	AC5	SOFTWARE	NAG A:1430	BINDING SITE FOR RESIDUE NAG A 1431
06	AC6	SOFTWARE	ASN A:674	BINDING SITE FOR RESIDUE NAG A 1674
07	AC7	SOFTWARE	THR A:394 , ASN A:511	BINDING SITE FOR RESIDUE CL A 801
08	AC8	SOFTWARE	GLU B:138 , GLY B:139 , GLN B:140 , ASN B:141	BINDING SITE FOR RESIDUE NAG B 1141
09	AC9	SOFTWARE	ASN B:398 , LEU B:443 , ASN B:445	BINDING SITE FOR RESIDUE NAG B 1398
10	BC1	SOFTWARE	ALA B:426 , ARG B:427 , ASN B:430	BINDING SITE FOR RESIDUE NAG B 1430
11	BC2	SOFTWARE	ARG B:523 , ASN B:674	BINDING SITE FOR RESIDUE NAG B 1674

Asymmetric Unit

No.	Residues
1	A:116	-	A:573
2	A:133	-	A:529
3	A:207	-	A:271
4	A:364	-	A:412
5	A:596	-	A:633
6	B:116	-	B:573
7	B:133	-	B:529
8	B:207	-	B:271
9	B:364	-	B:412
10	B:596	-	B:633

Asymmetric Unit

No.	Residues
1	His A:177	-	Arg A:178
2	Tyr A:282	-	Pro A:283
3	His B:177	-	Arg B:178
4	Tyr B:282	-	Pro B:283

(no "SAP(SNP)/Variant" information available for 4L1R)

(no "PROSITE Motif" information available for 4L1R)

(no "Exon" information available for 4L1R)

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:608
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4l1ra_ A: Glycoprotein B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee........ee...................eeeeeeee....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhh.....ee..eeeeee..eeeeee.hhh....ee.ee.........eee...............eeeeeeeeeeeeeeeee......eee....ee..........hhhhh....hhh.eeeeeee..ee....ee....eeeeeee....eeeee..........eeeeeee..eeeee....eeeee....eeeee.....hhhhh..hhhhhhhhhhhhhhhhhhhh...eee....eeeee...eeeeeeeeee.hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.eeehhh.eee............ee...eeee........eeeee....eee.....ee......eeeeee..eeeeee..eeeeeee.hhh.........................hhhhhhh....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1r A 103 DIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNTIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIH 724
                                   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       472    || 496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716        
                                                                                                                                                                                                                                                                                                                                                                                                                477|                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                 492

Chain B from PDB  Type:PROTEIN  Length:608
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4l1rb_ B: Glycoprotein B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee........ee................ee.eeeeeeee....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhee..eeeeee..eeeeee.hhh....ee.ee.........eee..............eeeeeeeeeeeeeeeeee......eee....ee........hhhhh..........eee....................eeeee....eeeee..........eeeeeee..eeeee...eeeeee....eeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhh...eee....eeeee...eeeeeeeeee.hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee.eeehhh.eeee..........eee...eeee........eeeee.hhh.ee.....eee.....eeeeee..eeeeee..eeeeeee.hhh.........................hhhhhhh....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l1r B 103 DIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNTIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIH 724
                                   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       472    || 496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716        
                                                                                                                                                                                                                                                                                                                                                                                                                477|                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                 492

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Viral glycoprotein ectodomain-like (10)

Superfamily: Viral glycoprotein ectodomain-like (10)

Family: Glycoprotein B-like (7)

Protein domain: Glycoprotein B (7)

Human herpesvirus 1 [TaxId: 10298] (7)

1a	d4l1ra_	A:
1b	d4l1rb_	B:

(no "CATH Domain" information available for 4L1R)

(no "Pfam Domain" information available for 4L1R)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		His A:177 - Arg A:178	[ RasMol ]
		His B:177 - Arg B:178	[ RasMol ]
		Tyr A:282 - Pro A:283	[ RasMol ]
		Tyr B:282 - Pro B:283	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4l1r
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		Orientation in Membranes	:	OPM
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UniProtKB/Swiss-Prot
	GB_HHV1K \| P06437	:	2gum 3nw8 3nwa 3nwd 3nwf 3wv0 4bom 4hsi 5fz2

2gum	WILD-TYPE STRUCTURE, NEUTRAL PH.
3nw8	Y179S MUTANT, HIGH PH.
3nwa	W174R MUTANT, LOW PH.
3nwd	Y179S MUTANT, LOW PH.
3nwf	WILD-TYPE STRUCTURE, LOW PH.
4hsi	A504P/R505G/Q507G/N511G MUTANT, LOW PH.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (14, 14)

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