3WV0 - JenaLib

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Title :   O-GLYCAN ATTACHED TO HERPES SIMPLEX VIRUS TYPE 1 GLYCOPROTEIN GB IS RECOGNIZED BY THE IG V-SET DOMAIN OF HUMAN PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR ALPHA

Authors :   K. Kuroki, J. Wang, T. Ose, M. Yamaguchi, S. Tabata, N. Maita, S. Nakamur M. Kajikawa, A. Kogure, T. Satoh, H. Arase, K. Maenaka

Date :   10 May 14 (Deposition) - 11 Jun 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Immunoglobulin-Like, Immunological Receptor, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kuroki, J. Wang, T. Ose, M. Yamaguchi, S. Tabata, N. Maita, S. Nakamura, M. Kajikawa, A. Kogure, T. Satoh, H. Arase, K. Maenaka
Structural Basis For Simultaneous Recognition Of An O-Glyca And Its Attached Peptide Of Mucin Family By Immune Receptor Pilr Alpha
Proc. Natl. Acad. Sci. Usa V. 111 8877 2014
PubMed-ID: 24889612 | Reference-DOI: 10.1073/PNAS.1324105111

Molecule 1 - PAIRED IMMUNOGLOBULIN-LIKE TYPE 2 RECEPTOR ALPHA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGMT7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	V-SET DOMAIN, UNP RESIDUES 32-150
	Gene	:	PILRA
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - ENVELOPE GLYCOPROTEIN B
	Chains	:	X, Y
	Engineered	:	YES
	Fragment	:	O-GLYCAN WITH ATTACHED PEPTIDE, UNP RESIDUES 50-56
	Organism Common	:	HHV-1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10306
	Other Details	:	O-GLYCAN WITH PEPTIDE DERIVED FROM HUMAN HERPESVIRUS 1
	Synonym	:	GB, GB-1, GB1
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	X	Y
Biological Unit 1 (1x)	:	A		X
Biological Unit 2 (1x)	:		B		Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	A2G	2	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	SIA	2	Ligand/Ion	O-SIALIC ACID
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	SIA	1	Ligand/Ion	O-SIALIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	SIA	1	Ligand/Ion	O-SIALIC ACID
3	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:40 , LYS A:106 , SER A:107 , HOH A:312 , PRO X:56	BINDING SITE FOR RESIDUE SO4 A 201
02	AC2	SOFTWARE	ARG A:132 , ILE A:149 , HOH A:359 , HOH A:366	BINDING SITE FOR RESIDUE SO4 A 202
03	AC3	SOFTWARE	ARG A:73 , HIS A:90 , ASP A:92 , TYR A:93 , ARG B:132	BINDING SITE FOR RESIDUE SO4 A 203
04	AC4	SOFTWARE	GLN B:105 , LYS B:106 , SER B:107 , HOH B:361	BINDING SITE FOR RESIDUE SO4 B 201
05	AC5	SOFTWARE	ARG B:68 , SER B:70 , ARG B:72 , SER B:80 , SER B:83 , ARG B:126 , HOH B:309	BINDING SITE FOR RESIDUE SO4 B 202
06	AC6	SOFTWARE	ARG B:73 , HIS B:90 , TYR B:93 , HOH B:364	BINDING SITE FOR RESIDUE SO4 B 203
07	AC7	SOFTWARE	HIS B:75 , PHE B:76 , HIS B:77 , HOH B:332 , HOH B:344 , HOH B:357 , PRO Y:56	BINDING SITE FOR RESIDUE SO4 B 204
08	AC8	SOFTWARE	HIS B:77 , GLU B:128 , ARG B:136 , GLN B:138 , A2G Y:102 , HOH Y:201	BINDING SITE FOR RESIDUE SO4 B 205
09	AC9	SOFTWARE	TYR A:33 , ARG A:126 , ARG A:136 , GLN A:137 , GLN A:138 , TRP A:139 , GLN A:140 , ILE A:142 , HOH A:322 , A2G X:102 , HOH X:202 , HOH X:203 , HOH X:208	BINDING SITE FOR RESIDUE SIA X 101
10	BC1	SOFTWARE	HIS A:77 , THR X:53 , PRO X:54 , ALA X:55 , PRO X:56 , SIA X:101 , HOH X:205 , HOH X:207	BINDING SITE FOR RESIDUE A2G X 102
11	BC2	SOFTWARE	TYR B:33 , ARG B:126 , GLN B:137 , GLN B:138 , TRP B:139 , GLN B:140 , ILE B:142 , HOH B:356 , A2G Y:102 , HOH Y:201 , HOH Y:202 , HOH Y:203 , HOH Y:206	BINDING SITE FOR RESIDUE SIA Y 101
12	BC3	SOFTWARE	PHE B:76 , HIS B:77 , ARG B:136 , SO4 B:205 , THR Y:53 , PRO Y:54 , ALA Y:55 , PRO Y:56 , SIA Y:101	BINDING SITE FOR RESIDUE A2G Y 102

(no "SS Bond" information available for 3WV0)

Asymmetric Unit

No.	Residues
1	Arg A:85	-	Pro A:86
2	Arg B:85	-	Pro B:86

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060361	R	78	G	PILRA_HUMAN	Polymorphism	1859788	A/B	G	78	G

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060361	R	78	G	PILRA_HUMAN	Polymorphism	1859788	A	G	78	G

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060361	R	78	G	PILRA_HUMAN	Polymorphism	1859788	B	G	78	G

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

(no "PROSITE Motif" information available for 3WV0)

(no "Exon" information available for 3WV0)

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:119
 aligned with C9JGG1_HUMAN | C9JGG1 from UniProtKB/TrEMBL  Length:166

    Alignment length:119
                                    40        50        60        70        80        90       100       110       120       130       140         
         C9JGG1_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee......eeeeeeee...........eeeeee........ee....ee.......eeee......eeeeee...hhhhheeeeeeeeee.....eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv0 A  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
                                    40        50        60        70        80        90       100       110       120       130       140

Chain A from PDB  Type:PROTEIN  Length:119
 aligned with PILRA_HUMAN | Q9UKJ1 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:119
                                    40        50        60        70        80        90       100       110       120       130       140         
          PILRA_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee......eeeeeeee...........eeeeee........ee....ee.......eeee......eeeeee...hhhhheeeeeeeeee.....eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv0 A  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
                                    40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with C9JGG1_HUMAN | C9JGG1 from UniProtKB/TrEMBL  Length:166

    Alignment length:119
                                    40        50        60        70        80        90       100       110       120       130       140         
         C9JGG1_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee......eeeeeeee...........eeeeee........ee.............eeee......eeeeee...hhhhh.eeeeeeeee.....eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv0 B  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
                                    40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with PILRA_HUMAN | Q9UKJ1 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:119
                                    40        50        60        70        80        90       100       110       120       130       140         
          PILRA_HUMAN    31 YLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHRQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee......eeeeeeee...........eeeeee........ee.............eeee......eeeeee...hhhhh.eeeeeeeee.....eeeee....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------G----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv0 B  31 MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSI 149
                                    40        50        60        70        80        90       100       110       120       130       140

Chain X from PDB  Type:PROTEIN  Length:7
 aligned with GB_HHV1K | P06437 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:7
             GB_HHV1K    50 GPATPAP  56
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3wv0 X  50 GPATPAP  56

Chain Y from PDB  Type:PROTEIN  Length:6
 aligned with GB_HHV1K | P06437 from UniProtKB/Swiss-Prot  Length:904

    Alignment length:6
             GB_HHV1K    51 PATPAP  56
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3wv0 Y  51 PATPAP  56

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 3WV0)

(no "CATH Domain" information available for 3WV0)

(no "Pfam Domain" information available for 3WV0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PILRA_HUMAN | Q9UKJ1)

molecular function
	GO:0042288	MHC class I protein binding	Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	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.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (C9JGG1_HUMAN | C9JGG1)

Chain X,Y (GB_HHV1K | P06437)

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:0044177	host cell Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic host cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
	GO:0044178	host cell Golgi membrane	The lipid bilayer surrounding any of the compartments of the host cell Golgi apparatus.
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	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.

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	Cis Peptide Bonds
		Arg A:85 - Pro A:86	[ RasMol ]
		Arg B:85 - Pro B:86	[ RasMol ]

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	3wv0
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UniProtKB/Swiss-Prot
	C9JGG1_HUMAN \| C9JGG1	:	3wuz
	GB_HHV1K \| P06437	:	2gum 3nw8 3nwa 3nwd 3nwf 4bom 4hsi 4l1r 5fz2
	PILRA_HUMAN \| Q9UKJ1	:	3wuz 4nfb

3wuz	THE SAME PROTEIN FREE FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (22, 25)

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Related Entries

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