2X57 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 2

Authors :   A. C. W. Pike, A. J. Barr, A. Quigley, N. Burgess Brown, A. De Riso, A. Bu G. Berridge, J. R. C. Muniz, A. Chaikaud, M. Vollmar, T. Krojer, E. Ugoc F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, E. P. Carpenter

Date :   05 Feb 10 (Deposition) - 09 Mar 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)

Keywords :   G-Protein Coupled Receptor, Circadian Rhythm, Male Reproduction, Hormone Binding, Growth, Receptor, Transducer, Class B Gpcr, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. W. Pike, A. J. Barr, A. Quigley, N. Burgess Brown, A. De Riso, A. Bullock, G. Berridge, J. R. C. Muniz, A. Chaikaud, M. Vollmar, T. Krojer, E. Ugochukwu, F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, E. P. Carpenter
Crystal Structure Of The Extracellular Domain Of Human Vasoactive Intestinal Polypeptide Receptor 2
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (0, 0)

SS Bonds (9, 9)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011811	A	39	T	VIPR2_HUMAN	Polymorphism	1062609	A/B/C	A	39	T

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

Biological Unit 1 (1, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011811	A	39	T	VIPR2_HUMAN	Polymorphism	1062609	A/B/C	A	39	T

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_011811	A	39	T	VIPR2_HUMAN	Polymorphism	1062609	A	A	39	T

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011811	A	39	T	VIPR2_HUMAN	Polymorphism	1062609	B	A	39	T

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011811	A	39	T	VIPR2_HUMAN	Polymorphism	1062609	C	A	39	T

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

PROSITE Motifs (2, 6)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	VIPR2_HUMAN	37-113	3	A:37-113 B:37-113 C:37-113
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	VIPR2_HUMAN	52-76	3	A:52-76 B:52-76 C:52-76

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	VIPR2_HUMAN	37-113	6	A:37-113 B:37-113 C:37-113
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	VIPR2_HUMAN	52-76	6	A:52-76 B:52-76 C:52-76

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	VIPR2_HUMAN	37-113	1	A:37-113 - -
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	VIPR2_HUMAN	52-76	1	A:52-76 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	VIPR2_HUMAN	37-113	1	- B:37-113 -
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	VIPR2_HUMAN	52-76	1	- B:52-76 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F2_3	PS50227	G-protein coupled receptors family 2 profile 1.	VIPR2_HUMAN	37-113	1	- - C:37-113
2	G_PROTEIN_RECEP_F2_1	PS00649	G-protein coupled receptors family 2 signature 1.	VIPR2_HUMAN	52-76	1	- - C:52-76

Exons (0, 0)

Sequences/Alignments

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:103
 aligned with VIPR2_HUMAN | P41587 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:103
                                    21        31        41        51        61        71        81        91       101       111   
          VIPR2_HUMAN    12 CWLLAPVNSIHPECRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee..eee.......eeeee.hhhhhhh.....eeeeeee..ee.....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------T--------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------G_PROTEIN_RECEP_F2_3  PDB: A:37-113 UniProt: 37-113                          - PROSITE (1)
                PROSITE (2) ----------------------------------------G_PROTEIN_RECEP_F2_1     -------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2x57 A -13 GVDLGTENLYFQSmRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
                                    -4   ||   31        41        51        61        71        81        91       101       111   
                                         0-MSE                                                                                     
                                         26

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with VIPR2_HUMAN | P41587 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:105
                                    19        29        39        49        59        69        79        89        99       109     
          VIPR2_HUMAN    10 LTCWLLAPVNSIHPECRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee.......eeeee.hhhhhhh.....eeeeeee..ee.....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------T--------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------G_PROTEIN_RECEP_F2_3  PDB: B:37-113 UniProt: 37-113                          - PROSITE (1)
                PROSITE (2) ------------------------------------------G_PROTEIN_RECEP_F2_1     -------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2x57 B -15 SSGVDLGTENLYFQSmRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
                                    -6     || 29        39        49        59        69        79        89        99       109     
                                           0-MSE                                                                                     
                                           26

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with VIPR2_HUMAN | P41587 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:103
                                    21        31        41        51        61        71        81        91       101       111   
          VIPR2_HUMAN    12 CWLLAPVNSIHPECRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------HRM-2x57C01 C:49-112                                            -- Pfam domains (1)
           Pfam domains (2) -------------------------------------HRM-2x57C02 C:49-112                                            -- Pfam domains (2)
           Pfam domains (3) -------------------------------------HRM-2x57C03 C:49-112                                            -- Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee..eee.......eeeee.hhhhhhh.....eeeeeee..ee.....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------T--------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------G_PROTEIN_RECEP_F2_3  PDB: C:37-113 UniProt: 37-113                          - PROSITE (1)
                PROSITE (2) ----------------------------------------G_PROTEIN_RECEP_F2_1     -------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2x57 C -13 GVDLGTENLYFQSmRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPANVGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDP 114
                                    -4   ||   31        41        51        61        71        81        91       101       111   
                                         0-MSE                                                                                     
                                         26

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (VIPR2_HUMAN | P41587)

molecular function
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0004999	vasoactive intestinal polypeptide receptor activity	Combining with vasoactive intestinal polypeptide to initiate a change in cell activity.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0007190	activation of adenylate cyclase activity	Any process that initiates the activity of the inactive enzyme adenylate cyclase.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0048662	negative regulation of smooth muscle cell proliferation	Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
	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.
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: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.

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	2x57
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