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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE P55 PDZ T85C DOMAIN COMPLEXED WITH THE GLYCOPHORIN C F127C PEPTIDE

Authors :   H. Kusunoki, T. Kohno

Date :   22 Mar 07 (Deposition) - 12 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Gpc, Maguk, P55, Pdz, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Kusunoki, T. Kohno
Structural Insight Into The Interaction Between The P55 Pdz Domain And Glycophorin C
Biochem. Biophys. Res. Commun. V. 359 972 2007
PubMed-ID: 17572384 | Reference-DOI: 10.1016/J.BBRC.2007.05.215
(for further references see the PDB file header)

Molecule 1 - 55 KDA ERYTHROCYTE MEMBRANE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN, RESIDUES 69-153
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	P55, MEMBRANE PROTEIN, PALMITOYLATED 1

Molecule 2 - GLYCOPHORIN C
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PUBK19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL REGION, RESIDUES 117-128
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PAS-2', GLYCOPROTEIN BETA, GLPC, GLYCOCONNECTIN, SIALOGLYCOPROTEIN D, GLYCOPHORIN D, GPD, CD236 ANTIGEN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2EJY)

NMR Structure

No.	Residues
1	A:85	-	B:127

(no "Cis Peptide Bond" information available for 2EJY)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021342	K	124	E	GLPC_HUMAN	Polymorphism	28370000	B	K	124	E

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	EM55_HUMAN	71-152	1	A:71-152

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000259254	1a	ENSE00001832190	chr2:127413509-127413888	380	GLPC_HUMAN	1-17	17	0	-	-
1.5	ENST00000259254	5	ENSE00000857228	chr2:127447831-127447887	57	GLPC_HUMAN	17-36	20	0	-	-
1.6	ENST00000259254	6	ENSE00000925795	chr2:127451440-127451523	84	GLPC_HUMAN	36-64	29	0	-	-
1.7c	ENST00000259254	7c	ENSE00001896060	chr2:127453522-127454246	725	GLPC_HUMAN	64-128	65	1	B:123-128	6

2.2b	ENST00000369534	2b	ENSE00001842847	X:154033796-154033547	250	EM55_HUMAN	1-34	34	0	-	-
2.5c	ENST00000369534	5c	ENSE00001622979	X:154020560-154020417	144	EM55_HUMAN	35-82	48	1	A:69-82	14
2.6a	ENST00000369534	6a	ENSE00001697405	X:154020122-154020044	79	EM55_HUMAN	83-109	27	1	A:83-109	27
2.7b	ENST00000369534	7b	ENSE00001607029	X:154019343-154019258	86	EM55_HUMAN	109-137	29	1	A:109-137	29
2.8b	ENST00000369534	8b	ENSE00002179637	X:154018297-154018229	69	EM55_HUMAN	138-160	23	1	A:138-153	16
2.9c	ENST00000369534	9c	ENSE00001675460	X:154014675-154014479	197	EM55_HUMAN	161-226	66	0	-	-
2.10d	ENST00000369534	10d	ENSE00001691038	X:154013432-154013326	107	EM55_HUMAN	226-262	37	0	-	-
2.11b	ENST00000369534	11b	ENSE00001641741	X:154012383-154012303	81	EM55_HUMAN	262-289	28	0	-	-
2.12a	ENST00000369534	12a	ENSE00001684797	X:154011782-154011702	81	EM55_HUMAN	289-316	28	0	-	-
2.12g	ENST00000369534	12g	ENSE00001658958	X:154010077-154009875	203	EM55_HUMAN	316-383	68	0	-	-
2.13b	ENST00000369534	13b	ENSE00001612210	X:154009588-154009514	75	EM55_HUMAN	384-408	25	0	-	-
2.14e	ENST00000369534	14e	ENSE00001863406	X:154007628-154006959	670	EM55_HUMAN	409-466	58	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:85
 aligned with EM55_HUMAN | Q00013 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:85
                                    78        88        98       108       118       128       138       148     
           EM55_HUMAN    69 VRLIQFEKVTEEPMGITLKLNEKQSCTVARILHGGMIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMISLKVIPNQQ 153
               SCOP domains d2ejya_ A: automated matches                                                          SCOP domains
               CATH domains 2ejyA00 A:69-153  [code=2.30.42.10, no name defined]                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeee.....eeeeee...hhhhhhh......eeeee.........hhhhhhhhhhh.eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: A:71-152 UniProt: 71-152                                                - PROSITE
           Transcript 2 (1) Exon 2.5c     Exon 2.6a  PDB: A:83-109   ----------------------------Exon 2.8b        Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------Exon 2.7b  PDB: A:109-137    ---------------- Transcript 2 (2)
                 2ejy A  69 VRLIQFEKVTEEPMGICLKLNEKQSCTVARILHGGMIHRQGSLHVGDEILEINGTNVTNHSVDQLQKAMKETKGMISLKVIPNQQ 153
                                    78        88        98       108       118       128       138       148

Chain B from PDB  Type:PROTEIN  Length:6
 aligned with GLPC_HUMAN | P04921 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:6
           GLPC_HUMAN   123 RKEYFI 128
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) -E---- SAPs(SNPs)
                    PROSITE ------ PROSITE
               Transcript 1 1.7c   Transcript 1
                 2ejy B 123 RKEYCI 128

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: PDZ domain (180)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (34)

d2ejya_

NMR Structure

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

Homologous Superfamily: [code=2.30.42.10, no name defined] (191)

Human (Homo sapiens) (120)

2ejyA00

A:69-153

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

NMR Structure(hide GO term definitions)

Chain A (EM55_HUMAN | Q00013)

molecular function
	GO:0004385	guanylate kinase activity	Catalysis of the reaction: ATP + GMP = ADP + GDP.
	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:0046710	GDP metabolic process	The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
	GO:0046037	GMP metabolic process	The chemical reactions and pathways involving GMP, guanosine monophosphate.
	GO:0090022	regulation of neutrophil chemotaxis	Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	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:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0030863	cortical cytoskeleton	The portion of the cytoskeleton that lies just beneath the plasma 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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0032420	stereocilium	An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.

Chain B (GLPC_HUMAN | P04921)

molecular function
	GO:0070492	oligosaccharide binding	Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
	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).
cellular component
	GO:0030863	cortical cytoskeleton	The portion of the cytoskeleton that lies just beneath the plasma membrane.
	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.

NMR Structure
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ejy)

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	2ejy
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	EM55_HUMAN \| Q00013
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UniProtKB/Swiss-Prot
	EM55_HUMAN \| Q00013	:	2ev8 3ney

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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Exons (5, 5)

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