4E35 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAIN BOUND TO ICAL36-L (ANSRWPTSIL) PEPTIDE

Authors :   J. F. Amacher, D. R. Madden

Date :   09 Mar 12 (Deposition) - 26 Dec 12 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Pdz-Peptide Complex, Protein Transport-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Amacher, P. R. Cushing, C. D. Bahl, T. Beck, D. R. Madden
Stereochemical Determinants Of C-Terminal Specificity In Pd Peptide-Binding Domains: A Novel Contribution Of The Carboxylate-Binding Loop.
J. Biol. Chem. V. 288 5114 2013
PubMed-ID: 23243314 | Reference-DOI: 10.1074/JBC.M112.401588

Molecule 1 - GOLGI-ASSOCIATED PDZ AND COILED-COIL MOTIF-CONTAINING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN (UNP RESIDUES 284-370)
	Gene	:	GOPC, CAL, FIG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAL, CFTR-ASSOCIATED LIGAND, FUSED IN GLIOBLASTOMA, PDZ PROTEIN INTERACTING SPECIFICALLY WITH TC10, PIST

Molecule 2 - ICAL50 PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:322 , HOH A:528 , HOH A:562 , GLY B:284 , PRO B:285 , ILE B:286 , VAL B:368 , HOH B:570 , ILE C:9	BINDING SITE FOR RESIDUE GOL A 401
2	AC2	SOFTWARE	LEU A:292 , LYS A:293 , GLU A:294 , LYS A:350 , HOH A:521 , HOH A:525	BINDING SITE FOR RESIDUE GOL A 402
3	AC3	SOFTWARE	ASP A:346 , LYS A:348 , GLU A:351 , HOH A:580 , LYS B:288 , LEU B:290 , GLU B:364 , GOL B:402 , HOH B:547 , HOH B:566	BINDING SITE FOR RESIDUE GOL B 401
4	AC4	SOFTWARE	HIS A:296 , VAL A:342 , ASN A:343 , LYS B:288 , GOL B:401 , HOH B:566	BINDING SITE FOR RESIDUE GOL B 402
5	AC5	SOFTWARE	SER A:357 , LYS B:288 , GLU B:364 , GLU B:366 , HOH B:511 , HOH B:546	BINDING SITE FOR RESIDUE GOL B 403
6	AC6	SOFTWARE	GLY A:298 , LEU A:299 , GLY A:300 , ILE A:301 , SER A:302 , ILE A:303 , THR A:304 , HIS A:309 , HIS A:349 , VAL A:353 , LEU A:356 , GOL A:401 , HOH A:528 , HOH A:573 , ILE B:286 , ARG B:345 , HOH C:102 , HOH C:103 , HOH C:104 , HOH C:106 , HOH C:112	BINDING SITE FOR CHAIN C OF ICAL50 PEPTIDE
7	AC7	SOFTWARE	GLY A:284 , PRO A:285 , ILE A:286 , ASP A:325 , VAL A:370 , LEU B:292 , GLY B:298 , LEU B:299 , GLY B:300 , ILE B:301 , SER B:302 , ILE B:303 , THR B:304 , HIS B:309 , VAL B:311 , HIS B:349 , VAL B:353 , LEU B:356 , ARG B:360 , GLY B:361 , GLU B:362 , HOH B:513 , HOH B:515 , HOH B:537 , HOH D:101 , HOH D:102 , HOH D:104 , HOH D:108 , HOH D:109 , HOH D:110 , HOH D:111 , HOH D:114	BINDING SITE FOR CHAIN D OF ICAL50 PEPTIDE

(no "SS Bond" information available for 4E35)

(no "Cis Peptide Bond" information available for 4E35)

(no "SAP(SNP)/Variant" information available for 4E35)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	GOPC_HUMAN	288-371	2	A:288-370 B:288-370

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	GOPC_HUMAN	288-371	1	A:288-370 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	GOPC_HUMAN	288-371	1	- B:288-370

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000368498	1b	ENSE00001931189	chr6:117923527-117923167	361	GOPC_HUMAN	1-95	95	0	-	-
1.2	ENST00000368498	2	ENSE00000840039	chr6:117900227-117900063	165	GOPC_HUMAN	96-150	55	0	-	-
1.3	ENST00000368498	3	ENSE00001371009	chr6:117898634-117898611	24	GOPC_HUMAN	151-158	8	0	-	-
1.4	ENST00000368498	4	ENSE00000762781	chr6:117896515-117896340	176	GOPC_HUMAN	159-217	59	0	-	-
1.5a	ENST00000368498	5a	ENSE00000762780	chr6:117894795-117894630	166	GOPC_HUMAN	217-272	56	0	-	-
1.6	ENST00000368498	6	ENSE00002164938	chr6:117892118-117892023	96	GOPC_HUMAN	273-304	32	2	A:284-304 B:284-304	21 21
1.7	ENST00000368498	7	ENSE00002151421	chr6:117890899-117890735	165	GOPC_HUMAN	305-359	55	2	A:305-359 B:305-359	55 55
1.8	ENST00000368498	8	ENSE00002152146	chr6:117888197-117888017	181	GOPC_HUMAN	360-420	61	2	A:360-370 B:360-370	11 11
1.9	ENST00000368498	9	ENSE00001017893	chr6:117884547-117881432	3116	GOPC_HUMAN	420-462	43	0	-	-

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:87
 aligned with GOPC_HUMAN | Q9HD26 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:87
                                   293       303       313       323       333       343       353       363       
           GOPC_HUMAN   284 GPIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYV 370
               SCOP domains d4e35a_ A: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........eeeeeehhhheeeeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:288-370 UniProt: 288-371                                                PROSITE
               Transcript 1 Exon 1.6 [INCOMPLETE]Exon 1.7  PDB: A:305-359 UniProt: 305-359              Exon 1.8    Transcript 1
                 4e35 A 284 GPIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYV 370
                                   293       303       313       323       333       343       353       363

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with GOPC_HUMAN | Q9HD26 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:87
                                   293       303       313       323       333       343       353       363       
           GOPC_HUMAN   284 GPIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYV 370
               SCOP domains d4e35b_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeeeeehhhheeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:288-370 UniProt: 288-371                                                PROSITE
               Transcript 1 Exon 1.6 [INCOMPLETE]Exon 1.7  PDB: B:305-359 UniProt: 305-359              Exon 1.8    Transcript 1
                 4e35 B 284 GPIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRCGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYV 370
                                   293       303       313       323       333       343       353       363

Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...eeee Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4e35 C   4 RWPTSIL  10

Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......eee Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4e35 D   1 ANSRWPTSIL  10
                                    10

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: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d4e35a_	A:
1b	d4e35b_	B:

(no "CATH Domain" information available for 4E35)

(no "Pfam Domain" information available for 4E35)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GOPC_HUMAN | Q9HD26)

molecular function
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	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:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0006893	Golgi to plasma membrane transport	The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
	GO:0045176	apical protein localization	Any process in which a protein is transported to, or maintained in, apical regions of the cell.
	GO:0043004	cytoplasmic sequestering of CFTR protein	The selective interaction of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein with specific molecules in the cytoplasm, thereby inhibiting its transport to the cell membrane.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0030660	Golgi-associated vesicle membrane	The lipid bilayer surrounding a vesicle associated with the Golgi apparatus.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	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.
	GO:0014069	postsynaptic density of dendrite	An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
	GO:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0030140	trans-Golgi network transport vesicle	A vesicle that mediates transport between the trans-Golgi network and other parts of the cell.

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Description

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Ligands, Modified Residues, Ions (1, 5)

Sites (7, 7)

SS Bonds (0, 0)

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