3JXT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF SAP-102 IN COMPLEX WITH A FLUOROGENIC PEPTIDE-BASED LIGAND

Authors :   M. Sainlos, N. B. Olivier, B. Imperiali

Date :   21 Sep 09 (Deposition) - 29 Sep 10 (Release) - 10 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Sap102, Dlg3, Stargazin, 4-Dmap, 4Db, Pdz Domain, Solvatochromic Flurophore, Fluorogenic Probe, Calcium Channel, Calcium Transport, Ion Transport, Ionic Channel, Transport, Voltage-Gated Channel, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sainlos, W. S. Iskenderian-Epps, N. B. Olivier, D. Choquet, B. Imperiali
Caged Mono- And Divalent Ligands For Light-Assisted Disruption Of Pdz Domain-Mediated Interactions.
J. Am. Chem. Soc. V. 135 4580 2013
PubMed-ID: 23480637 | Reference-DOI: 10.1021/JA309870Q

Molecule 1 - DISKS LARGE HOMOLOG 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-NO, MODIFIED PET32
	Expression System Strain	:	BL21-RIL
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	THIRD PDZ DOMAIN: UNP RESIDUES 393-493
	Gene	:	DLG3, DLGH3
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	SYNAPSE-ASSOCIATED PROTEIN 102, SAP102, PSD-95/SAP90-RELATED PROTEIN 1

Molecule 2 - VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	C-TERMINAL MOTIF OF STARGAZIN: UNP O88602 RESIDUES 318-323
	Mutation	:	YES
	Other Details	:	PEPTIDE LIGAND OBTAINED BY SOLID PHASE PEPTIDE SYNTHESIS
	Synonym	:	NEURONAL VOLTAGE-GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT, STARGAZIN
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	4DB	2	Mod. Amino Acid	(2S)-2-AMINO-4-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]BUTANOIC ACID
2	ACE	2	Mod. Amino Acid	ACETYL GROUP
3	ACT	1	Ligand/Ion	ACETATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	4DB	1	Mod. Amino Acid	(2S)-2-AMINO-4-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]BUTANOIC ACID
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	ACT	1	Ligand/Ion	ACETATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	4DB	1	Mod. Amino Acid	(2S)-2-AMINO-4-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]BUTANOIC ACID
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	ACT	-1	Ligand/Ion	ACETATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:417 , SER A:430 , PHE A:431 , ASN B:417 , SER B:430 , PHE B:431 , ARG B:446 , THR C:103 , THR D:103	BINDING SITE FOR RESIDUE ACT A 1

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

(no "Cis Peptide Bond" information available for 3JXT)

(no "SAP(SNP)/Variant" information available for 3JXT)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DLG3_RAT	149-236 244-331 404-485	2	- - A:404-485 B:404-485

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DLG3_RAT	149-236 244-331 404-485	1	- - A:404-485 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	DLG3_RAT	149-236 244-331 404-485	1	- - - B:404-485

(no "Exon" information available for 3JXT)

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:96
 aligned with DLG3_RAT | Q62936 from UniProtKB/Swiss-Prot  Length:849

    Alignment length:97
                                   406       416       426       436       446       456       466       476       486       
             DLG3_RAT   397 DFTREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFES 493
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.......eeeee......eeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhhh-.eeeeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:404-485 UniProt: 404-485                                              -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3jxt A 397 DFTREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRA-QSVTIVAQYRPEEYSRFES 493
                                   406       416       426       436       446       456       466      |476       486       
                                                                                                      473 |                  
                                                                                                        475

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with DLG3_RAT | Q62936 from UniProtKB/Swiss-Prot  Length:849

    Alignment length:95
                                   408       418       428       438       448       458       468       478       488     
             DLG3_RAT   399 TREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFES 493
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PDZ_aPDZ-3jxtB01 B:404-482                                                          ----------- Pfam domains (1)
           Pfam domains (2) PDZ_aPDZ-3jxtB02 B:404-482                                                          ----------- Pfam domains (2)
         Sec.struct. author ....eeeee........eeeee......eeeeee...hhhhhhh.....eeeeee..ee....hhhhhhhhhhh....eeeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: B:404-485 UniProt: 404-485                                              -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3jxt B 399 TREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFES 493
                                   408       418       428       438       448       458       468       478       488

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with CCG2_MOUSE | O88602 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:7
           CCG2_MOUSE   317 NRRTTPV 323
               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
                 3jxt C 100 xxRTTPV 106
                            ||     
                            ||     
                          100-ACE  
                           101-4DB

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with CCG2_MOUSE | O88602 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:7
           CCG2_MOUSE   317 NRRTTPV 323
               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
                 3jxt D 100 xxRTTPV 106
                            ||     
                            ||     
                          100-ACE  
                           101-4DB

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 3JXT)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Rattus norvegicus (Rat) (23)

1a	PDZ-3jxtB01	B:404-482
1b	PDZ-3jxtB02	B:404-482

Clan: no clan defined [family: PDZ_assoc] (8)

Family: PDZ_assoc (8)

Rattus norvegicus (Rat) (5)

2a	PDZ_assoc-3jxtB03	B:399-403
2b	PDZ_assoc-3jxtB04	B:399-403

Asymmetric Unit(hide GO term definitions)

Chain A,B (DLG3_RAT | Q62936)

molecular function
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	GO:0004385	guanylate kinase activity	Catalysis of the reaction: ATP + GMP = ADP + GDP.
	GO:0035255	ionotropic glutamate receptor binding	Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	GO:0019902	phosphatase binding	Interacting selectively and non-covalently with any phosphatase.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
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:0007268	chemical synaptic transmission	The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
	GO:0001736	establishment of planar polarity	Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
	GO:0045197	establishment or maintenance of epithelial cell apical/basal polarity	Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
	GO:0010923	negative regulation of phosphatase activity	Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0043113	receptor clustering	The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
	GO:0097120	receptor localization to synapse	Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
cellular component
	GO:0032281	AMPA glutamate receptor complex	An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043198	dendritic shaft	Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0008328	ionotropic glutamate receptor complex	A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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: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.

Chain C,D (CCG2_MOUSE | O88602)

molecular function
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0016247	channel regulator activity	Modulates the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel.
	GO:0035255	ionotropic glutamate receptor binding	Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
	GO:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
	GO:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0051899	membrane depolarization	The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.
	GO:0060081	membrane hyperpolarization	The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential.
	GO:0050877	nervous system process	A organ system process carried out by any of the organs or tissues of neurological system.
	GO:0007528	neuromuscular junction development	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
	GO:2000311	regulation of AMPA receptor activity	Any process that modulates the frequency, rate or extent of AMPA selective glutamate receptor activity.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0042391	regulation of membrane potential	Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
	GO:0019226	transmission of nerve impulse	The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
	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:0032281	AMPA glutamate receptor complex	An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
	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:0005891	voltage-gated calcium channel complex	A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

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	CCG2_MOUSE \| O88602	:	4x3h 5kbs 5kbt 5kbu

(no "Related Entries Specified in the PDB File" available for 3JXT)

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Ligands, Modified Residues, Ions (3, 5)

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