1KJW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SH3-GUANYLATE KINASE MODULE FROM PSD-95

Authors :   A. W. Mcgee, S. R. Dakoji, O. Olsen, D. S. Bredt, W. A. Lim, K. E. Prehoda

Date :   05 Dec 01 (Deposition) - 09 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Protein-Protein Interaction, Scaffold, Neuropeptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. W. Mcgee, S. R. Dakoji, O. Olsen, D. S. Bredt, W. A. Lim, K. E. Prehoda
Structure Of The Sh3-Guanylate Kinase Module From Psd-95 Suggests A Mechanism For Regulated Assembly Of Maguk Scaffolding Proteins
Mol. Cell V. 8 1291 2001
PubMed-ID: 11779504 | Reference-DOI: 10.1016/S1097-2765(01)00411-7
(for further references see the PDB file header)

Molecule 1 - POSTSYNAPTIC DENSITY PROTEIN 95
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SH3 DOMAIN/GUANYLATE KINASE DOMAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	PSD-95, POSTSYNAPTIC PROTEIN SAP90, SYNAPSE- ASSOCIATED PROTEIN 90

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:102 , HOH A:124 , THR A:543 , LYS A:544 , ASP A:545	BINDING SITE FOR RESIDUE SO4 A 188
2	AC2	SOFTWARE	ARG A:475 , HIS A:477 , SER A:478 , ASP A:479 , GLY A:515 , ARG A:516	BINDING SITE FOR RESIDUE SO4 A 189

(no "SS Bond" information available for 1KJW)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:713	-	Pro A:714

(no "SAP(SNP)/Variant" information available for 1KJW)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	DLG4_RAT	534-709	1	A:534-709
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	DLG4_RAT	566-583	1	A:566-583

(no "Exon" information available for 1KJW)

Asymmetric/Biological 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:292
 aligned with DLG4_RAT | P31016 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:295
                                   439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719     
             DLG4_RAT   430 GFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL 724
               SCOP domains d1kjwa1 A:430-525 Psd-95                                                                        d1kjwa2 A:526-724 Guanylate kinase-like domain of Psd-95                                                                                                                                                SCOP domains
               CATH domains 1kjwA01 A:430-503,A:522-531,A:714-724 SH3 Domains                         ------------------1kjwA01   1kjwA02 A:532-562,A:624-713    1kjwA03 A:563-623 Guanylate Kinase phosphate binding domain  1kjwA02 A:532-562,A:624-713 P-loop containing nucleotide triphosphate hydrolases          1kjwA01     CATH domains
               Pfam domains --SH3_2-1kjwA02 A:432-496                                          ------------------------------------Guanylate_kin-1kjwA01 A:533-711                                                                                                                                                    ------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhh............eeeeee.....eeeeee..........eeeehhhhhhhhhhh...---................eeeeeeee......eeee..hhhhhhhhhhhhh...ee....ee..............ee..hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhh..eeee....hhhhhhhhh....eeeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhh..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------GUANYLATE_KINASE_2  PDB: A:534-709 UniProt: 534-709                                                                                                                             --------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------GUANYLATE_KINASE_1--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kjw A 430 GFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLK---WGSSSGSQGREDSVLSYETVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL 724
                                   439       449       459       469       479       489       499   |   509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719     
                                                                                                   503 507

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Guanylate Kinase phosphate binding domain (22)

Homologous Superfamily: Guanylate Kinase phosphate binding domain (22)

Norway rat (Rattus norvegicus) (3)

1kjwA03

A:563-623

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Norway rat (Rattus norvegicus) (38)

1kjwA02

A:532-562,A:624-713

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Norway rat (Rattus norvegicus) (12)

1kjwA01

A:430-503,A:522-531,A:714-724

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Guanylate_kin (23)

Rattus norvegicus (Rat) (7)

Guanylate_kin-1kjwA01

A:533-711

Clan: SH3 (175)

Family: SH3_2 (30)

Rattus norvegicus (Rat) (3)

SH3_2-1kjwA02

A:432-496

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DLG4_RAT | P31016)

molecular function
	GO:0031748	D1 dopamine receptor binding	Interacting selectively and non-covalently with a D1 dopamine receptor.
	GO:0031812	P2Y1 nucleotide receptor binding	Interacting selectively and non-covalently with a P2Y1 nucleotide receptor.
	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:0033130	acetylcholine receptor binding	Interacting selectively and non-covalently with an acetylcholine receptor.
	GO:0031697	beta-1 adrenergic receptor binding	Interacting selectively and non-covalently with a beta-1 adrenergic receptor.
	GO:0035254	glutamate receptor binding	Interacting selectively and non-covalently with a glutamate receptor.
	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:0097109	neuroligin family protein binding	Interacting selectively and non-covalently with a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0097110	scaffold protein binding	Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
biological process
	GO:0097113	AMPA glutamate receptor clustering	The glutamate receptor clustering process in which alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors are localized to distinct domains in the cell membrane.
	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:0060997	dendritic spine morphogenesis	The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	GO:0045184	establishment of protein localization	The directed movement of a protein to a specific location.
	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:0035641	locomotory exploration behavior	The specific movement from place to place of an organism in response to a novel environment.
	GO:0002091	negative regulation of receptor internalization	Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization.
	GO:0050885	neuromuscular process controlling balance	Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
	GO:0045161	neuronal ion channel clustering	The process in which voltage-gated ion channels become localized to distinct subcellular domains in the neuron. Specific targeting, clustering, and maintenance of these channels in their respective domains are essential to achieve high conduction velocities of action potential propagation.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:2000463	positive regulation of excitatory postsynaptic potential	Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
	GO:0050806	positive regulation of synaptic transmission	Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0035418	protein localization to synapse	Any process in which a protein 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.
	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.
	GO:2000310	regulation of NMDA receptor activity	Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity.
	GO:2000821	regulation of grooming behavior	Any process that modulates the frequency, rate or extent of grooming behavior.
	GO:0048169	regulation of long-term neuronal synaptic plasticity	A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
	GO:0035176	social behavior	Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
	GO:0016188	synaptic vesicle maturation	Steps required to form an initiated synaptic vesicle into a fully formed and transmissible synaptic vesicle.
	GO:0071625	vocalization behavior	The behavior in which an organism produces sounds by a mechanism involving its respiratory system.
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:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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: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:0032839	dendrite cytoplasm	All of the contents of a dendrite, excluding the surrounding plasma membrane.
	GO:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0060076	excitatory synapse	A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	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:0044224	juxtaparanode region of axon	A region of an axon near a node of Ranvier that is between the paranode and internode regions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0044306	neuron projection terminus	The specialized, terminal region of a neuron projection such as an axon or a dendrite.
	GO:0044309	neuron spine	A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck.
	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.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

Asymmetric/Biological Unit
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		Gly A:713 - Pro A:714	[ RasMol ]

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	1kjw
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(no "Related Entries Specified in the PDB File" available for 1KJW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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