2FN5 - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

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Title :   NMR STRUCTURE OF THE NEURABIN PDZ DOMAIN (502-594)

Authors :   B. Dancheck, W. Peti

Date :   10 Jan 06 (Deposition) - 09 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Pdz, Neurabin, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Kelker, B. Dancheck, T. Ju, R. P. Kessler, J. Hudak, A. C. Nairn, W. Peti
Structural Basis For Spinophilin-Neurabin Receptor Interaction.
Biochemistry V. 46 2333 2007
PubMed-ID: 17279777 | Reference-DOI: 10.1021/BI602341C
(for further references see the PDB file header)

Molecule 1 - NEURABIN-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cell Line	:	IRL
	Expression System Plasmid	:	RP1B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN
	Gene	:	PPP1R9A
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	NEURABIN-I, NEURAL TISSUE-SPECIFIC F-ACTIN BINDING PROTEIN I, PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 9A, P180, PP1BP175


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2FN5)

(no "Site" information available for 2FN5)

(no "SS Bond" information available for 2FN5)

(no "Cis Peptide Bond" information available for 2FN5)

(no "SAP(SNP)/Variant" information available for 2FN5)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	NEB1_RAT	505-593	1	A:7-94

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000011756	1	ENSRNOE00000234466	chr4:29656850-29658247	1398	NEB1_RAT	1-466	466	0	-	-
1.2	ENSRNOT00000011756	2	ENSRNOE00000234458	chr4:29818404-29818536	133	NEB1_RAT	467-511	45	1	A:1-13	13
1.3	ENSRNOT00000011756	3	ENSRNOE00000234449	chr4:29827866-29827986	121	NEB1_RAT	511-551	41	1	A:13-53	41
1.4	ENSRNOT00000011756	4	ENSRNOE00000234443	chr4:29836250-29836274	25	NEB1_RAT	551-559	9	1	A:53-61	9
1.5	ENSRNOT00000011756	5	ENSRNOE00000234429	chr4:29836279-29836320	42	NEB1_RAT	560-573	14	1	A:62-75	14
1.6	ENSRNOT00000011756	6	ENSRNOE00000234423	chr4:29836325-29836356	32	NEB1_RAT	574-584	11	1	A:76-86	11
1.7	ENSRNOT00000011756	7	ENSRNOE00000234414	chr4:29845516-29845651	136	NEB1_RAT	584-629	46	1	A:86-94	9
1.8	ENSRNOT00000011756	8	ENSRNOE00000234405	chr4:29868210-29868365	156	NEB1_RAT	630-681	52	0	-	-
1.9	ENSRNOT00000011756	9	ENSRNOE00000234396	chr4:29880214-29880267	54	NEB1_RAT	682-699	18	0	-	-
1.10b	ENSRNOT00000011756	10b	ENSRNOE00000287107	chr4:29882803-29883032	230	NEB1_RAT	700-776	77	0	-	-
1.11	ENSRNOT00000011756	11	ENSRNOE00000234490	chr4:29884329-29884425	97	NEB1_RAT	776-808	33	0	-	-
1.12	ENSRNOT00000011756	12	ENSRNOE00000234485	chr4:29884519-29884690	172	NEB1_RAT	809-866	58	0	-	-
1.15	ENSRNOT00000011756	15	ENSRNOE00000233971	chr4:29902418-29902575	158	NEB1_RAT	866-918	53	0	-	-
1.16	ENSRNOT00000011756	16	ENSRNOE00000083456	chr4:29924526-29924645	120	NEB1_RAT	919-958	40	0	-	-
1.17	ENSRNOT00000011756	17	ENSRNOE00000233957	chr4:29925420-29925443	24	NEB1_RAT	959-966	8	0	-	-
1.18	ENSRNOT00000011756	18	ENSRNOE00000083487	chr4:29926495-29926677	183	NEB1_RAT	967-1027	61	0	-	-
1.19	ENSRNOT00000011756	19	ENSRNOE00000083535	chr4:29927942-29928142	201	NEB1_RAT	1028-1093	66	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:94
 aligned with NEB1_RAT | O35867 from UniProtKB/Swiss-Prot  Length:1095

    Alignment length:94
                                   508       518       528       538       548       558       568       578       588    
             NEB1_RAT   499 EKLELFPVELEKDEDGLGISIIGMGVGADAGLEKLGIFVKTVTEGGAAQRDGRIQVNDQIVEVDGISLVGVTQNFAATVLRNTKGNVRFVIGRE 592
               SCOP domains d2fn5a_ A: automated matches                                                                   SCOP domains
               CATH domains 2fn5A00 A:1-94  [code=2.30.42.10, no name defined]                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeee.............eeeee..................eeee........hhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: A:7-94 UniProt: 505-593                                                        PROSITE
           Transcript 1 (1) Exon 1.2     ---------------------------------------Exon 1.4 Exon 1.5      Exon 1.6   -------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: A:13-53 UniProt: 511-551  --------------------------------Exon 1.7  Transcript 1 (2)
                 2fn5 A   1 GHMELFPVELEKDEDGLGISIIGMGVGADAGLEKLGIFVKTVTEGGAAQRDGRIQVNDQIVEVDGISLVGVTQNFAATVLRNTKGNVRFVIGRE  94
                                    10        20        30        40        50        60        70        80        90

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(

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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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (9)

d2fn5a_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

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

Norway rat (Rattus norvegicus) (26)

2fn5A00

A:1-94

(no "Pfam Domain" information available for 2FN5)

NMR Structure(hide GO term definitions)

Chain A (NEB1_RAT | O35867)

molecular function
	GO:0051020	GTPase binding	Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	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: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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0008157	protein phosphatase 1 binding	Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
biological process
	GO:0007015	actin filament organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0097237	cellular response to toxic substance	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
	GO:0060079	excitatory postsynaptic potential	A process that leads to 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:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:1900272	negative regulation of long-term synaptic potentiation	Any process that stops, prevents or reduces the frequency, rate or extent of long-term synaptic potentiation.
	GO:1904049	negative regulation of spontaneous neurotransmitter secretion	Any process that stops, prevents or reduces the frequency, rate or extent of spontaneous neurotransmitter secretion.
	GO:0051497	negative regulation of stress fiber assembly	Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly a stress fiber, a bundle of microfilaments and other proteins found in fibroblasts.
	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:0048666	neuron development	The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
	GO:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0060999	positive regulation of dendritic spine development	Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
	GO:1900454	positive regulation of long term synaptic depression	Any process that activates or increases the frequency, rate or extent of long term synaptic depression.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0030833	regulation of actin filament polymerization	Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
	GO:0061001	regulation of dendritic spine morphogenesis	Any process that modulates the rate, frequency, or extent of 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:0051489	regulation of filopodium assembly	Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	GO:0051963	regulation of synapse assembly	Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
	GO:0051823	regulation of synapse structural plasticity	Any process that modulates the frequency, rate or extent of synapse structural plasticity. Synapse structural plasticity is a type of cytoskeletal remodeling; this remodeling is induced by stimuli that can lead to long term potentiation and it can be activity-dependent or -independent. Examples of cytoskeletal changes include the formation of new spines and increase in spine size; this can be accompanied by the insertion of greater numbers of glutamate (or other neurotransmitter) receptors into the post-synaptic membrane.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	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:0030864	cortical actin cytoskeleton	The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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:0044326	dendritic spine neck	Part of the dendritic spine that connects the dendritic shaft to the head of the dendritic spine.
	GO:0030175	filopodium	Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:1990761	growth cone lamellipodium	A thin sheetlike process extended by the leading edge of an axonal or dendritic growth cone; contains a dense meshwork of actin filaments.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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: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.

NMR Structure
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	2fn5
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	NEB1_RAT \| O35867	:	2gle 3hvq

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