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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF HARMONIN PDZ2 IN COMPLEX WITH THE CARBOXYL TAIL PEPTIDE OF CADHERIN23

Authors :   L. Pan, J. Yan, L. Wu, M. Zhang

Date :   05 Dec 08 (Deposition) - 31 Mar 09 (Release) - 21 Apr 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

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

Keywords :   Protein Complex, Alternative Splicing, Coiled Coil, Deafness, Hearing, Non-Syndromic Deafness, Polymorphism, Retinitis Pigmentosa, Sensory Transduction, Usher Syndrome, Vision, Calcium, Cell Adhesion, Cell Membrane, Disease Mutation, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Structural Protein/Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Pan, J. Yan, L. Wu, M. Zhang
Assembling Stable Hair Cell Tip Link Complex Via Multidentate Interactions Between Harmonin And Cadherin 23
Proc. Natl. Acad. Sci. Usa V. 106 5575 2009
PubMed-ID: 19297620 | Reference-DOI: 10.1073/PNAS.0901819106
(for further references see the PDB file header)

Molecule 1 - HARMONIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET32A
	Expression System Vector Type	:	VECTOR
	Fragment	:	PDZ2 DOMAIN, UNP RESIDUES 208-299
	Gene	:	HARMONIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	USHER SYNDROME TYPE-1C PROTEIN, AUTOIMMUNE ENTEROPATHY-RELATED ANTIGEN AIE-75, ANTIGEN NY-CO-38/NY-CO- 37, PDZ-73 PROTEIN, RENAL CARCINOMA ANTIGEN NY-REN-3

Molecule 2 - OCTAMERIC PEPTIDE FROM CADHERIN-23
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET32A
	Expression System Vector Type	:	VECTOR
	Fragment	:	CARBOXYL TAIL, UNP RESIDUES 3347-3354
	Gene	:	CADHERIN23
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	OTOCADHERIN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2KBS)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	USH1C_HUMAN	87-155 211-281 452-525	1	- A:12-82 -

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000318024	1a	ENSE00001481272	chr11:17565963-17565819	145	USH1C_HUMAN	1-12	12	0	-	-
1.3b	ENST00000318024	3b	ENSE00001356343	chr11:17554869-17554802	68	USH1C_HUMAN	13-35	23	0	-	-
1.4b	ENST00000318024	4b	ENSE00000705394	chr11:17553089-17552946	144	USH1C_HUMAN	35-83	49	0	-	-
1.5a	ENST00000318024	5a	ENSE00000705392	chr11:17552839-17552701	139	USH1C_HUMAN	83-129	47	0	-	-
1.6	ENST00000318024	6	ENSE00000705391	chr11:17548878-17548770	109	USH1C_HUMAN	130-166	37	0	-	-
1.7	ENST00000318024	7	ENSE00000705390	chr11:17548587-17548563	25	USH1C_HUMAN	166-174	9	0	-	-
1.8	ENST00000318024	8	ENSE00000705389	chr11:17548357-17548300	58	USH1C_HUMAN	174-193	20	0	-	-
1.9	ENST00000318024	9	ENSE00000705388	chr11:17547988-17547894	95	USH1C_HUMAN	194-225	32	1	A:9-26	18
1.10	ENST00000318024	10	ENSE00000705386	chr11:17546082-17545998	85	USH1C_HUMAN	225-253	29	1	A:26-54	29
1.11	ENST00000318024	11	ENSE00000705385	chr11:17545025-17544966	60	USH1C_HUMAN	254-273	20	1	A:55-74	20
1.12	ENST00000318024	12	ENSE00000705384	chr11:17544814-17544758	57	USH1C_HUMAN	274-292	19	1	A:75-93	19
1.13c	ENST00000318024	13c	ENSE00000705383	chr11:17544473-17544331	143	USH1C_HUMAN	293-340	48	1	A:94-100	7
1.14	ENST00000318024	14	ENSE00000705382	chr11:17542958-17542893	66	USH1C_HUMAN	340-362	23	0	-	-
1.15a	ENST00000318024	15a	ENSE00000339040	chr11:17542541-17542417	125	USH1C_HUMAN	362-404	43	0	-	-
1.16	ENST00000318024	16	ENSE00000705380	chr11:17539021-17538948	74	USH1C_HUMAN	404-428	25	0	-	-
1.25b	ENST00000318024	25b	ENSE00000705348	chr11:17523527-17523486	42	USH1C_HUMAN	429-442	14	0	-	-
1.26	ENST00000318024	26	ENSE00000705285	chr11:17523082-17523029	54	USH1C_HUMAN	443-460	18	0	-	-
1.27b	ENST00000318024	27b	ENSE00000705266	chr11:17522697-17522598	100	USH1C_HUMAN	461-494	34	0	-	-
1.28	ENST00000318024	28	ENSE00000705265	chr11:17519818-17519709	110	USH1C_HUMAN	494-530	37	0	-	-
1.29b	ENST00000318024	29b	ENSE00001386158	chr11:17518360-17518305	56	USH1C_HUMAN	531-549	19	0	-	-
1.31h	ENST00000318024	31h	ENSE00002163620	chr11:17515923-17515442	482	USH1C_HUMAN	549-552	4	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:92
 aligned with USH1C_HUMAN | Q9Y6N9 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:92
                                   217       227       237       247       257       267       277       287       297  
         USH1C_HUMAN    208 KEKKVFISLVGSRGLGCSISSGPIQKPGIFISHVKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVNVLKSSRSLTISIVAAAGRELFMT  299
               SCOP domains d2kbsa_ A: automated matches                                                                 SCOP domains
               CATH domains 2kbsA00 A:9-100  [code=2.30.42.10, no name defined]                                          CATH domains
               Pfam domains ---PDZ-2kbsA01 A:12-91                                                             --------- Pfam domains
         Sec.struct. author .eeeeee.........eeeee.......eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeee...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:12-82 UniProt: 211-281                                     ------------------ PROSITE
           Transcript 1 (1) -----------------Exon 1.10  PDB: A:26-54      Exon 1.11           Exon 1.12          1.13c   Transcript 1 (1)
           Transcript 1 (2) Exon 1.9          -------------------------------------------------------------------------- Transcript 1 (2)
                2kbs A    9 KEKKVFISLVGSRGLGCSISSGPIQKPGIFISHVKPGSLSAEVGLEIGDQIVEVNGVDFSNLDHKEAVNVLKSSRSLTISIVAAAGRELFMT  100
                                    18        28        38        48        58        68        78        88        98

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with CAD23_HUMAN | Q9H251 from UniProtKB/Swiss-Prot  Length:3354

    Alignment length:8
         CAD23_HUMAN   3347 TPLEITEL 3354
               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
                2kbs B  111 TPLEITEL  118

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	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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

d2kbsa_

NMR Structure

Classes(

)

Architectures( (-)

)

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)

2kbsA00

A:9-100

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

PDZ-2kbsA01

A:12-91

NMR Structure(hide GO term definitions)

Chain A (USH1C_HUMAN | Q9Y6N9)

molecular function
	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:0032029	myosin tail binding	Interacting selectively and non-covalently with the tail region of a myosin heavy chain.
	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:0030507	spectrin binding	Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
	GO:0000086	G2/M transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	GO:1904970	brush border assembly	The aggregation, arrangement and bonding together of adjacent microvilli through the formation of Ca(2+)-dependent adhesion links between them, forming a brush border.
	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:0043623	cellular protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
	GO:0050957	equilibrioception	The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion.
	GO:0045494	photoreceptor cell maintenance	Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
	GO:1904106	protein localization to microvillus	A process in which a protein is transported to, or maintained in, a location within a microvillus.
	GO:0032532	regulation of microvillus length	A process that modulates the length of a microvillus.
	GO:0050953	sensory perception of light stimulus	The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
	GO:0007605	sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	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: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:0005902	microvillus	Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
	GO:0001917	photoreceptor inner segment	The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
	GO:0001750	photoreceptor outer segment	The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
	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: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.
	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 B (CAD23_HUMAN | Q9H251)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0016339	calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	The attachment of one cell to another cell via adhesion molecules that require the presence of calcium for the interaction.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0050957	equilibrioception	The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion.
	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
	GO:0060122	inner ear receptor stereocilium organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of inner ear receptor cells.
	GO:0007626	locomotory behavior	The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
	GO:0045494	photoreceptor cell maintenance	Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
	GO:0051480	regulation of cytosolic calcium ion concentration	Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0050953	sensory perception of light stimulus	The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
	GO:0007605	sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	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: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: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.

NMR Structure
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UniProtKB/Swiss-Prot
	CAD23_HUMAN \| Q9H251	:	2kbr 2lsr
	USH1C_HUMAN \| Q9Y6N9	:	1x5n 2kbq 2kbr 2lsr 3k1r 5f3x 5xbf

2kbq	HARMONIN N TERMINAL DOMAIN
2kbr	HARMONIN N TERMINAL DOMAIN IN COMPLEX WITH A INTERNAL PEPTIDE OF CADHERIN23

Description

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Ligands, Modified Residues, Ions (0, 0)

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Exons (5, 5)

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