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Title :   SOLUTION STRUCTURE OF THE FIRST C2 DOMAIN FROM HUMAN KIAA1005 PROTEIN

Authors :   T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   02 Apr 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Beta Sandwich, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The First C2 Domain From Human Kiaa1005 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN FANTOM
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050719-05
	Expression System Vector Type	:	PLASMID
	Fragment	:	C2 DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	KIAA1005 PROTEIN, RPGR-INTERACTING PROTEIN 1-LIKE PROTEIN, RPGRIP1-LIKE PROTEIN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2YRB)

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

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

NMR Structure (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_039393	T	615	P	FTM_HUMAN	Disease (JBTS7)	121918198	A	T	615	P
2	UniProt	VAR_076825	C	633	R	FTM_HUMAN	Disease (JBTS7)	---	A	C	633	R
3	UniProt	VAR_066480	V	647	I	FTM_HUMAN	Polymorphism	145572901	A	V	647	I
4	UniProt	VAR_063805	S	659	P	FTM_HUMAN	Disease (COACHS)	267607020	A	S	659	P
5	UniProt	VAR_039394	T	677	I	FTM_HUMAN	Disease (JBTS7)	532768944	A	T	677	I
6	UniProt	VAR_039395	A	695	P	FTM_HUMAN	Disease (JBTS7)	121918200	A	A	695	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2YRB)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000379925	1	ENSE00001519128	chr16:53737771-53737715	57	FTM_HUMAN	-	0	0	-	-
1.2	ENST00000379925	2	ENSE00001608510	chr16:53734642-53734551	92	FTM_HUMAN	1-29	29	0	-	-
1.3	ENST00000379925	3	ENSE00001746874	chr16:53730207-53730063	145	FTM_HUMAN	29-77	49	0	-	-
1.4	ENST00000379925	4	ENSE00001618773	chr16:53726276-53725978	299	FTM_HUMAN	77-177	101	0	-	-
1.5	ENST00000379925	5	ENSE00001483076	chr16:53721877-53721775	103	FTM_HUMAN	177-211	35	0	-	-
1.6	ENST00000379925	6	ENSE00001141083	chr16:53720488-53720345	144	FTM_HUMAN	211-259	49	0	-	-
1.7	ENST00000379925	7	ENSE00000852643	chr16:53709034-53708929	106	FTM_HUMAN	259-294	36	0	-	-
1.8	ENST00000379925	8	ENSE00000852644	chr16:53706928-53706782	147	FTM_HUMAN	295-343	49	0	-	-
1.9	ENST00000379925	9	ENSE00000852645	chr16:53705495-53705422	74	FTM_HUMAN	344-368	25	0	-	-
1.10	ENST00000379925	10	ENSE00001141059	chr16:53698921-53698782	140	FTM_HUMAN	368-415	48	0	-	-
1.11	ENST00000379925	11	ENSE00001141051	chr16:53692790-53692684	107	FTM_HUMAN	415-450	36	0	-	-
1.12	ENST00000379925	12	ENSE00001206164	chr16:53692376-53692326	51	FTM_HUMAN	451-467	17	0	-	-
1.13	ENST00000379925	13	ENSE00001141040	chr16:53691544-53691365	180	FTM_HUMAN	468-527	60	0	-	-
1.14	ENST00000379925	14	ENSE00001206157	chr16:53690501-53690384	118	FTM_HUMAN	528-567	40	0	-	-
1.15	ENST00000379925	15	ENSE00001108330	chr16:53686899-53686447	453	FTM_HUMAN	567-718	152	1	A:588-718	131
1.16	ENST00000379925	16	ENSE00001108326	chr16:53683027-53682876	152	FTM_HUMAN	718-768	51	1	A:718-740 (gaps)	46
1.17	ENST00000379925	17	ENSE00001108338	chr16:53679915-53679537	379	FTM_HUMAN	769-895	127	1	A:741-743	3
1.18	ENST00000379925	18	ENSE00001108337	chr16:53675387-53675197	191	FTM_HUMAN	895-958	64	0	-	-
1.19	ENST00000379925	19	ENSE00001108328	chr16:53675028-53674945	84	FTM_HUMAN	959-986	28	0	-	-
1.20	ENST00000379925	20	ENSE00001483058	chr16:53672323-53672222	102	FTM_HUMAN	987-1020	34	0	-	-
1.21	ENST00000379925	21	ENSE00001108336	chr16:53671766-53671607	160	FTM_HUMAN	1021-1074	54	0	-	-
1.22	ENST00000379925	22	ENSE00001108334	chr16:53670424-53670351	74	FTM_HUMAN	1074-1098	25	0	-	-
1.23	ENST00000379925	23	ENSE00001483054	chr16:53656268-53656131	138	FTM_HUMAN	1099-1144	46	0	-	-
1.24	ENST00000379925	24	ENSE00000684191	chr16:53653120-53652937	184	FTM_HUMAN	1145-1206	62	0	-	-
1.25	ENST00000379925	25	ENSE00000684189	chr16:53644963-53644879	85	FTM_HUMAN	1206-1234	29	0	-	-
1.26	ENST00000379925	26	ENSE00000684188	chr16:53639526-53639393	134	FTM_HUMAN	1234-1279	46	0	-	-
1.27	ENST00000379925	27	ENSE00001125799	chr16:53636100-53633824	2277	FTM_HUMAN	1279-1315	37	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
	(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:156
 aligned with FTM_HUMAN | Q68CZ1 from UniProtKB/Swiss-Prot  Length:1315

    Alignment length:195
                                   597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777     
            FTM_HUMAN   588 DDSVDEFDETIHLERGENLFEIHINKVTFSSEVLQASGDKEPVTFCTYAFYDFELQTTPVVRGLHPEYNFTSQYLVHVNDLFLQYIQKNTITLEVHQAYSTEYETIAACQLKFHEILEKSGRIFCTASLIGTKGDIPNFGTVEYWFRLRVPMDQAIRLYRERAKALGYITSNFKGPEHMQSLSQQAPKTAQLSST 782
               SCOP domains --------d2yrba1 A:596-737 Fantom                                                                                                                      --------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeeeee..hhhhhhhh.....eeeeee.......ee...ee.......eeeeeee..hhhhhhhhhhh.eeeeeeee....eeeeeeeee..hhhhhh...eeeeeee..........eeeeeeeeeee.-----------------------..----------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------P-----------------R-------------I-----------P-----------------I-----------------P--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15  PDB: A:588-718 UniProt: 567-718 [INCOMPLETE]                                                                            --------------------------------------------------Exon 1.17      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.16  PDB: A:718-740 (gaps) UniProt: 718-768  -------------- Transcript 1 (2)
                 2yrb A 588 GSSGSSGDETIHLERGENLFEIHINKVTFSSEVLQASGDKEPVTFCTYAFYDFELQTTPVVRGLHPEYNFTSQYLVHVNDLFLQYIQKNTITLEVHQAYSTEYETIAACQLKFHEILEKSGRIFCTASLIGTKGDIPNFGTVEYWFRLRVS-----------------------GP----------------SSG 743
                                   597       607       617       627       637       647       657       667       677       687       697       707       717       727       737|        -         -    ||   -         -  |  
                                                                                                                                                                                738                     739|              741  
                                                                                                                                                                                                         740

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: C2 domain (Calcium/lipid-binding domain, CaLB) (148)

Family: PLC-like (P variant) (81)

Protein domain: Fantom (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2yrba1

A:596-737

(no "CATH Domain" information available for 2YRB)

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

NMR Structure(hide GO term definitions)

Chain A (FTM_HUMAN | Q68CZ1)

molecular function
	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:0031870	thromboxane A2 receptor binding	Interacting selectively and non-covalently with a thromboxane A2 receptor.
biological process
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0021549	cerebellum development	The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
	GO:0060271	cilium assembly	The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
	GO:0090102	cochlea development	The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound.
	GO:0022038	corpus callosum development	The process whose specific outcome is the progression of the corpus callosum over time, from its formation to the mature structure. The corpus callosum is a thick bundle of nerve fibers comprising a commissural plate connecting the two cerebral hemispheres. It consists of contralateral axon projections that provide communication between the right and left cerebral hemispheres.
	GO:0007368	determination of left/right symmetry	The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.
	GO:0035115	embryonic forelimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
	GO:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	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:0007163	establishment or maintenance of cell polarity	Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
	GO:0060322	head development	The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	GO:0021670	lateral ventricle development	The process whose specific outcome is the progression of the lateral ventricles over time, from the formation to the mature structure. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle.
	GO:0035108	limb morphogenesis	The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0045744	negative regulation of G-protein coupled receptor protein signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
	GO:0021532	neural tube patterning	The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube.
	GO:0043584	nose development	The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity).
	GO:0021772	olfactory bulb development	The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex.
	GO:0060039	pericardium development	The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
	GO:0008589	regulation of smoothened signaling pathway	Any process that modulates the frequency, rate or extent of smoothened signaling.
	GO:0044767	single-organism developmental process	A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism.
	GO:0021537	telencephalon development	The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived.
cellular component
	GO:0005930	axoneme	The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
	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: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: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:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0036064	ciliary basal body	A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
	GO:0035869	ciliary transition zone	A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.
	GO:0005929	cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
	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:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.

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(no "Cis Peptide Bonds" information available for 2yrb)

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