2BE4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO DR.36843

Authors :   G. E. Wesenberg, G. N. Phillips Jr. , B. W. Han, E. Bitto, C. A. Bingman, E Center For Eukaryotic Structural Genomics (Cesg)

Date :   21 Oct 05 (Deposition) - 01 Nov 05 (Release) - 06 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Dr. 36843, Bc083168, Calicium Binding, Ef-Hand Superfamily, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Bitto, C. A. Bingman, L. Bittova, R. O. Frederick, B. G. Fox, G. N. Phillips Jr.
X-Ray Structure Of Danio Rerio Secretagogin: A Hexa-Ef-Hand Calcium Sensor.
Proteins V. 76 477 2009
PubMed-ID: 19241471 | Reference-DOI: 10.1002/PROT.22362

Molecule 1 - HYPOTHETICAL PROTEIN LOC449832
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP 16
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DR.36843, BC083168
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2BE4)

(no "SS Bond" information available for 2BE4)

(no "Cis Peptide Bond" information available for 2BE4)

(no "SAP(SNP)/Variant" information available for 2BE4)

Asymmetric/Biological Unit (2, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	SEGN_DANRE	8-43 53-89 101-136 145-180 193-228 237-272	6	A:8-43 A:53-89 A:101-136 A:145-180 A:193-228 A:237-272
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	SEGN_DANRE	21-33 114-126 158-170 206-218 250-262	5	A:21-33 A:114-126 A:158-170 A:206-218 A:250-262

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSDART00000081649	1	ENSDARE00000591909	chr16:7591269-7591115	155	SEGN_DANRE	1-24	24	1	A:3-24	22
1.2	ENSDART00000081649	2	ENSDARE00000591894	chr16:7590988-7590918	71	SEGN_DANRE	24-47	24	1	A:24-47	24
1.3	ENSDART00000081649	3	ENSDARE00000591881	chr16:7590114-7590022	93	SEGN_DANRE	48-78	31	1	A:48-78	31
1.4	ENSDART00000081649	4	ENSDARE00000591869	chr16:7582425-7582336	90	SEGN_DANRE	79-108	30	1	A:79-108	30
1.5	ENSDART00000081649	5	ENSDARE00000591865	chr16:7582258-7582202	57	SEGN_DANRE	109-127	19	1	A:109-127	19
1.6	ENSDART00000081649	6	ENSDARE00000591855	chr16:7579700-7579623	78	SEGN_DANRE	128-153	26	1	A:128-153	26
1.7	ENSDART00000081649	7	ENSDARE00000591848	chr16:7576718-7576663	56	SEGN_DANRE	154-172	19	1	A:154-172	19
1.8	ENSDART00000081649	8	ENSDARE00000591842	chr16:7575820-7575775	46	SEGN_DANRE	172-187	16	1	A:172-187	16
1.9	ENSDART00000081649	9	ENSDARE00000591836	chr16:7572866-7572807	60	SEGN_DANRE	188-207	20	1	A:188-207	20
1.10	ENSDART00000081649	10	ENSDARE00000591826	chr16:7572650-7572582	69	SEGN_DANRE	208-230	23	1	A:208-230	23
1.11	ENSDART00000081649	11	ENSDARE00000591818	chr16:7570886-7570047	840	SEGN_DANRE	231-272	42	1	A:231-272	42

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
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Chain A from PDB  Type:PROTEIN  Length:270
 aligned with SEGN_DANRE | Q5XJX1 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
           SEGN_DANRE     3 SAFANLDAAGFLQIWQHFDADDNGYIEGKELDDFFRHMLKKLQPKDKITDERVQQIKKSFMSAYDATFDGRLQIEELANMILPQEENFLLIFRREAPLDNSVEFMKIWRKYDADSSGYISAAELKNFLKDLFLQHKKKIPPNKLDEYTDAMMKIFDKNKDGRLDLNDLARILALQENFLLQFKMDASSQVERKRDFEKIFAHYDVSRTGALEGPEVDGFVKDMMELVRPSISGGDLDKFRECLLTHCDMNKDGKIQKSELALCLGLKHKP 272
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....eee..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....eeehhhhhhhh............hhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeehhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----EF_HAND_2  PDB: A:8-43 UniProt: 8-43---------EF_HAND_2  PDB: A:53-89              -----------EF_HAND_2  PDB: A:101-136           --------EF_HAND_2  PDB: A:145-180           ------------EF_HAND_2  PDB: A:193-228           --------EF_HAND_2  PDB: A:237-272            PROSITE (1)
                PROSITE (2) ------------------EF_HAND_1    --------------------------------------------------------------------------------EF_HAND_1    -------------------------------EF_HAND_1    -----------------------------------EF_HAND_1    -------------------------------EF_HAND_1    ---------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:3-24 -----------------------Exon 1.3  PDB: A:48-78         Exon 1.4  PDB: A:79-108       Exon 1.5           Exon 1.6  PDB: A:128-153  Exon 1.7           ---------------Exon 1.9            Exon 1.10              Exon 1.11  PDB: A:231-272 UniProt: 231-272 Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.2  PDB: A:24-47  ----------------------------------------------------------------------------------------------------------------------------Exon 1.8        ------------------------------------------------------------------------------------- Transcript 1 (2)
                 2be4 A   3 SAFANLDAAGFLQIWQHFDADDNGYIEGKELDDFFRHmLKKLQPKDKITDERVQQIKKSFmSAYDATFDGRLQIEELANmILPQEENFLLIFRREAPLDNSVEFmKIWRKYDADSSGYISAAELKNFLKDLFLQHKKKIPPNKLDEYTDAmmKIFDKNKDGRLDLNDLARILALQENFLLQFKmDASSQVERKRDFEKIFAHYDVSRTGALEGPEVDGFVKDmmELVRPSISGGDLDKFRECLLTHCDmNKDGKIQKSELALCLGLKHKP 272
                                    12        22        32       |42        52        62|       72        82        92       102    |  112       122       132       142       152||     162       172       182   |   192       202       212       222  ||   232       242       252       262       272
                                                                40-MSE                 63-MSE             82-MSE                  107-MSE                                       153-MSE                          186-MSE                                225-MSE                   251-MSE                 
                                                                                                                                                                                 154-MSE                                                                 226-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "SCOP Domain" information available for 2BE4)

(no "CATH Domain" information available for 2BE4)

(no "Pfam Domain" information available for 2BE4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SEGN_DANRE | Q5XJX1)

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.
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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.

Asymmetric/Biological Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 11)

Exons (11, 11)

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