1LV4 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   HUMAN CATESTATIN 21-MER

Authors :   D. T. O'Connor, N. E. Preece

Date :   24 May 02 (Deposition) - 19 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (25x)

Keywords :   Glycoprotein, Amidation, Phosphorylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. E. Preece, M. Nguyen, M. Mahata, S. K. Mahata, N. R. Mahapatra, I. Tsigelny, D. T. O'Connor
Conformational Preferences And Activities Of Peptides From The Catecholamine Release-Inhibitory (Catestatin) Region Of Chromogranin A.
Regul. Pept. V. 118 75 2004
PubMed-ID: 14759560 | Reference-DOI: 10.1016/J.REGPEP.2003.10.035
(for further references see the PDB file header)

Molecule 1 - CATESTATIN
	Chains	:	A
	Engineered	:	YES
	Fragment	:	RESIDUES 370-390
	Other Details	:	SOLID-PHASE SYNTHESIS. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS.
	Synonym	:	CHROMOGRANIN A
	Synthetic	:	YES


NMR Structure (25x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1LV4)

(no "Site" information available for 1LV4)

(no "SS Bond" information available for 1LV4)

NMR Structure

No.	Model	Residues
1	1, 4, 7, 10, 11, 14, 16, 25	Arg A:8	-	Ala A:9
2	1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25	Gly A:16	-	Pro A:17
3	1, 2, 4, 6, 7, 8, 10, 11, 12, 14, 15, 22, 23, 24	Pro A:19	-	Gln A:20
4	2, 7, 14	Ser A:2	-	Met A:3
5	2, 3, 10, 11, 12, 13, 15, 17, 19, 23, 24, 25	Ser A:6	-	Phe A:7
6	2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25	Gly A:18	-	Pro A:19
7	3, 6, 8, 13, 20, 22, 23, 25	Lys A:4	-	Leu A:5
8	3, 16, 17, 18	Ala A:11	-	Tyr A:12
9	4, 8, 9, 10, 12, 13	Met A:3	-	Lys A:4
10	4, 11, 12, 20, 24	Tyr A:12	-	Gly A:13
11	5, 9, 16, 18, 19, 24, 25	Phe A:7	-	Arg A:8
12	5, 9, 13, 15, 22, 23	Ala A:9	-	Arg A:10
13	6, 20	Phe A:14	-	Arg A:15
14	9	Gly A:13	-	Phe A:14
15	10, 12, 24	Pro A:17	-	Gly A:18
16	20, 23	Leu A:5	-	Ser A:6

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025643	G	382	S	CMGA_HUMAN	Polymorphism	9658667	A	G	13	S
2	UniProt	VAR_025644	P	388	L	CMGA_HUMAN	Polymorphism	9658668	A	P	19	L

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

(no "PROSITE Motif" information available for 1LV4)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000216492	1	ENSE00001362941	chr14:93389445-93389750	306	CMGA_HUMAN	1-16	16	0	-	-
1.2	ENST00000216492	2	ENSE00000808703	chr14:93390544-93390590	47	CMGA_HUMAN	16-31	16	0	-	-
1.3	ENST00000216492	3	ENSE00000808704	chr14:93392950-93393043	94	CMGA_HUMAN	32-63	32	0	-	-
1.4	ENST00000216492	4	ENSE00001098306	chr14:93393895-93393963	69	CMGA_HUMAN	63-86	24	0	-	-
1.5	ENST00000216492	5	ENSE00000659901	chr14:93396062-93396160	99	CMGA_HUMAN	86-119	34	0	-	-
1.6	ENST00000216492	6	ENSE00000659902	chr14:93397595-93398047	453	CMGA_HUMAN	119-270	152	0	-	-
1.7	ENST00000216492	7	ENSE00000659903	chr14:93398715-93399196	482	CMGA_HUMAN	270-430	161	1	A:1-21	21
1.8	ENST00000216492	8	ENSE00001098305	chr14:93401146-93401636	491	CMGA_HUMAN	431-457	27	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:21
 aligned with CMGA_HUMAN | P10645 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:21
                                   379       389 
           CMGA_HUMAN   370 SSMKLSFRARAYGFRGPGPQL 390
               SCOP domains d1lv4a_ A:            SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains Granin-1lv4A01 A:1-21 Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) ------------S-----L-- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
               Transcript 1 Exon 1.7  PDB: A:1-21 Transcript 1
                 1lv4 A   1 SSMKLSFRARAYGFRGPGPQL  21
                                    10        20

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: Peptides (792)

Fold: Catestatin fragment from chromogranin A (2)

Superfamily: Catestatin fragment from chromogranin A (2)

Family: Catestatin fragment from chromogranin A (2)

Protein domain: Catestatin fragment from chromogranin A (2)

Synthetic, human sequence-based (2)

d1lv4a_

(no "CATH Domain" information available for 1LV4)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Granin] (2)

Family: Granin (2)

Homo sapiens (Human) (1)

Granin-1lv4A01

A:1-21

NMR Structure(hide GO term definitions)

Chain A (CMGA_HUMAN | P10645)

biological process
	GO:0086030	adrenergic receptor signaling pathway involved in cardiac muscle relaxation	An adrenergic receptor signaling pathway that contributes to a reduction in cardiac muscle contraction. Beta-adrenergic receptor-induced cardiac relaxation is achieved by a GPCR-activated adenylate cyclase generating cAMP; cAMP then activates the cAMP-dependent protein kinase A (PKA), which phosphorylates the sarcoplasmic reticulum (SR) membrane protein PLB. In its non-phosphorylated state, PLB acts as an inhibitor of the ATPase Ca(2+) pump of the cardiac SR (SERCA2a); inhibition of the pump is relieved upon phosphorylation. The pump removes Ca(2+) from the cytoplasm, thereby preventing cytosolic Ca(2+)-dependent activation of contractile proteins, leading to enhanced muscle relaxation.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
	GO:0045576	mast cell activation	The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors.
	GO:0002551	mast cell chemotaxis	The movement of a mast cell in response to an external stimulus.
	GO:0032762	mast cell cytokine production	Any process that contributes to cytokine production by a mast cell.
	GO:0043303	mast cell degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a mast cell.
	GO:0033604	negative regulation of catecholamine secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine.
	GO:1901215	negative regulation of neuron death	Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
	GO:0006996	organelle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
	GO:0042698	ovulation cycle	The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
	GO:0030816	positive regulation of cAMP metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0060452	positive regulation of cardiac muscle contraction	Any process that increases the frequency, rate or extent of cardiac muscle contraction.
	GO:2000707	positive regulation of dense core granule biogenesis	Any process that activates or increases the frequency, rate or extent of dense core granule biogenesis.
	GO:1900738	positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of phospholipase C-activating G-protein coupled receptor signaling pathway.
	GO:1901899	positive regulation of relaxation of cardiac muscle	Any process that activates or increases the frequency, rate or extent of relaxation of cardiac muscle.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	GO:0002026	regulation of the force of heart contraction	Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
cellular component
	GO:0042583	chromaffin granule	Specialized secretory vesicle found in the cells of adrenal glands and various other organs, which is concerned with the synthesis, storage, metabolism, and secretion of epinephrine and norepinephrine.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0042629	mast cell granule	Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
	GO:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

NMR Structure
	Complete Structure
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 1lv4)

	Cis Peptide Bonds
		Ala A:11 - Tyr A:12	[ RasMol ]
		Ala A:9 - Arg A:10	[ RasMol ]
		Arg A:8 - Ala A:9	[ RasMol ]
		Gly A:13 - Phe A:14	[ RasMol ]
		Gly A:16 - Pro A:17	[ RasMol ]
		Gly A:18 - Pro A:19	[ RasMol ]
		Leu A:5 - Ser A:6	[ RasMol ]
		Lys A:4 - Leu A:5	[ RasMol ]
		Met A:3 - Lys A:4	[ RasMol ]
		Phe A:14 - Arg A:15	[ RasMol ]
		Phe A:7 - Arg A:8	[ RasMol ]
		Pro A:17 - Gly A:18	[ RasMol ]
		Pro A:19 - Gln A:20	[ RasMol ]
		Ser A:2 - Met A:3	[ RasMol ]
		Ser A:6 - Phe A:7	[ RasMol ]
		Tyr A:12 - Gly A:13	[ RasMol ]

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	1lv4
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1cfk	HOMOLOGY MODEL
1krk	CYCLIC VERSION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (16, 126)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (32, 32)

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