1G8I - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN FREQUENIN (NEURONAL CALCIUM SENSOR 1)

Authors :   Y. Bourne, J. Dannenberg, V. Pollmann, P. Marchot, O. Pongs

Date :   17 Nov 00 (Deposition) - 09 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Calcium Binding-Protein, Ef-Hand, Calcium Ion, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Bourne, J. Dannenberg, V. Pollmann, P. Marchot, O. Pongs
Immunocytochemical Localization And Crystal Structure Of Human Frequenin (Neuronal Calcium Sensor 1).
J. Biol. Chem. V. 276 11949 2001
PubMed-ID: 11092894 | Reference-DOI: 10.1074/JBC.M009373200
(for further references see the PDB file header)

Molecule 1 - NEURONAL CALCIUM SENSOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FREQUENIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	1PE	3	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	6	Ligand/Ion	CALCIUM ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	NA	2	Ligand/Ion	SODIUM ION
5	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	NA	-1	Ligand/Ion	SODIUM ION
5	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	NA	-1	Ligand/Ion	SODIUM ION
5	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR B:17 , THR B:20 , PHE B:22 , HOH B:568	BINDING SITE FOR RESIDUE NA B 1595
02	AC2	SOFTWARE	ALA A:175 , HOH A:501	BINDING SITE FOR RESIDUE NA A 1596
03	AC3	SOFTWARE	ASP A:73 , ASN A:75 , ASP A:77 , ARG A:79 , GLU A:84 , HOH A:733	BINDING SITE FOR RESIDUE CA A 1597
04	AC4	SOFTWARE	ASP A:109 , ASP A:111 , ASP A:113 , TYR A:115 , GLU A:120 , HOH A:507	BINDING SITE FOR RESIDUE CA A 1598
05	AC5	SOFTWARE	ASP A:157 , ASN A:159 , ASP A:161 , LYS A:163 , GLU A:168 , HOH A:565	BINDING SITE FOR RESIDUE CA A 1599
06	AC6	SOFTWARE	ASP B:73 , ASN B:75 , ASP B:77 , ARG B:79 , GLU B:84 , HOH B:696	BINDING SITE FOR RESIDUE CA B 1600
07	AC7	SOFTWARE	ASP B:109 , ASP B:111 , ASP B:113 , TYR B:115 , GLU B:120 , HOH B:583	BINDING SITE FOR RESIDUE CA B 1601
08	AC8	SOFTWARE	ASP B:157 , ASN B:159 , ASP B:161 , LYS B:163 , GLU B:168 , HOH B:701	BINDING SITE FOR RESIDUE CA B 1602
09	AC9	SOFTWARE	TYR A:108 , VAL A:125 , ARG A:148 , PHE A:169 , SER A:173 , ILE A:179 , LEU A:183 , HOH A:676 , HOH A:735 , 1PE A:952	BINDING SITE FOR RESIDUE 1PE A 951
10	BC1	SOFTWARE	THR A:92 , TRP A:103 , HOH A:676 , HOH A:710 , 1PE A:951	BINDING SITE FOR RESIDUE 1PE A 952
11	BC2	SOFTWARE	TYR B:108 , ARG B:148 , PHE B:169 , SER B:173 , ILE B:179 , LEU B:183 , HOH B:627 , HOH B:737	BINDING SITE FOR RESIDUE 1PE B 953
12	BC3	SOFTWARE	TRP A:30 , PHE A:85 , LEU A:89 , SER A:93 , ARG A:94 , ASP A:187 , HOH A:755	BINDING SITE FOR RESIDUE P6G A 954
13	BC4	SOFTWARE	GLU A:26 , TYR A:186 , HOH A:541	BINDING SITE FOR RESIDUE EDO A 901
14	BC5	SOFTWARE	PHE B:22 , TRP B:30 , SER B:93 , ASP B:187	BINDING SITE FOR RESIDUE EDO B 902

(no "SS Bond" information available for 1G8I)

(no "Cis Peptide Bond" information available for 1G8I)

(no "SAP(SNP)/Variant" information available for 1G8I)

Asymmetric Unit (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	NCS1_HUMAN	60-95 96-131 144-179	6	A:60-95 B:60-95 A:96-131 B:96-131 A:144-179 B:144-179
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	NCS1_HUMAN	73-85 109-121 157-169	6	A:73-85 B:73-85 A:109-121 B:109-121 A:157-169 B:157-169

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	NCS1_HUMAN	60-95 96-131 144-179	3	A:60-95 - A:96-131 - A:144-179 -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	NCS1_HUMAN	73-85 109-121 157-169	3	A:73-85 - A:109-121 - A:157-169 -

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	NCS1_HUMAN	60-95 96-131 144-179	3	- B:60-95 - B:96-131 - B:144-179
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	NCS1_HUMAN	73-85 109-121 157-169	3	- B:73-85 - B:109-121 - B:157-169

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000372398	1	ENSE00001457688	chr9:132934857-132935006	150	NCS1_HUMAN	1-22	22	2	A:4-22 B:3-22	19 20
1.4	ENST00000372398	4	ENSE00001052774	chr9:132963237-132963261	25	NCS1_HUMAN	22-30	9	2	A:22-30 B:22-30	9 9
1.5b	ENST00000372398	5b	ENSE00000927338	chr9:132980111-132980249	139	NCS1_HUMAN	30-76	47	2	A:30-76 B:30-76	47 47
1.6	ENST00000372398	6	ENSE00000927339	chr9:132982004-132982082	79	NCS1_HUMAN	77-103	27	2	A:77-103 B:77-103	27 27
1.7	ENST00000372398	7	ENSE00000927340	chr9:132984929-132985017	89	NCS1_HUMAN	103-132	30	2	A:103-132 B:103-132	30 30
1.8	ENST00000372398	8	ENSE00000927341	chr9:132985361-132985438	78	NCS1_HUMAN	133-158	26	2	A:138-158 B:133-158	21 26
1.9	ENST00000372398	9	ENSE00001052772	chr9:132988668-132988783	116	NCS1_HUMAN	159-190	32	2	A:159-190 B:159-188	32 30
1.10	ENST00000372398	10	ENSE00001457687	chr9:132995269-132999583	4315	NCS1_HUMAN	-	0	0	-	-

Asymmetric 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:182
 aligned with NCS1_HUMAN | P62166 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       
           NCS1_HUMAN     4 SNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQMVGNTVELPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDGLV 190
               SCOP domains d1g8ia_ A: Frequenin (neuronal calcium sensor 1)                                                                                                                                            SCOP domains
               CATH domains --------1g8iA01 A:12-96 EF-hand                                                              1g8iA02 A:97-189 EF-hand                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhh-----.hhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_2  PDB: A:60-95             EF_HAND_2  PDB: A:96-131            ------------EF_HAND_2  PDB: A:144-179           ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------------------EF_HAND_1    --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1           -------Exon 1.5b  PDB: A:30-76 UniProt: 30-76         Exon 1.6  PDB: A:77-103    -----------------------------Exon 1.8  PDB: A:138-158  Exon 1.9  PDB: A:159-190         Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.4 ------------------------------------------------------------------------Exon 1.7  PDB: A:103-132      ---------------------------------------------------------- Transcript 1 (2)
                 1g8i A   4 SNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQMV-----LPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDGLV 190
                                    13        23        33        43        53        63        73        83        93       103       113       123        |-    |  143       153       163       173       183       
                                                                                                                                                          132   138

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with NCS1_HUMAN | P62166 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           NCS1_HUMAN     3 KSNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQMVGNTVELPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDG 188
               SCOP domains d1g8ib_ B: Frequenin (neuronal calcium sensor 1)                                                                                                                                           SCOP domains
               CATH domains ---------1g8iB01 B:12-96 EF-hand                                                              1g8iB02 B:97-187 EF-hand                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh...hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------EF_HAND_2  PDB: B:60-95             EF_HAND_2  PDB: B:96-131            ------------EF_HAND_2  PDB: B:144-179           --------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    -----------------------------------EF_HAND_1    ------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:3-2-------Exon 1.5b  PDB: B:30-76 UniProt: 30-76         Exon 1.6  PDB: B:77-103    -----------------------------Exon 1.8  PDB: B:133-158  Exon 1.9  PDB: B:159-188       Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.4 ------------------------------------------------------------------------Exon 1.7  PDB: B:103-132      -------------------------------------------------------- Transcript 1 (2)
                 1g8i B   3 KSNSKLKPEVVEELTRKTYFTEKEVQQWYKGFIKDCPSGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDENKDGRIEFSEFIQALSVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQMVGNTVELPEEENTPEKRVDRIFAMMDKNADGKLTLQEFQEGSKADPSIVQALSLYDG 188
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Frequenin (neuronal calcium sensor 1) (5)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1g8ia_	A:
1b	d1g8ib_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Human (Homo sapiens) (106)

1a	1g8iA01	A:12-96
1b	1g8iB02	B:97-187
1c	1g8iA02	A:97-189
1d	1g8iB01	B:12-96

(no "Pfam Domain" information available for 1G8I)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NCS1_HUMAN | P62166)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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).
	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:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0045921	positive regulation of exocytosis	Any process that activates or increases the frequency, rate or extent of exocytosis.
	GO:0010975	regulation of neuron projection development	Any process that modulates 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).
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0031045	dense core granule	Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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: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: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:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	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.

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	1g8i
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	NCS1_HUMAN \| P62166
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NCS1_HUMAN \| P62166	:	2lcp 4guk

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 12)

Exons (7, 14)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (26, 26)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File