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(-) Description

Title :  CRYSTAL STRUCTURE OF CALCIUM-FREE HUMAN SORCIN: A MEMBER OF THE PENTA-EF-HAND PROTEIN FAMILY
 
Authors :  X. Xie
Date :  24 Aug 01  (Deposition) - 30 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Calcium-Binding Proteins, Penta-Ef-Hand, Pef, X-Ray, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xie, M. D. Dwyer, L. Swenson, M. H. Parker, M. C. Botfield
Crystal Structure Of Calcium-Free Human Sorcin: A Member Of The Penta-Ef-Hand Protein Family.
Protein Sci. V. 10 2419 2001
PubMed-ID: 11714909  |  Reference-DOI: 10.1110/PS.PS.36701
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SORCIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1JUO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 12)

Asymmetric/Biological Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.SORCN_HUMAN45-64
 
100-135
 
70-98
 
151-169
 		  8A:45-64
B:45-64
A:100-135
B:100-135
A:70-98
B:70-98
A:151-169
B:151-169
2EF_HAND_1PS00018 EF-hand calcium-binding domain.SORCN_HUMAN83-95
 
113-125
 		  4A:83-95
B:83-95
A:113-125
B:113-125

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002657292aENSE00000877269chr7:87849394-87849291104SORCN_HUMAN1-17170--
1.3ENST000002657293ENSE00000454471chr7:87848257-8784817484SORCN_HUMAN18-45282A:27-45
B:27-45		19
19
1.4ENST000002657294ENSE00001650311chr7:87846506-8784643770SORCN_HUMAN46-69242A:46-69
B:46-69		24
24
1.6aENST000002657296aENSE00001746532chr7:87840240-8784019744SORCN_HUMAN69-83152A:69-83
B:69-83		15
15
1.7cENST000002657297cENSE00001612675chr7:87839445-87839298148SORCN_HUMAN84-133502A:84-133
B:84-133		50
50
1.8aENST000002657298aENSE00001711742chr7:87838767-87838654114SORCN_HUMAN133-171392A:133-171
B:133-171		39
39
1.9aENST000002657299aENSE00001618133chr7:87837880-8783782259SORCN_HUMAN171-190202A:171-190
B:171-190		20
20
1.10eENST0000026572910eENSE00001811340chr7:87835819-878344331387SORCN_HUMAN191-19882A:191-198
B:191-198		8
8

(-) Sequences/Alignments

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
(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:172
 aligned with SORCN_HUMAN | P30626 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:172
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  
          SORCN_HUMAN    27 FPGQTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFNEFKELWAVLNGWRQHFISFDTDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKITFDDYIACCVKLRALTDSFRRRDTAQQGVVNFPYDDFIQCVMSV 198
               SCOP domains d1juoa_ A: Sorcin                                                                                                                                                            SCOP domains
               CATH domains 1juoA00 A:27-198 EF-hand                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh...eehhhhhhhhhhhhh........hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------EF_HAND_2           -----EF_HAND_2  PDB: A:70-98      -EF_HAND_2  PDB: A:100-135           ---------------EF_HAND_2          ----------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3           Exon 1.4  PDB: A:46-69  --------------Exon 1.7c  PDB: A:84-133 UniProt: 84-133          -------------------------------------Exon 1.9a           1.10e    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.6a      -------------------------------------------------Exon 1.8a  PDB: A:133-171              --------------------------- Transcript 1 (2)
                 1juo A  27 FPGQTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFNEFKELWAVLNGWRQHFISFDTDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKITFDDYIACCVKLRALTDSFRRRDTAQQGVVNFPYDDFIQCVMSV 198
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with SORCN_HUMAN | P30626 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:172
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  
          SORCN_HUMAN    27 FPGQTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFNEFKELWAVLNGWRQHFISFDTDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKITFDDYIACCVKLRALTDSFRRRDTAQQGVVNFPYDDFIQCVMSV 198
               SCOP domains d1juob_ B: Sorcin                                                                                                                                                            SCOP domains
               CATH domains 1juoB00 B:27-198 EF-hand                                                                                                                                                     CATH domains
           Pfam domains (1) ------------------EF_hand_6-1juoB03 B:45-102                                -EF_hand_5-1juoB01 B:104-163                                 ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------EF_hand_6-1juoB04 B:45-102                                -EF_hand_5-1juoB02 B:104-163                                 ----------------------------------- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------EF_HAND_2           -----EF_HAND_2  PDB: B:70-98      -EF_HAND_2  PDB: B:100-135           ---------------EF_HAND_2          ----------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3           Exon 1.4  PDB: B:46-69  --------------Exon 1.7c  PDB: B:84-133 UniProt: 84-133          -------------------------------------Exon 1.9a           1.10e    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.6a      -------------------------------------------------Exon 1.8a  PDB: B:133-171              --------------------------- Transcript 1 (2)
                 1juo B  27 FPGQTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDMSGTMGFNEFKELWAVLNGWRQHFISFDTDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKITFDDYIACCVKLRALTDSFRRRDTAQQGVVNFPYDDFIQCVMSV 198
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (53, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SORCN_HUMAN | P30626)
molecular function
    GO:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004198    calcium-dependent cysteine-type endopeptidase activity    Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
biological process
    GO:0001508    action potential    A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
    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:0042994    cytoplasmic sequestering of transcription factor    The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0006880    intracellular sequestering of iron ion    The process of binding or confining iron ions in an intracellular area such that they are separated from other components of a biological system.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0010459    negative regulation of heart rate    Any process that stops, prevents or reduces the frequency or rate of heart contraction.
    GO:0060315    negative regulation of ryanodine-sensitive calcium-release channel activity    Any process that decreases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    GO:2000678    negative regulation of transcription regulatory region DNA binding    Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0035774    positive regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051924    regulation of calcium ion transport    Any process that modulates the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0086004    regulation of cardiac muscle cell contraction    Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
    GO:0010649    regulation of cell communication by electrical coupling    Any process that modulates the frequency, rate or extent of cell communication via electrical coupling. Cell communication via electrical coupling is the process that mediates signaling interactions between one cell and another cell by transfer of current between their adjacent cytoplasms via intercellular protein channels.
    GO:1901844    regulation of cell communication by electrical coupling involved in cardiac conduction    Any process that modulates the frequency, rate or extent of cell communication by electrical coupling involved in cardiac conduction.
    GO:0008016    regulation of heart contraction    Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
    GO:1901841    regulation of high voltage-gated calcium channel activity    Any process that modulates the frequency, rate or extent of high voltage-gated calcium channel activity.
    GO:1901077    regulation of relaxation of muscle    Any process that modulates the frequency, rate or extent of relaxation of muscle.
    GO:0010880    regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum    Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
    GO:0006942    regulation of striated muscle contraction    Any process that modulates the frequency, rate or extent of striated muscle contraction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030315    T-tubule    Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0042584    chromaffin granule membrane    The lipid bilayer surrounding a chromaffin granule, a 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: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:0044326    dendritic spine neck    Part of the dendritic spine that connects the dendritic shaft to the head of the dendritic spine.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0016529    sarcoplasmic reticulum    A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
    GO:0033017    sarcoplasmic reticulum membrane    The lipid bilayer surrounding the sarcoplasmic reticulum.
    GO:0005790    smooth endoplasmic reticulum    The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SORCN_HUMAN | P30626: 2jc2 4u8d 4upg 4usl

(-) Related Entries Specified in the PDB File

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