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(-) Description

Title :  NMR STRUCTURE OF METAL-BINDING DOMAIN 1 OF ATP7B
 
Authors :  C. Yu, W. Lee, O. Dmitriev
Date :  27 Sep 15  (Deposition) - 28 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Copper Binding, Hydrolase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Yu, W. Lee, O. Dmitriev
Metal-Binding Domain 1 Of Atp7B
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COPPER-TRANSPORTING ATPASE 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB12
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentMETAL BINDING DOMAIN (UNP RESIDUES 56-127)
    GeneATP7B, PWD, WC1, WND
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOPPER PUMP 2, WILSON DISEASE-ASSOCIATED PROTEIN, WND/140 KDA

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2N7Y)

(-) Sites  (0, 0)

(no "Site" information available for 2N7Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2N7Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2N7Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000703G85VATP7B_HUMANDisease (WD)786204643AG34V
2UniProtVAR_000704G96DATP7B_HUMANPolymorphism  ---AG45D
3UniProtVAR_076730C108RATP7B_HUMANUnclassified (WD)  ---AC57R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000703G85VATP7B_HUMANDisease (WD)786204643AG34V
2UniProtVAR_000704G96DATP7B_HUMANPolymorphism  ---AG45D
3UniProtVAR_076730C108RATP7B_HUMANUnclassified (WD)  ---AC57R

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2N7Y)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002428391ENSE00002179667chr13:52585630-52585423208ATP7B_HUMAN1-17170--
1.5bENST000002428395bENSE00001793840chr13:52549304-525480711234ATP7B_HUMAN18-4294121A:1-76 (gaps)83
1.6ENST000002428396ENSE00001750372chr13:52544885-52544628258ATP7B_HUMAN429-515870--
1.7ENST000002428397ENSE00001626066chr13:52542743-52542580164ATP7B_HUMAN515-569550--
1.8aENST000002428398aENSE00001663793chr13:52539169-52539008162ATP7B_HUMAN570-623540--
1.9ENST000002428399ENSE00001778246chr13:52536049-5253597377ATP7B_HUMAN624-649260--
1.10ENST0000024283910ENSE00001797943chr13:52534458-52534284175ATP7B_HUMAN649-707590--
1.11ENST0000024283911ENSE00001661412chr13:52532680-52532447234ATP7B_HUMAN708-785780--
1.12ENST0000024283912ENSE00001780518chr13:52531743-5253165292ATP7B_HUMAN786-816310--
1.13ENST0000024283913ENSE00001691729chr13:52524535-52524408128ATP7B_HUMAN816-859440--
1.14ENST0000024283914ENSE00001628540chr13:52524297-52524143155ATP7B_HUMAN859-910520--
1.15ENST0000024283915ENSE00001610847chr13:52523932-52523798135ATP7B_HUMAN911-955450--
1.16bENST0000024283916bENSE00001682155chr13:52520614-52520420195ATP7B_HUMAN956-1020650--
1.17ENST0000024283917ENSE00001721174chr13:52518427-52518245183ATP7B_HUMAN1021-1081610--
1.18ENST0000024283918ENSE00001706162chr13:52516690-52516522169ATP7B_HUMAN1082-1138570--
1.19aENST0000024283919aENSE00001770820chr13:52515360-52515217144ATP7B_HUMAN1138-1186490--
1.20ENST0000024283920ENSE00001687534chr13:52513329-52513187143ATP7B_HUMAN1186-1233480--
1.21ENST0000024283921ENSE00001595712chr13:52511815-52511612204ATP7B_HUMAN1234-1301680--
1.22ENST0000024283922ENSE00001612752chr13:52511529-52511412118ATP7B_HUMAN1302-1341400--
1.23ENST0000024283923ENSE00001665491chr13:52509831-52509729103ATP7B_HUMAN1341-1375350--
1.24bENST0000024283924bENSE00001813320chr13:52509165-525068092357ATP7B_HUMAN1375-1465910--

(-) Sequences/Alignments

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:76
 aligned with ATP7B_HUMAN | P35670 from UniProtKB/Swiss-Prot  Length:1465

    Alignment length:83
                                    54        64        74        84        94       104       114       124   
          ATP7B_HUMAN    45 EGGLDGLGPSSQVATSTVRILGMTCQSCVKSIEDRISNLKGIISMKVSLEQGSATVKYVPSVVCLQQVCHQIGDMGFEASIAE 127
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------....eeeeeeee..hhhhhhhhhhhhhhhh....eeeee....eeeeee.....hhhhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------V----------D-----------R------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.5b  PDB: A:1-76 (gaps) UniProt: 18-429 [INCOMPLETE]                          Transcript 1
                 2n7y A   1 AG-------HMQVATSTVRILGMTCQSCVKSIEDRISNLKGIISMKVSLEQGSATVKYVPSVVCLQQVCHQIGDMGFEASIAE  76
                             |       3        13        23        33        43        53        63        73   
                             2       3                                                                         

   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  (0, 0)

(no "SCOP Domain" information available for 2N7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2N7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2N7Y)

(-) Gene Ontology  (43, 43)

NMR Structure(hide GO term definitions)
Chain A   (ATP7B_HUMAN | P35670)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019829    cation-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0005375    copper ion transmembrane transporter activity    Catalysis of the transfer of copper (Cu) ions from one side of a membrane to the other.
    GO:0004008    copper-exporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Cu2+(in) -> ADP + phosphate + Cu2+(out).
    GO:0043682    copper-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Cu2+ = ADP + phosphate + Cu2+, directly driving the transport of the copper ions across a membrane.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006878    cellular copper ion homeostasis    Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
    GO:0006882    cellular zinc ion homeostasis    Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0060003    copper ion export    The directed movement of copper ions out of a cell or organelle.
    GO:0015677    copper ion import    The directed movement of copper ions into a cell or organelle.
    GO:0035434    copper ion transmembrane transport    The directed movement of copper cation across a membrane.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015680    intracellular copper ion transport    The directed movement of copper (Cu) ions within a cell.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0046688    response to copper ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    GO:0051208    sequestering of calcium ion    The process of binding or confining calcium ions such that they are separated from other components of a biological system.
    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: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:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    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: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:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATP7B_HUMAN | P356702arf 2ew9 2koy 2lqb 2rop

(-) Related Entries Specified in the PDB File

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