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(-) Description

Title :  SOLUTION STRUCTURE OF DOMAINS 3 AND 4 OF HUMAN ATP7B
 
Authors :  L. Banci, I. Bertini, F. Cantini, A. C. Rosenzweig, L. A. Yatsunyk
Date :  04 Apr 08  (Deposition) - 21 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Wilson Protein, Mobility, Protein-Protein Interaction, Alternative Splicing, Atp-Binding, Copper, Copper Transport, Cytoplasm, Disease Mutation, Golgi Apparatus, Hydrolase, Ion Transport, Magnesium, Membrane, Metal-Binding, Mitochondrion, Nucleotide-Binding, Phosphoprotein, Polymorphism, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Banci, I. Bertini, F. Cantini, A. C. Rosenzweig, L. A. Yatsunyk
Metal Binding Domains 3 And 4 Of The Wilson Disease Protein: Solution Structure And Interaction With The Copper(I) Chaperone Hah1
Biochemistry V. 47 7423 2008
PubMed-ID: 18558714  |  Reference-DOI: 10.1021/BI8004736
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER-TRANSPORTING ATPASE 2
    ChainsA
    EC Number3.6.3.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET32XA/LIC
    FragmentHMA 3 AND HMA 4, THIRD SOLUBLE DOMAIN AND FOURTH SOLUBLE DOMAIN
    GeneATP7B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHE CONSTRUCT USED IN THE EXPERIMENT IS 202 AA LONG AND CONTAINS THE SOLUBLE DOMAINS 3 AND 4 OF ATP7B NAMED ALSO WILSON PROTEIN, THE INTER-DOMAIN LINKER (31 AA), A 17 AA PORTION OF THE LINKER CONNECTING DOMAINS 2-3, A 12 AA PORTION OF THE LINKER CONNECTING DOMAINS 4-5, AND NO TAGS.
    SynonymCOPPER PUMP 2, WILSON DISEASE-ASSOCIATED PROTEIN, WND/140 KDA

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2ROP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044453V290LATP7B_HUMANPolymorphism  ---AV53L
2UniProtVAR_076695S382CATP7B_HUMANUnclassified (WD)774102085AS145C
3UniProtVAR_000705I390VATP7B_HUMANPolymorphism770903362AI153V
4UniProtVAR_000706S406AATP7B_HUMANPolymorphism1801243AA169A

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMA_2PS50846 Heavy-metal-associated domain profile.ATP7B_HUMAN59-125
144-210
258-327
360-426
489-555
565-631
  2-
-
A:21-90
A:123-189
-
-
2HMA_1PS01047 Heavy-metal-associated domain.ATP7B_HUMAN64-93
149-178
263-292
365-394
494-523
570-599
  2-
-
A:26-55
A:128-157
-
-

(-) 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:20-190 (gaps)171
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:142
 aligned with ATP7B_HUMAN | P35670 from UniProtKB/Swiss-Prot  Length:1465

    Alignment length:171
                                   266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426 
          ATP7B_HUMAN   257 VTLQLRIDGMHCKSCVLNIEENIGQLLGVQSIQVSLENKTAQVKYDPSCTSPVALQRAIEALPPGNFKVSLPDGAEGSGTDHRSSSSHSPGSPPRNQVQGTCSTTLIAIAGMTCASCVHSIEGMISQLEGVQQISVSLAEGTATVLYNPSVISPEELRAAIEDMGFEASVV 427
               SCOP domains d2ropa1 A:20-81 automated matches                             ----------------------------------------------d2ropa2 A:128-190 automated matches                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------HMA-2ropA01 A:125-186                                         ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------HMA-2ropA02 A:125-186                                         ---- Pfam domains (2)
         Sec.struct. author .eeeeeeehhhhhhhhhhhhhhh.....eeeeeee....eeeeee.....hhhhhhhhhh.......eee.-----------------------------..eeeeeee.....hhhhhhhhhhhhhh..eeeeeee....eeeeee.....hhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------L-------------------------------------------------------------------------------------------C-------V---------------A--------------------- SAPs(SNPs)
                PROSITE (1) -HMA_2  PDB: A:21-90 UniProt: 258-327                                  --------------------------------HMA_2  PDB: A:123-189 UniProt: 360-426                             - PROSITE (1)
                PROSITE (2) ------HMA_1  PDB: A:26-55           ------------------------------------------------------------------------HMA_1  PDB: A:128-157         --------------------------------- PROSITE (2)
               Transcript 1 Exon 1.5b  PDB: A:20-190 (gaps) UniProt: 18-429 [INCOMPLETE]                                                                                                                Transcript 1
                 2rop A  20 VTLQLRIDGMHCKSCVLNIEENIGQLLGVQSIQVSLENKTAQVKYDPSCTSPVALQRAIEALPPGNFKVSL-----------------------------TCSTTLIAIAGMTCASCVHSIEGMISQLEGVQQISVSLAEGTATVLYNPAVISPEELRAAIEDMGFEASVV 190
                                    29        39        49        59        69        79        89|        -         -         -|      129       139       149       159       169       179       189 
                                                                                                 90                           120                                                                      

   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)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Family: HMA (41)
1aHMA-2ropA01A:125-186
1bHMA-2ropA02A:125-186

(-) 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)

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        ATP7B_HUMAN | P356702arf 2ew9 2koy 2lqb 2n7y

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