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- PDB-1fvs: SOLUTION STRUCTURE OF THE YEAST COPPER TRANSPORTER DOMAIN CCC2A I... -

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Basic information

Entry
Database: PDB / ID: 1fvs
TitleSOLUTION STRUCTURE OF THE YEAST COPPER TRANSPORTER DOMAIN CCC2A IN THE APO AND CU(I) LOAD STATES
ComponentsCOPPER-TRANSPORTING ATPASE
KeywordsHYDROLASE / Cu(I)-Ccc2a / babbab
Function / homology
Function and homology information


trans-Golgi network transport vesicle membrane / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion homeostasis / copper ion transport / ATPase-coupled monoatomic cation transmembrane transporter activity / transmembrane transport / intracellular iron ion homeostasis ...trans-Golgi network transport vesicle membrane / P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion homeostasis / copper ion transport / ATPase-coupled monoatomic cation transmembrane transporter activity / transmembrane transport / intracellular iron ion homeostasis / copper ion binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-transporting ATPase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics restrained energy minimization
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Ciofi Baffoni, S. / Huffman, D.L. / O'Halloran, T.V.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Solution structure of the yeast copper transporter domain Ccc2a in the apo and Cu(I)-loaded states.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Huffman, D.L. / O'Halloran, T.V.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9532
Polymers7,8901
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein COPPER-TRANSPORTING ATPASE


Mass: 7889.924 Da / Num. of mol.: 1 / Fragment: CCC2A DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PDLHV021 / Production host: Escherichia coli (E. coli) / References: UniProt: P38995, EC: 3.6.1.36
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 1.2mM Cu(I)-Ccc2a; 100mM phosphate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate / pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRprocessing
XEASYEccles, Guentert, Billeter, Wuethrichdata analysis
DIANAGuentert, Mumenthaler, Wuethrichstructure solution
CORMABorgias, Thomas, Jamesiterative matrix relaxation
Amber6Case, Kollman et al.refinement
RefinementMethod: simulated annealing torsion angle dynamics restrained energy minimization
Software ordinal: 1 / Details: 1944 meaningful NOEs
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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