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- PDB-2rsq: Copper(I) loaded form of the first domain of the human copper cha... -

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Basic information

Entry
Database: PDB / ID: 2rsq
TitleCopper(I) loaded form of the first domain of the human copper chaperone for SOD1, CCS
ComponentsCopper chaperone for superoxide dismutase
KeywordsMETAL BINDING PROTEIN / copper chaperone / human CCS / human SOD1
Function / homology
Function and homology information


protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / superoxide metabolic process / Detoxification of Reactive Oxygen Species / protein-disulfide reductase activity / removal of superoxide radicals / cellular response to oxidative stress / cadherin binding / copper ion binding / nucleus ...protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / superoxide metabolic process / Detoxification of Reactive Oxygen Species / protein-disulfide reductase activity / removal of superoxide radicals / cellular response to oxidative stress / cadherin binding / copper ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily ...Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone for superoxide dismutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsfewest violations, model1
AuthorsBanci, L. / Bertini, I. / Cantini, F. / Kozyreva, T. / Rubino, J.T.
CitationJournal: To be Published
Title: Copper(I) loaded form of the first domain of the human copper chaperone for SOD1, CCS
Authors: Banci, L. / Bertini, I. / Cantini, F. / Kozyreva, T. / Rubino, J.T.
History
DepositionMay 15, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_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 chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4362
Polymers9,3731
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Copper chaperone for superoxide dismutase / Superoxide dismutase copper chaperone / D1CCS


Mass: 9372.544 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCS / Production host: Escherichia coli (E. coli) / References: UniProt: O14618
#2: Chemical ChemComp-CU1 / COPPER (I) ION


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 1H-15N HSQC
2222D 1H-13C HSQC
3332D 1H-1H NOESY
2423D CBCA(CO)NH
2523D HNCO
2623D HNCA
2723D HN(CA)CB
2823D HN(CO)CA
1913D 1H-15N NOESY
21023D 1H-13C NOESY aliphatic
21123D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 15N] D1CCS-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] D1CCS-2, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM D1CCS-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMD1CCS-1[U-99% 15N]1
0.5 mMD1CCS-2[U-99% 13C; U-99% 15N]2
0.5 mMD1CCS-33
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaPi, 0.1M NaCl 6 ambient 298 K
20.1 NaPi, 0.1 NaCl 6.0 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
XEASYBartels et al.data analysis
CARAKeller, R. and W thrich, K.chemical shift assignment
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmanrefinement
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20 / Representative conformer: 1

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