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- PDB-2hrf: Solution Structure of Cu(I) P174L HSco1 -

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Basic information

Entry
Database: PDB / ID: 2hrf
TitleSolution Structure of Cu(I) P174L HSco1
ComponentsSCO1 protein homolog, mitochondrial
KeywordsMETAL TRANSPORT / Chaperone / Mitochondrion / Metal-binding / Disease mutation / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


Complex IV assembly / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / myofibril / intracellular copper ion homeostasis / mitochondrial inner membrane / copper ion binding / mitochondrion
Similarity search - Function
Synthesis of cytochrome c oxidase, Sco1/Sco2 / Copper chaperone SCO1/SenC / SCO1/SenC / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Protein SCO1 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Leontari, I. / Martinelli, M. / Palumaa, P. / Sillard, R. / Wang, S. / Structural Proteomics in Europe (SPINE)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Human Sco1 functional studies and pathological implications of the P174L mutant.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Leontari, I. / Martinelli, M. / Palumaa, P. / Sillard, R. / Wang, S.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCO1 protein homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7922
Polymers19,7281
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -target function
Representativeminimized average structure

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Components

#1: Protein SCO1 protein homolog, mitochondrial


Mass: 19728.320 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 132-301) / Mutation: P174L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HUMAN / Gene: SCO1, SCOD1 / Plasmid: PETG-30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 GOLD / References: UniProt: O75880
#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
1113D 13C-separated NOESY
1223D 15N-separated NOESY
131HNCA
141HN(CO)CA
151CBCA(CO)NH
161(H)CCH-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Cu(I)P174LHSco1 U-15N,13C, 50mM phosphate buffer NA, 90% H2O, 10% D2O90% H2O/10% D2O
21mM Cu(I)P174LHSco1 U-15N, 50mM phosphate buffer NA, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionClassification
XwinNMR3.6collection
XwinNMR3.6processing
CARA2data analysis
DYANA1.5structure solution
Amber8refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers submitted total number: 1

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