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- PDB-2rli: Solution structure of Cu(I) human Sco2 -

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Basic information

Entry
Database: PDB / ID: 2rli
TitleSolution structure of Cu(I) human Sco2
ComponentsSCO2 protein homolog, mitochondrial
KeywordsMETAL TRANSPORT / Copper protein / thioredoxin fold / Structural Genomics / SPINE2-Complexes / Structural Proteomics in Europe / SPINE / Structural Proteomics in Europe 2 / SPINE-2
Function / homology
Function and homology information


Complex IV assembly / muscle system process / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / eye development / myofibril / protein-disulfide reductase activity / intracellular copper ion homeostasis / respiratory electron transport chain / response to activity ...Complex IV assembly / muscle system process / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / eye development / myofibril / protein-disulfide reductase activity / intracellular copper ion homeostasis / respiratory electron transport chain / response to activity / TP53 Regulates Metabolic Genes / in utero embryonic development / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / mitochondrion
Similarity search - Function
Synthesis of cytochrome c oxidase, Sco1/Sco2 / Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Protein SCO2 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Ciofi-baffoni, S. / Gerothanassis, I.P. / Leontari, I. / Martinelli, M. / Wang, S. / Structural Proteomics in Europe (SPINE) / Structural Proteomics in Europe 2 (SPINE-2)
CitationJournal: Structure / Year: 2007
Title: A Structural Characterization of Human SCO2
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gerothanassis, I.P. / Leontari, I. / Martinelli, M. / Wang, S.
History
DepositionJul 11, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_keywords / 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_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCO2 protein homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5562
Polymers19,4931
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)31 / 350structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein SCO2 protein homolog, mitochondrial


Mass: 19492.826 Da / Num. of mol.: 1 / Fragment: soluble domain of human Sco2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCO2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 GOLD / References: UniProt: O43819
#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
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D (H)CCH-TOCSY
1823D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(CO)CA
NMR detailsText: the structure was determined using NOE and dihedral angle constrains

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] entity_1, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 15N] entity_1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1[U-100% 13C; U-100% 15N]1
0.8 mMentity_1[U-100% 15N]2
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
XwinNMR3.6Bruker Biospinprocessing
CARA2Keller and Wuthrichdata analysis
CARA2Keller and Wuthrichchemical shift assignment
CARA2Keller and Wuthrichpeak picking
DYANA1.5Guntert, Braun and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2296 / NOE intraresidue total count: 364 / NOE long range total count: 719 / NOE medium range total count: 619 / NOE sequential total count: 594
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 350 / Conformers submitted total number: 31

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