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- PDB-5nf8: Solution structure of detergent-solubilized Rcf1, a yeast mitocho... -

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Basic information

Entry
Database: PDB / ID: 5nf8
TitleSolution structure of detergent-solubilized Rcf1, a yeast mitochondrial inner membrane protein involved in respiratory Complex III/IV supercomplex formation
ComponentsRespiratory supercomplex factor 1, mitochondrial
KeywordsMEMBRANE PROTEIN / Homodimer / solution structure / Charged dimer interface
Function / homology
Function and homology information


: / regulation of proton transport / mitochondrial cytochrome c oxidase assembly / mitochondrial respirasome assembly / mitochondrial respirasome / mitochondrial membrane / membrane => GO:0016020 / mitochondrion
Similarity search - Function
Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile.
Similarity search - Domain/homology
Respiratory supercomplex factor 1, mitochondrial / Respiratory supercomplex factor 1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsZhou, S. / Pettersson, P. / Sjoholm, J. / Sjostrand, D. / Hogbom, M. / Brzezinski, P. / Maler, L. / Adelroth, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Solution NMR structure of yeast Rcf1, a protein involved in respiratory supercomplex formation.
Authors: Zhou, S. / Pettersson, P. / Huang, J. / Sjoholm, J. / Sjostrand, D. / Pomes, R. / Hogbom, M. / Brzezinski, P. / Maler, L. / Adelroth, P.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Respiratory supercomplex factor 1, mitochondrial
B: Respiratory supercomplex factor 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)40,7772
Polymers40,7772
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1860 Å2
ΔGint8 kcal/mol
Surface area27560 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Respiratory supercomplex factor 1, mitochondrial / Altered inheritance of mitochondria protein 31


Mass: 20388.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RCF1, AIM31, SCRG_01865 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B3LLM2, UniProt: Q03713*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic12D 1H-15N HSQC
232isotropic13D HN(CA)CB
242isotropic23D HN(COCA)CB
252isotropic13D HNCO
262isotropic13D HN(CA)CO
272isotropic13D HNCA
282isotropic13D HN(CO)CA
292isotropic13D N-NOESY-HSQC
3103isotropic13D (H)CCH-TOCSY
3113isotropic13D CC(CO)NH
3123isotropic13D H(CCO)NH
3133isotropic12D 1H-13C HSQC
3143isotropic13D N-NOESY-HSQC
3153isotropic13D C-NOESY-HSQC
4164isotropic12D 1H-13C HSQC
4174isotropic13D N-NOESY-HSQC
4184isotropic13D C-NOESY-HSQC
5195isotropic12D 1H-13C HSQC
5205isotropic13D C-NOESY-HSQC
6216isotropic13D F1-13C/15N-filtered, F3-15N-edited-NOESY-HSQC
6226isotropic13D F1-13C/15N-filtered, F3-13C-edited-NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.4 mM [U-15N] rcf1, 90% H2O/10% D2O15N_rcf190% H2O/10% D2O
micelle20.4 mM [U-13C; U-15N; U-2H] rcf1, 90% H2O/10% D2O13C, 15N, 2H_rcf190% H2O/10% D2O
micelle30.4 mM [U-13C; U-15N] rcf1, 90% H2O/10% D2O13C, 15N_rcf190% H2O/10% D2O
micelle40.4 mM [U-13C; U-15N; 50% U-2H] rcf1, 90% H2O/10% D2O50%-2H, 13C, 15N_rcf190% H2O/10% D2O
micelle50.4 mM [U-15N; U-2H; 99%-1HD, 13CD-IL; 99%-1HG, 13CG-V] rcf1, 90% H2O/10% D2O2H, 15N, IVL-13C_rcf190% H2O/10% D2O
micelle60.4 mM [U-50% 13C; U-50% 15N; U-50% 12C; U-50% 14N] rcf1, 90% H2O/10% D2O50% 13C, 15N; 50% 12C, 14N_rcf190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMrcf1[U-15N]1
0.4 mMrcf1[U-13C; U-15N; U-2H]2
0.4 mMrcf1[U-13C; U-15N]3
0.4 mMrcf1[U-13C; U-15N; 50% U-2H]4
0.4 mMrcf1[U-15N; U-2H; 99%-1HD, 13CD-IL; 99%-1HG, 13CG-V]5
0.4 mMrcf1[U-50% 13C; U-50% 15N; U-50% 12C; U-50% 14N]6
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 Not definedconditions_15.0 1 Pa323 K
20 Not definedconditions_25.0 1 Pa323 K
30 Not definedconditions_35.0 1 Pa323 K
40 Not definedconditions_45.0 1 Pa323 K
50 Not definedconditions_55.0 1 Pa323 K
60 Not definedconditions_65.0 1 Pa323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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