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- PDB-2mv3: The N-domain of the AAA metalloproteinase Yme1 from Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 2mv3
TitleThe N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae
ComponentsMitochondrial inner membrane i-AAA protease supercomplex subunit YME1
KeywordsNUCLEOTIDE BINDING PROTEIN / AAA ATPase / substrate recognition domain / metalloprotease
Function / homology
Function and homology information


i-AAA complex / Cellular response to mitochondrial stress / protein import into mitochondrial intermembrane space / protein import into mitochondrial matrix / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein maturation / mitochondrion organization / protein catabolic process ...i-AAA complex / Cellular response to mitochondrial stress / protein import into mitochondrial intermembrane space / protein import into mitochondrial matrix / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein maturation / mitochondrion organization / protein catabolic process / metalloendopeptidase activity / protein folding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
: / Yme1-like, N-terminal / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...: / Yme1-like, N-terminal / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing, NOESY back-calculation
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsScharfenberg, F. / Serek-Heuberger, J. / Martin, J. / Lupas, A.N. / Coles, M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Evolution of N-domains in AAA Metalloproteases.
Authors: Scharfenberg, F. / Serek-Heuberger, J. / Coles, M. / Hartmann, M.D. / Habeck, M. / Martin, J. / Lupas, A.N. / Alva, V.
History
DepositionSep 22, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1


Theoretical massNumber of molelcules
Total (without water)10,0561
Polymers10,0561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 / Protein OSD1 / Tat-binding homolog 11 / Yeast mitochondrial escape protein 1 / Yme1-N


Mass: 10056.246 Da / Num. of mol.: 1 / Fragment: N-domain (UNP residues 97-176)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: YME1, OSD1, YTA11, YPR024W, YP9367.04 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P32795

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D C(CO)NH
1323D (H)CCH-TOCSY
1423D CCH NOESY
1523D CNH NOESY
1613D 1H-15N NOESY
1723D 1H-13C NOESY
1813D HNHA
1913D HNHB
11023D 3JHBHA(CO)NH
11113D NNH NOESY
11223D HN(CA)NNH
11323D HNCA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] Yme1-N, 20 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] Yme1-N, 20 mM Tris, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMYme1-N-1[U-100% 15N]1
20 mMTris-21
300 mMsodium chloride-31
0.5 mMYme1-N-4[U-100% 13C; U-100% 15N]2
20 mMTris-52
300 mMsodium chloride-62
Sample conditionsIonic strength: 0.34 / pH: 7.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorerefinement
NMR-SPIRIT1.1In houserefinement
RefinementMethod: simulated annealing, NOESY back-calculation / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 47 / Protein other angle constraints total count: 34 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 94
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 23 / Maximum lower distance constraint violation: 0.02 Å / Maximum torsion angle constraint violation: 0.3 ° / Maximum upper distance constraint violation: 0.08 Å
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.001 Å

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