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- PDB-2lna: Solution NMR Structure of the mitochondrial inner membrane domain... -

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Basic information

Entry
Database: PDB / ID: 2lna
TitleSolution NMR Structure of the mitochondrial inner membrane domain (residues 164-251), FtsH_ext, from the paraplegin-like protein AFG3L2 from Homo sapiens, Northeast Structural Genomics Consortium Target HR6741A
ComponentsAFG3-like protein 2
KeywordsHYDROLASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / MPP / Mitochondrial Protein Partnership
Function / homology
Function and homology information


cellular response to glutathione / m-AAA complex / mitochondrial protein processing / mitochondrial protein quality control / regulation of calcium import into the mitochondrion / Processing of SMDT1 / mitochondrial calcium ion homeostasis / membrane protein proteolysis / calcium import into the mitochondrion / righting reflex ...cellular response to glutathione / m-AAA complex / mitochondrial protein processing / mitochondrial protein quality control / regulation of calcium import into the mitochondrion / Processing of SMDT1 / mitochondrial calcium ion homeostasis / membrane protein proteolysis / calcium import into the mitochondrion / righting reflex / cristae formation / Hydrolases; Acting on acid anhydrides / nerve development / muscle cell development / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / mitochondrial fusion / neuromuscular junction development / ATP-dependent peptidase activity / protein maturation / protein autoprocessing / regulation of multicellular organism growth / Mitochondrial protein degradation / myelination / axonogenesis / protein catabolic process / metalloendopeptidase activity / protein processing / metallopeptidase activity / unfolded protein binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / proteolysis / zinc ion binding / ATP binding
Similarity search - Function
name from scop - #20 / : / name from scop / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain ...name from scop - #20 / : / name from scop / Peptidase M41, FtsH extracellular / FtsH Extracellular / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial inner membrane m-AAA protease component AFG3L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Yang, Y. / Lee, H. / Janua, H. / Kohan, E. / Shastry, R. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. ...Ramelot, T.A. / Yang, Y. / Lee, H. / Janua, H. / Kohan, E. / Shastry, R. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP)
CitationJournal: Febs Lett. / Year: 2013
Title: NMR structure and MD simulations of the AAA protease intermembrane space domain indicates peripheral membrane localization within the hexaoligomer.
Authors: Ramelot, T.A. / Yang, Y. / Sahu, I.D. / Lee, H.W. / Xiao, R. / Lorigan, G.A. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Structure summary
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jun 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_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_seq_dif.details
Revision 1.4May 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: AFG3-like protein 2


Theoretical massNumber of molelcules
Total (without water)11,4941
Polymers11,4941
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein AFG3-like protein 2 / Paraplegin-like protein


Mass: 11493.874 Da / Num. of mol.: 1 / Fragment: UNP residues 164-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFG3L2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q9Y4W6, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-13C NOESYaliph
1813D 1H-15N NOESY
1922D 1H-13C HSQC aliphatic
11022D 1H-15N hetNOE
11113D HN(CO)CA
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
11413D H(CCO)NH
11513D C(CO)NH
11613D HBHA(CO)NH
11734D CC-HMQC-NOESY-HMQC
11832D 1H-15N HSQC
11933D CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] HR6741A, 200 mM sodium chloride, 20 mM MES, 5 mM calcium chloride, 10 mM DTT, 10 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM NC5 HR6741A, 200 mM sodium chloride, 20 mM MES, 5 mM calcium chloride, 10 mM DTT, 10 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-100% 13C; U-100% 15N] HR6741A, 200 mM sodium chloride, 20 mM MES, 5 mM calcium chloride, 10 mM DTT, 10 uM DSS, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHR6741A-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-21
20 mMMES-31
5 mMcalcium chloride-41
10 mMDTT-51
10 uMDSS-61
0.02 %sodium azide-71
1.0 mMHR6741A-8NC52
200 mMsodium chloride-92
20 mMMES-102
5 mMcalcium chloride-112
10 mMDTT-122
10 uMDSS-132
0.02 %sodium azide-142
0.7 mMHR6741A-15[U-100% 13C; U-100% 15N]3
200 mMsodium chloride-163
20 mMMES-173
5 mMcalcium chloride-183
10 mMDTT-193
10 uMDSS-203
0.02 %sodium azide-213
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAVANCE III8501
Varian INOVAVarianINOVA6002
Bruker AvanceIIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
NMRPipe2008 linux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1.4 and 3.1Bruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.113Goddarddata analysis
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALES2000PALES (Zweckstetter, Bax)geometry optimization
PSVS1.4Bhattacharya, Montelionestructure solution
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: CNS refinement in explicit water + two sets of NH RDCs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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