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- PDB-5lci: Solution structure of BOLA1 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5lci
TitleSolution structure of BOLA1 from Homo sapiens
ComponentsBolA-like protein 1
KeywordsPROTEIN BINDING / class II KH-like fold / mitochondrial protein / Fe/S protein biogenesis
Function / homologyBolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / mitochondrion / 2-Layer Sandwich / Alpha Beta / BolA-like protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsNasta, V. / Ciofi Baffoni, S. / Banci, L.
CitationJournal: Elife / Year: 2016
Title: Mitochondrial Bol1 and Bol3 function as assembly factors for specific iron-sulfur proteins.
Authors: Uzarska, M.A. / Nasta, V. / Weiler, B.D. / Spantgar, F. / Ciofi-Baffoni, S. / Saviello, M.R. / Gonnelli, L. / Muhlenhoff, U. / Banci, L. / Lill, R.
History
DepositionJun 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BolA-like protein 1


Theoretical massNumber of molelcules
Total (without water)12,8751
Polymers12,8751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40target function
RepresentativeModel #1medoid

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Components

#1: Protein BolA-like protein 1 / hBolA


Mass: 12875.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GIDPFT sequence at the N-terminus is added by cloning. The mitochondrial-targeting sequence (MLSGRLVLGLVSMAGRVCLC) has been removed.
Source: (gene. exp.) Homo sapiens (human) / Gene: BOLA1, CGI-143 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9Y3E2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
222anisotropic12D 1H-13C HSQC aliphatic
232anisotropic13D HNCO
242anisotropic13D HNCA
252anisotropic13D HN(CO)CA
292anisotropic13D HN(CA)CB
282anisotropic13D CBCA(CO)NH
272anisotropic13D HN(CA)CO
262anisotropic13D HBHA(CBCACO)NH
2102anisotropic13D HN(CA)CB
2122anisotropic13D (H)CCH-TOCSY
2112anisotropic23D 1H-13C NOESY
1131anisotropic12D 1H-1H TOCSY
1141anisotropic32D 1H-1H NOESY
1151anisotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 15N] mitochondrial BOLA1 protein, 50 mM potassium phosphate, 5 mM DTT, 90% H2O/10% D2O15N_BOLA190% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] mitochondrial BOLA1 protein, 50 mM potassium phosphate, 5 mM DTT, 90% H2O/10% D2O13C_15N_BOLA190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmitochondrial BOLA1 protein[U-100% 15N]1
50 mMpotassium phosphatenatural abundance1
5 mMDTTnatural abundance1
1 mMmitochondrial BOLA1 protein[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphatenatural abundance2
5 mMDTTnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM15N_BOLA17 1 atm298 K
250 mM13C_15N_BOLA17 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE9002
Bruker AVANCEBrukerAVANCE9503

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
UNIOSerrano, Pedrini, Mohanty, Geralt, Herrmann and Wuthrich,structure calculation
CARA2Keller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
UNIOSerrano, Pedrini, Mohanty, Geralt, Herrmann and Wuthrich,peak picking
TopSpinBruker Biospinprocessing
TALOS+Cornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 20

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