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- PDB-5lnf: Solution NMR structure of farnesylated PEX19, C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5lnf
TitleSolution NMR structure of farnesylated PEX19, C-terminal domain
ComponentsPeroxisomal biogenesis factor 19
KeywordsCHAPERONE / PEX19 / farnesylation / post translational modification / allostery
Function / homology
Function and homology information


peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / peroxisome organization / protein carrier chaperone ...peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / Class I peroxisomal membrane protein import / peroxisome organization / protein carrier chaperone / ABC transporters in lipid homeostasis / peroxisome fission / peroxisomal membrane / : / brush border membrane / peroxisome / ATPase binding / protein stabilization / protein-containing complex / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Pex19, mPTS binding domain / Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FARNESYL / Peroxisomal biogenesis factor 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsEmmanouilidis, L. / Schuetz, U. / Tripsianes, K. / Madl, T. / Radke, J. / Rucktaeschel, R. / Wilmanns, M. / Schliebs, W. / Erdmann, R. / Sattler, M.
CitationJournal: Nat Commun / Year: 2017
Title: Allosteric modulation of peroxisomal membrane protein recognition by farnesylation of the peroxisomal import receptor PEX19.
Authors: Emmanouilidis, L. / Schutz, U. / Tripsianes, K. / Madl, T. / Radke, J. / Rucktaschel, R. / Wilmanns, M. / Schliebs, W. / Erdmann, R. / Sattler, M.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 11, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Peroxisomal biogenesis factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8712
Polymers15,6651
Non-polymers2061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area630 Å2
ΔGint4 kcal/mol
Surface area9120 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein Peroxisomal biogenesis factor 19 / 33 kDa housekeeping protein / Peroxin-19 / Peroxisomal farnesylated protein


Mass: 15664.643 Da / Num. of mol.: 1 / Fragment: UNP residues 161-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX19, HK33, PXF, OK/SW-cl.22 / Production host: Escherichia coli (E. coli) / References: UniProt: P40855
#2: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D (H)CCH-TOCSY
151isotropic23D 1H-13C NOESY
161isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM {U-1H,13C,15N; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2Odoubly labeled90% H2O/10% D2O
solution21 mM {U-2H,12C,15N; Leu-[1H,13C,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2OLeucine labeled90% H2O/10% D2O
solution31 mM {U-2H,12C,15N; Lle-[1H,13C,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2OIsoleucine labeled90% H2O/10% D2O
solution41 mM {U-2H,12C,15N; Met-[1H,13CH3,15N]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2OMethionine labeled90% H2O/10% D2O
solution51 mM {U-2H,12C,15N; Ile(delta1),Leu(delta),Val(gamma)-[13CH3]; farnesyl-[1H,12C]} PEX19, 90% H2O/10% D2OILV methyl labeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPEX19{U-1H,13C,15N; farnesyl-[1H,12C]}1
1 mMPEX19{U-2H,12C,15N; Leu-[1H,13C,15N]; farnesyl-[1H,12C]}2
1 mMPEX19{U-2H,12C,15N; Lle-[1H,13C,15N]; farnesyl-[1H,12C]}3
1 mMPEX19{U-2H,12C,15N; Met-[1H,13CH3,15N]; farnesyl-[1H,12C]}4
1 mMPEX19{U-2H,12C,15N; Ile(delta1),Leu(delta),Val(gamma)-[13CH3]; farnesyl-[1H,12C]}5
Sample conditionsIonic strength: 50 mM / Label: NMR buffer / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7501
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR softwareName: CNS / Developer: BRUNGER A. T. ET.AL. / Classification: refinement
NMR ensembleConformers submitted total number: 20

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