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- PDB-2w85: Structure of Pex14 in complex with Pex19 -

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Basic information

Entry
Database: PDB / ID: 2w85
TitleStructure of Pex14 in complex with Pex19
Components
  • PEROXIN-19
  • PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14
KeywordsPROTEIN TRANSPORT / ZELLWEGER SYNDROME / ALTERNATIVE SPLICING / TRANSLOCATION / PHOSPHOPROTEIN / PROTEIN COMPLEX / PEROXISOME BIOGENESIS DISORDER / PEROXISOME TARGETING SIGNAL / PEROXISOME / PRENYLATION / LIPOPROTEIN / POLYMORPHISM / PTS / MEMBRANE / PEROXISOME IMPORT / PEROXISOME BIOGENESIS / RECEPTOR-CARGO COMPLEX
Function / homology
Function and homology information


peroxisome transport along microtubule / peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome ...peroxisome transport along microtubule / peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / peroxisomal importomer complex / microtubule anchoring / protein import into peroxisome matrix / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / protein carrier chaperone / peroxisome organization / peroxisome fission / ABC transporters in lipid homeostasis / peroxisomal membrane / beta-tubulin binding / protein transmembrane transporter activity / chaperone-mediated protein folding / negative regulation of protein binding / Peroxisomal protein import / brush border membrane / negative regulation of DNA-binding transcription factor activity / fibrillar center / cellular response to reactive oxygen species / transcription corepressor activity / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / protein-macromolecule adaptor activity / ATPase binding / microtubule binding / protein-containing complex assembly / protein stabilization / signaling receptor binding / negative regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family / Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peroxisomal membrane protein PEX14 / Peroxisomal biogenesis factor 19
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNeufeld, C. / Filipp, F.V. / Simon, B. / Neuhaus, A. / Schueller, N. / David, C. / Kooshapur, H. / Madl, T. / Erdmann, R. / Schliebs, W. ...Neufeld, C. / Filipp, F.V. / Simon, B. / Neuhaus, A. / Schueller, N. / David, C. / Kooshapur, H. / Madl, T. / Erdmann, R. / Schliebs, W. / Wilmanns, M. / Sattler, M.
CitationJournal: Embo J. / Year: 2009
Title: Structural Basis for Competitive Interactions of Pex14 with the Import Receptors Pex5 and Pex19.
Authors: Neufeld, C. / Filipp, F.V. / Simon, B. / Neuhaus, A. / Schueller, N. / David, C. / Kooshapur, H. / Madl, T. / Erdmann, R. / Schliebs, W. / Wilmanns, M. / Sattler, M.
History
DepositionJan 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14
B: PEROXIN-19


Theoretical massNumber of molelcules
Total (without water)9,1452
Polymers9,1452
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)10 / 100LOWEST ENERGY
Representative

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Components

#1: Protein PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14 / PEROXIN-14 / PTS1 RECEPTOR-DOCKING PROTEIN


Mass: 7639.655 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 16-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11_MOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75381
#2: Protein/peptide PEROXIN-19 / PEROXISOMAL FARNESYLATED PROTEIN / 33 KDA HOUSEKEEPING PROTEIN


Mass: 1505.603 Da / Num. of mol.: 1 / Fragment: F/YFXXXF MOTIF, RESIDUES 66-77 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P40855
Sequence detailsRESIDUES 101-112 IN THIS PDB-ENTRY CORRESPOND TO RESIDUES 66-77 IN THE CORRESPONDING GENBANK ENTRY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CA)CB
1313D C(CO)NH
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1613D H(CCO)NH
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1912D 1H-1H NOESY
NMR detailsText: THE STRUCUTRE WAS DETERMINED USING EDITED-FILTERED EXPERIMENTS ON 13C,15N LABELLED PEX14 - UNLABELLED PEX5 COMPLEXES

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Sample preparation

DetailsContents: 10%WATER/90%D2O, 100%D2O
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRView5.0.4structure solution
TopSpin1.3structure solution
NMRPipestructure solution
ARIAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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