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- PDB-2c0l: TPR DOMAIN OF HUMAN PEX5P IN COMPLEX WITH HUMAN MSCP2 -

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Basic information

Entry
Database: PDB / ID: 2c0l
TitleTPR DOMAIN OF HUMAN PEX5P IN COMPLEX WITH HUMAN MSCP2
Components
  • NONSPECIFIC LIPID-TRANSFER PROTEIN
  • PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
KeywordsTRANSPORT PROTEIN/RECEPTOR / TPR REPEAT / TRANSPORT / IMPORT RECEPTOR COMPLEX / PEROXISOME / DISEASE MUTATION / PROTEIN TRANSPORT / ZELLWEGER SYNDROME / ALTERNATIVE INITIATION / LIPID TRANSPORT / LIPID-BINDING / MITOCHONDRION / TRANSIT PEPTIDE / TRANSPORT PROTEIN-RECEPTOR COMPLEX
Function / homology
Function and homology information


positive regulation of intracellular cholesterol transport / positive regulation of steroid metabolic process / lipid hydroperoxide transport / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / progesterone biosynthetic process / protein import into peroxisome matrix, substrate release / acetyl-CoA C-myristoyltransferase activity / Beta-oxidation of pristanoyl-CoA ...positive regulation of intracellular cholesterol transport / positive regulation of steroid metabolic process / lipid hydroperoxide transport / propanoyl-CoA C-acyltransferase activity / propionyl-CoA C2-trimethyltridecanoyltransferase activity / acetyl-CoA C-myristoyltransferase / progesterone biosynthetic process / protein import into peroxisome matrix, substrate release / acetyl-CoA C-myristoyltransferase activity / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / phosphatidylcholine transfer activity / protein import into peroxisome matrix, translocation / propanoyl-CoA C-acyltransferase / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / long-chain fatty acyl-CoA binding / inositol trisphosphate biosynthetic process / protein targeting to peroxisome / phosphatidylinositol transfer activity / fatty acid beta-oxidation using acyl-CoA oxidase / peroxisome matrix targeting signal-1 binding / alpha-linolenic acid metabolic process / protein import into peroxisome matrix, receptor recycling / alpha-linolenic acid (ALA) metabolism / protein import into peroxisome matrix / acetyl-CoA C-acyltransferase / protein import into peroxisome matrix, docking / acetyl-CoA C-acyltransferase activity / protein carrier chaperone / regulation of phospholipid biosynthetic process / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / intracellular cholesterol transport / cell development / fatty-acyl-CoA binding / oleic acid binding / pexophagy / bile acid biosynthetic process / phospholipid transport / steroid biosynthetic process / positive regulation of multicellular organism growth / cholesterol transfer activity / bile acid metabolic process / endoplasmic reticulum organization / mitochondrial membrane organization / peroxisomal membrane / neuromuscular process / cholesterol binding / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Pexophagy / protein localization to plasma membrane / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein-containing complex / mitochondrion / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. ...PEX5/PEX5L / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Thiolase-like / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sterol carrier protein 2 / Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStanley, W.A. / Kursula, P. / Wilmanns, M.
CitationJournal: Mol.Cell / Year: 2006
Title: Recognition of a Functional Peroxisome Type 1 Target by the Dynamic Import Receptor Pex5P.
Authors: Stanley, W.A. / Filipp, F.V. / Kursula, P. / Schuller, N. / Erdmann, R. / Schliebs, W. / Sattler, M. / Wilmanns, M.
History
DepositionSep 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: NONSPECIFIC LIPID-TRANSFER PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,6962
Polymers46,6962
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.480, 68.620, 137.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR / PEX5P / PEROXISMORE RECEPTOR 1 / PEROXIN-5 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT ...PEX5P / PEROXISMORE RECEPTOR 1 / PEROXIN-5 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR / PTS1-BP / PTS1 RECEPTOR


Mass: 33522.906 Da / Num. of mol.: 1 / Fragment: TPR REPEAT DOMAIN, RESIDUES 298-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P50542
#2: Protein NONSPECIFIC LIPID-TRANSFER PROTEIN / MSCP2 / STEROL CARRIER PROTEIN 2 / NSL-TP / SCP-2B / SCP-2 / STEROL CARRIER PROTEIN X / SCP-X / SCPX


Mass: 13173.263 Da / Num. of mol.: 1 / Fragment: SCP2 DOMAIN, RESIDUES 426-547
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P22307
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 39.83 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 17692 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.623 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.456 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 884 5 %RANDOM
Rwork0.202 ---
obs0.205 17681 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2---1.04 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 0 99 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213264
X-RAY DIFFRACTIONr_bond_other_d0.0020.023004
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.9734402
X-RAY DIFFRACTIONr_angle_other_deg0.70537004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6555411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.38124.765149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61915583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3321521
X-RAY DIFFRACTIONr_chiral_restr0.0540.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
X-RAY DIFFRACTIONr_nbd_refined0.2010.2841
X-RAY DIFFRACTIONr_nbd_other0.2270.23664
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.22432656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55543264
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61541387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.63951138
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 64
Rwork0.31 1224

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