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- PDB-1fch: CRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGION OF HUMA... -

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Basic information

Entry
Database: PDB / ID: 1fch
TitleCRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGION OF HUMAN PEX5
Components
  • PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
  • PTS1-CONTAINING PEPTIDE
KeywordsSIGNALING PROTEIN / PROTEIN-PEPTIDE COMPLEX / TETRATRICOPEPTIDE REPEAT / TPR / HELICAL REPEAT
Function / homology
Function and homology information


protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking ...protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / protein carrier chaperone / cell development / pexophagy / positive regulation of multicellular organism growth / endoplasmic reticulum organization / peroxisomal membrane / mitochondrial membrane organization / neuromuscular process / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Pexophagy / cellular response to reactive oxygen species / protein tetramerization / Peroxisomal protein import / small GTPase binding / neuron migration / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / enzyme binding / Golgi apparatus / protein-containing complex / mitochondrion / membrane / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGatto Jr., G.J. / Geisbrecht, B.V. / Gould, S.J. / Berg, J.M.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5.
Authors: Gatto Jr., G.J. / Geisbrecht, B.V. / Gould, S.J. / Berg, J.M.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PTS1-CONTAINING PEPTIDE
D: PTS1-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)83,2574
Polymers83,2574
Non-polymers00
Water4,342241
1
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PTS1-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)41,6292
Polymers41,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-3 kcal/mol
Surface area13430 Å2
MethodPISA
2
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
D: PTS1-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)41,6292
Polymers41,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-4 kcal/mol
Surface area13640 Å2
MethodPISA
3
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PTS1-CONTAINING PEPTIDE
D: PTS1-CONTAINING PEPTIDE

A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PTS1-CONTAINING PEPTIDE
D: PTS1-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)166,5158
Polymers166,5158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area13630 Å2
ΔGint-64 kcal/mol
Surface area45000 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-21 kcal/mol
Surface area24280 Å2
MethodPISA
5
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PTS1-CONTAINING PEPTIDE

B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
D: PTS1-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)83,2574
Polymers83,2574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4020 Å2
ΔGint-18 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.960, 73.510, 87.560
Angle α, β, γ (deg.)90.00, 120.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR / PEROXISMORE RECEPTOR 1 / PTS1-BP / PEROXIN-5 / PTS1 RECEPTOR


Mass: 40989.910 Da / Num. of mol.: 2 / Fragment: C-TERMINAL TPR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P50542
#2: Protein/peptide PTS1-CONTAINING PEPTIDE


Mass: 638.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium HEPES, Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: peptide solution was diluted 1:1 with reservoir
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.24 mMprotein1drop
250 mM1dropNaCl
35 mMHEPES1drop
41.9 mMpeptide1drop
50.58 MNa citrate1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 38298 / Num. obs: 38298 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.227 / Num. unique all: 1916 / % possible all: 98.8
Reflection shell
*PLUS
% possible obs: 98.8 % / Mean I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→29.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2170352.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3831 10 %RANDOM
Rwork0.194 ---
obs0.194 38295 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.56 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å20 Å20.12 Å2
2--8.07 Å20 Å2
3----4.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 0 241 4994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 642 10.2 %
Rwork0.212 5666 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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