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- PDB-7z0k: human PEX13 SH3 in complex with PEX5 W4 (WxxxF/Y) motif -

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Basic information

Entry
Database: PDB / ID: 7z0k
Titlehuman PEX13 SH3 in complex with PEX5 W4 (WxxxF/Y) motif
ComponentsPeroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor
KeywordsTRANSPORT PROTEIN / protein transport
Function / homology
Function and homology information


microtubule-based peroxisome localization / protein import into peroxisome matrix, substrate release / peroxisome targeting sequence binding / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / peroxisomal importomer complex / peroxisome matrix targeting signal-1 binding / fatty acid alpha-oxidation ...microtubule-based peroxisome localization / protein import into peroxisome matrix, substrate release / peroxisome targeting sequence binding / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / peroxisomal importomer complex / peroxisome matrix targeting signal-1 binding / fatty acid alpha-oxidation / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking / protein carrier chaperone / Class I peroxisomal membrane protein import / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / cell development / pexophagy / positive regulation of multicellular organism growth / endoplasmic reticulum organization / mitochondrial membrane organization / peroxisomal membrane / neuromuscular process / fatty acid beta-oxidation / suckling behavior / cerebral cortex cell migration / peroxisomal matrix / protein transmembrane transporter activity / negative regulation of protein-containing complex assembly / Pexophagy / locomotory behavior / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / Golgi apparatus / enzyme binding / protein-containing complex / mitochondrion / membrane / cytosol / cytoplasm
Similarity search - Function
Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / PEX5/PEX5L / Variant SH3 domain / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / PEX5/PEX5L / Variant SH3 domain / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Peroxisomal targeting signal 1 receptor / Peroxisomal membrane protein PEX13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGaussmann, S. / Napolitano, V. / sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR1905 Germany
CitationJournal: Biorxiv / Year: 2022
Title: Intramolecular autoinhibition of human PEX13 modulates peroxisomal import
Authors: Gaussmann, S. / Ott, J. / Zak, K.M. / Delhommel, F. / Popowicz, G.M. / Schliebs, W. / Erdmann, R. / Sattler, M.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor
B: Peroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor


Theoretical massNumber of molelcules
Total (without water)23,1452
Polymers23,1452
Non-polymers00
Water1,09961
1
A: Peroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor


Theoretical massNumber of molelcules
Total (without water)11,5731
Polymers11,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor


Theoretical massNumber of molelcules
Total (without water)11,5731
Polymers11,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.662, 87.662, 66.112
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGAA265 - 3565 - 96
2GLUGLUBB265 - 3445 - 84

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Components

#1: Protein Peroxisomal membrane protein PEX13,Peroxisomal targeting signal 1 receptor / Peroxin-13 / PTS1 receptor / PTS1R / PTS1-BP / Peroxin-5 / Peroxisomal C-terminal targeting signal ...Peroxin-13 / PTS1 receptor / PTS1R / PTS1-BP / Peroxin-5 / Peroxisomal C-terminal targeting signal import receptor / Peroxisome receptor 1


Mass: 11572.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX13, PEX5, PXR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92968, UniProt: P50542
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium sulfate 0.1 M Bis Tris propane pH 6.5 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.000029 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000029 Å / Relative weight: 1
ReflectionResolution: 2.3→49.91 Å / Num. obs: 13362 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.992 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1275 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z0J

7z0j


Resolution: 2.3→49.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.966 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 490 3.7 %RANDOM
Rwork0.1928 ---
obs0.1939 12854 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.14 Å2 / Biso mean: 50.489 Å2 / Biso min: 27.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å2-0 Å2
3----3.02 Å2
Refinement stepCycle: final / Resolution: 2.3→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 61 1398
Biso mean---54.14 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131386
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151323
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6381873
X-RAY DIFFRACTIONr_angle_other_deg1.2561.5963041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.822.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68915243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5771511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02328
Refine LS restraints NCS

Ens-ID: 1 / Number: 2236 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.257 963 -
obs--100 %

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