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- PDB-2c0m: apo form of the TPR domain of the pex5p receptor -

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Basic information

Entry
Database: PDB / ID: 2c0m
Titleapo form of the TPR domain of the pex5p receptor
ComponentsPEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
KeywordsTRANSPORT PROTEIN / TPR REPEAT / TRANSPORT / IMPORT RECEPTOR COMPLEX / PEROXISOME / DISEASE MUTATION / PROTEIN TRANSPORT / ZELLWEGER SYNDROME
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 / mitochondrial membrane organization / peroxisomal membrane / 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 / cytosol / cytoplasm
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
C: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
F: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)140,9874
Polymers140,9874
Non-polymers00
Water2,630146
1
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
F: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)35,2471
Polymers35,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.470, 85.550, 88.890
Angle α, β, γ (deg.)71.17, 89.99, 73.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41F
12A
22B
32C
42F
13C
23F

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSVALVALAA285 - 4032 - 120
211LYSLYSVALVALBB285 - 4032 - 120
311LYSLYSVALVALCC285 - 4032 - 120
411LYSLYSVALVALFD285 - 4032 - 120
112SERSERARGARGAA429 - 550146 - 267
212SERSERARGARGBB429 - 550146 - 267
312SERSERARGARGCC429 - 550146 - 267
412SERSERARGARGFD429 - 550146 - 267
122GLYGLYGLNGLNAA560 - 602277 - 319
222GLYGLYGLNGLNBB560 - 602277 - 319
322GLYGLYGLNGLNCC560 - 602277 - 319
422GLYGLYGLNGLNFD560 - 602277 - 319
113ARGARGASPASPCC420 - 428137 - 145
213ARGARGASPASPFD420 - 428137 - 145

NCS ensembles :
ID
1
2
3

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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: 35246.699 Da / Num. of mol.: 4 / Fragment: TPR REPEAT DOMAIN, RESIDUES 284-602
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.46 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 47257 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.31
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.54 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.84 / SU B: 38.188 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R: 0.832 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2363 5 %RANDOM
Rwork0.263 ---
obs0.265 44893 96.5 %-
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: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-1.4 Å2-0.37 Å2
2--6.45 Å2-0.8 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9406 0 0 146 9552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229669
X-RAY DIFFRACTIONr_bond_other_d0.0030.028787
X-RAY DIFFRACTIONr_angle_refined_deg1.391.97413123
X-RAY DIFFRACTIONr_angle_other_deg0.83320371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19351206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2824.122490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54151625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6441586
X-RAY DIFFRACTIONr_chiral_restr0.0720.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021974
X-RAY DIFFRACTIONr_nbd_refined0.2380.22749
X-RAY DIFFRACTIONr_nbd_other0.1890.29623
X-RAY DIFFRACTIONr_nbtor_refined0.1870.24741
X-RAY DIFFRACTIONr_nbtor_other0.0890.25745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.2147
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.53326454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73739577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08243984
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.45553546
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1810medium positional0.340.3
12B1810medium positional0.340.3
13C1810medium positional0.260.3
14F1810medium positional0.230.3
21A2378medium positional0.220.3
22B2378medium positional0.230.3
23C2378medium positional0.210.3
24F2378medium positional0.220.3
31C139medium positional0.810.3
11A1810medium thermal1.5325
12B1810medium thermal1.2625
13C1810medium thermal1.125
14F1810medium thermal1.0125
21A2378medium thermal1.7325
22B2378medium thermal1.1625
23C2378medium thermal1.1325
24F2378medium thermal1.0525
31C139medium thermal0.4925
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 151
Rwork0.383 2875

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