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- PDB-8p5p: Structure of TECPR1 N-terminal DysF domain -

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Basic information

Entry
Database: PDB / ID: 8p5p
TitleStructure of TECPR1 N-terminal DysF domain
ComponentsTectonin beta-propeller repeat-containing protein 1
KeywordsLIPID BINDING PROTEIN / Sphingomyelin binding
Function / homology
Function and homology information


regulation of autophagosome maturation / phosphatidylinositol-3-phosphate binding / autophagosome membrane / autophagosome maturation / macroautophagy / autophagy / cytoplasmic vesicle / lysosomal membrane / intracellular membrane-bounded organelle / protein-containing complex / nucleoplasm
Similarity search - Function
Peroxin domain / Integral peroxisomal membrane peroxin / Propeller / Tectonin domain / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / PH-like domain superfamily
Similarity search - Domain/homology
Tectonin beta-propeller repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBoyle, K.B. / Elliott, P.R. / Randow, F.
Funding support Canada, United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, Canada)U105170648 Canada
Wellcome Trust222503/Z/21/Z United Kingdom
CitationJournal: Embo J. / Year: 2023
Title: TECPR1 conjugates LC3 to damaged endomembranes upon detection of sphingomyelin exposure.
Authors: Boyle, K.B. / Ellison, C.J. / Elliott, P.R. / Schuschnig, M. / Grimes, K. / Dionne, M.S. / Sasakawa, C. / Munro, S. / Martens, S. / Randow, F.
History
DepositionMay 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / diffrn_source / pdbx_validate_planes
Item: _citation.journal_volume / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tectonin beta-propeller repeat-containing protein 1
B: Tectonin beta-propeller repeat-containing protein 1
C: Tectonin beta-propeller repeat-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4445
Polymers42,2603
Non-polymers1842
Water5,477304
1
A: Tectonin beta-propeller repeat-containing protein 1


  • defined by author
  • Evidence: gel filtration
  • 14.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,0871
Polymers14,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tectonin beta-propeller repeat-containing protein 1


  • defined by author
  • 14.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,0871
Polymers14,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tectonin beta-propeller repeat-containing protein 1
hetero molecules


  • defined by author
  • 14.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,2713
Polymers14,0871
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.715, 75.715, 122.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tectonin beta-propeller repeat-containing protein 1


Mass: 14086.729 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TECPR1, KIAA1358 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6L1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 6,000 100 mM LiCl 100 mM HEPES pH 75.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→44.83 Å / Num. obs: 31384 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2039 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.83 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 1601 5.11 %
Rwork0.1661 --
obs0.1681 31331 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 12 304 3103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112901
X-RAY DIFFRACTIONf_angle_d1.0743928
X-RAY DIFFRACTIONf_dihedral_angle_d11.183439
X-RAY DIFFRACTIONf_chiral_restr0.056344
X-RAY DIFFRACTIONf_plane_restr0.023495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.27511480.21692681X-RAY DIFFRACTION100
1.96-2.030.22791560.19692690X-RAY DIFFRACTION100
2.03-2.110.23731720.17792682X-RAY DIFFRACTION100
2.11-2.210.21681430.17962674X-RAY DIFFRACTION100
2.21-2.330.22621340.16282722X-RAY DIFFRACTION100
2.33-2.470.19461650.16192675X-RAY DIFFRACTION100
2.47-2.660.22131460.16452701X-RAY DIFFRACTION100
2.66-2.930.22771340.18472726X-RAY DIFFRACTION100
2.93-3.350.19151270.15812712X-RAY DIFFRACTION100
3.35-4.220.18731280.14752744X-RAY DIFFRACTION100
4.22-44.830.19881480.16432723X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.046-0.3217-0.62252.85191.8183.79810.12880.0208-0.0840.1289-0.0658-0.39080.14260.1598-0.02540.18290.02530.00360.13750.05160.32682.869854.045112.2154
24.07180.52990.08351.0307-0.12381.8401-0.0525-0.0560.11680.02380.0758-0.12620.04170.3814-0.0340.18250.07380.05410.35950.05870.20245.599171.3935-1.0086
32.6347-0.0817-0.05442.8074-1.87535.4442-0.0196-0.0901-0.01090.09380.23990.3251-0.0085-0.7698-0.13250.14490.01670.00240.27090.04960.1269-30.804266.22479.8729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 64 through 170)
2X-RAY DIFFRACTION2(chain 'B' and resid 66 through 170)
3X-RAY DIFFRACTION3(chain 'C' and resid 64 through 169)

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