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- PDB-4k8n: Crystal structure of human ceramide-1-phosphate transfer protein ... -

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Basic information

Entry
Database: PDB / ID: 4k8n
TitleCrystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 18:1 Ceramide-1-Phosphate (18:1-C1P)
ComponentsGlycolipid transfer protein domain-containing protein 1
KeywordsLIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid
Function / homology
Function and homology information


ceramide 1-phosphate transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-1 beta production / nuclear outer membrane / negative regulation of autophagy ...ceramide 1-phosphate transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-1 beta production / nuclear outer membrane / negative regulation of autophagy / phospholipid binding / endosome membrane / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Glycolipid transfer protein domain / Glycolipid transfer protein superfamily / Glycolipid transfer protein (GLTP) / Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1Q0 / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å
AuthorsSimanshu, D.K. / Brown, R.E. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids.
Authors: Simanshu, D.K. / Kamlekar, R.K. / Wijesinghe, D.S. / Zou, X. / Zhai, X. / Mishra, S.K. / Molotkovsky, J.G. / Malinina, L. / Hinchcliffe, E.H. / Chalfant, C.E. / Brown, R.E. / Patel, D.J.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycolipid transfer protein domain-containing protein 1
B: Glycolipid transfer protein domain-containing protein 1
C: Glycolipid transfer protein domain-containing protein 1
D: Glycolipid transfer protein domain-containing protein 1
E: Glycolipid transfer protein domain-containing protein 1
F: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,76812
Polymers146,9056
Non-polymers3,8646
Water27015
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1282
Polymers24,4841
Non-polymers6441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)236.983, 128.758, 66.663
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glycolipid transfer protein domain-containing protein 1


Mass: 24484.154 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTPD1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q5TA50
#2: Chemical
ChemComp-1Q0 / (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate


Mass: 643.918 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H70NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium malonate, 0.1 M Bis-Tris Propane pH 6.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 35765 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.1-3.2150.478198
3.21-3.3450.342199.1
3.34-3.494.90.283199.2
3.49-3.674.90.222199.7
3.67-3.94.90.16199.6
3.9-4.2150.12199.7
4.21-4.634.90.096199.7
4.63-5.294.90.085199.7
5.29-6.664.80.084199.6
6.66-304.90.055198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CPTP in complex with 2:0 ceramide-1-phosphate

Resolution: 3.102→30.052 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.35 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1784 4.99 %
Rwork0.225 --
obs0.2271 35733 98.52 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.3277 Å2
Baniso -1Baniso -2Baniso -3
1--11.1732 Å20 Å22.4873 Å2
2--10.6599 Å2-0 Å2
3---0.5133 Å2
Refinement stepCycle: LAST / Resolution: 3.102→30.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9865 0 219 15 10099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510304
X-RAY DIFFRACTIONf_angle_d0.87213945
X-RAY DIFFRACTIONf_dihedral_angle_d17.5563898
X-RAY DIFFRACTIONf_chiral_restr0.0581572
X-RAY DIFFRACTIONf_plane_restr0.0041762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1016-3.18540.47411060.34912388X-RAY DIFFRACTION89
3.1854-3.2790.31481420.29632578X-RAY DIFFRACTION99
3.279-3.38470.30741290.27042627X-RAY DIFFRACTION99
3.3847-3.50550.33311250.27582660X-RAY DIFFRACTION99
3.5055-3.64570.30851290.272613X-RAY DIFFRACTION100
3.6457-3.81130.29471330.24352625X-RAY DIFFRACTION100
3.8113-4.01180.28561500.2272621X-RAY DIFFRACTION99
4.0118-4.26250.27221410.21782642X-RAY DIFFRACTION100
4.2625-4.59050.22731410.19732626X-RAY DIFFRACTION100
4.5905-5.05050.25811310.19552645X-RAY DIFFRACTION100
5.0505-5.77680.25621600.21892628X-RAY DIFFRACTION100
5.7768-7.26120.24991490.23032653X-RAY DIFFRACTION99
7.2612-30.05360.20091480.17842643X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 38.5333 Å / Origin y: -63.1682 Å / Origin z: -3.6328 Å
111213212223313233
T0.2837 Å2-0.0396 Å2-0.0166 Å2-0.4712 Å20.0486 Å2--0.264 Å2
L0.6853 °20.0255 °2-0.0521 °2-0.4235 °20.0608 °2--0.5435 °2
S-0.0586 Å °0.0409 Å °-0.0724 Å °0.029 Å °0.0428 Å °-0.0469 Å °0.0593 Å °0.1751 Å °0.0087 Å °
Refinement TLS groupSelection details: all

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