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- PDB-4k85: Crystal structure of human ceramide-1-phosphate transfer protein ... -

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Basic information

Entry
Database: PDB / ID: 4k85
TitleCrystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 12:0 Ceramide-1-Phosphate (12:0-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 1-phosphate binding / ceramide transport / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...ceramide 1-phosphate transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / ceramide transport / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / 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-1PZ / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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 / _pdbx_database_related.db_name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1848
Polymers97,9374
Non-polymers2,2474
Water12,322684
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,4841
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,4841
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,4841
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0462
Polymers24,4841
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.191, 132.677, 62.107
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24484.154 Da / Num. of mol.: 4
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-1PZ / (2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate


Mass: 561.774 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H60NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium chloride, 0.1 M Hepes pH 7.0, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 70265 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.974.70.44193.1
1.97-2.055.20.346198.7
2.05-2.145.60.2591100
2.14-2.255.70.1941100
2.25-2.395.70.1421100
2.39-2.585.70.1141100
2.58-2.845.70.0891100
2.84-3.255.70.071100
3.25-4.095.60.0521100
4.09-505.60.042199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CPTP in complex with 2:0 ceramide-1-phosphate

Resolution: 1.901→31.232 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.23 / σ(F): 0.14 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 3402 5.04 %
Rwork0.1813 --
obs0.1837 67553 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3866 Å20 Å2-2.4213 Å2
2--10.0523 Å2-0 Å2
3----5.6656 Å2
Refinement stepCycle: LAST / Resolution: 1.901→31.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 152 684 7486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076968
X-RAY DIFFRACTIONf_angle_d0.9719424
X-RAY DIFFRACTIONf_dihedral_angle_d16.7722667
X-RAY DIFFRACTIONf_chiral_restr0.0621055
X-RAY DIFFRACTIONf_plane_restr0.0051192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9008-1.92790.28741110.23372209X-RAY DIFFRACTION77
1.9279-1.95670.3121340.22752262X-RAY DIFFRACTION82
1.9567-1.98730.27651300.20952423X-RAY DIFFRACTION88
1.9873-2.01990.2581250.19952552X-RAY DIFFRACTION90
2.0199-2.05470.25361290.18992573X-RAY DIFFRACTION92
2.0547-2.0920.23941280.19252620X-RAY DIFFRACTION93
2.092-2.13230.24931630.18352620X-RAY DIFFRACTION95
2.1323-2.17580.23841420.18252680X-RAY DIFFRACTION96
2.1758-2.22310.26221300.18152716X-RAY DIFFRACTION96
2.2231-2.27480.27031550.17812647X-RAY DIFFRACTION96
2.2748-2.33170.21791500.17562762X-RAY DIFFRACTION97
2.3317-2.39470.2071330.17042723X-RAY DIFFRACTION97
2.3947-2.46510.23861390.18342738X-RAY DIFFRACTION98
2.4651-2.54460.2361610.18932726X-RAY DIFFRACTION98
2.5446-2.63550.27651500.18912743X-RAY DIFFRACTION99
2.6355-2.7410.29081490.1862735X-RAY DIFFRACTION98
2.741-2.86570.23651530.19042767X-RAY DIFFRACTION99
2.8657-3.01660.24391430.18942780X-RAY DIFFRACTION99
3.0166-3.20550.23051420.19062794X-RAY DIFFRACTION99
3.2055-3.45270.23221370.17872815X-RAY DIFFRACTION100
3.4527-3.79960.20981160.16772827X-RAY DIFFRACTION100
3.7996-4.34810.19181730.14862810X-RAY DIFFRACTION100
4.3481-5.47340.18781500.16742802X-RAY DIFFRACTION100
5.4734-31.2360.19781590.1812827X-RAY DIFFRACTION99

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