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- PDB-4kf6: Crystal structure of human ceramide-1-phosphate transfer protein ... -

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Basic information

Entry
Database: PDB / ID: 4kf6
TitleCrystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 8:0 Ceramide-1-Phosphate (8:0-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-1T9 / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.195 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 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)149,93912
Polymers146,9056
Non-polymers3,0346
Water1629
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9902
Polymers24,4841
Non-polymers5061
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)24,9902
Polymers24,4841
Non-polymers5061
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)24,9902
Polymers24,4841
Non-polymers5061
Water0
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)24,9902
Polymers24,4841
Non-polymers5061
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)24,9902
Polymers24,4841
Non-polymers5061
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)24,9902
Polymers24,4841
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.884, 122.399, 149.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-1T9 / (2S,3R,4E)-3-hydroxy-2-(octanoylamino)octadec-4-en-1-yl dihydrogen phosphate


Mass: 505.668 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H52NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2009
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 25734 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 83.28 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.195→38.827 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1302 5.09 %Random
Rwork0.2219 ---
obs0.224 25604 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 251.39 Å2 / Biso mean: 81.1491 Å2 / Biso min: 25.86 Å2
Refinement stepCycle: LAST / Resolution: 3.195→38.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9757 0 149 9 9915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610129
X-RAY DIFFRACTIONf_angle_d0.99713739
X-RAY DIFFRACTIONf_chiral_restr0.0421560
X-RAY DIFFRACTIONf_plane_restr0.0051746
X-RAY DIFFRACTIONf_dihedral_angle_d15.8163762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1946-3.32250.3541320.32692640277299
3.3225-3.47360.32691260.280826922818100
3.4736-3.65660.3121500.265326442794100
3.6566-3.88550.28511430.23826902833100
3.8855-4.18520.26221480.207526612809100
4.1852-4.60570.2371590.197326852844100
4.6057-5.27080.22961610.198226882849100
5.2708-6.63520.33261460.241127392885100
6.6352-38.83030.2191370.19462863300099
Refinement TLS params.Method: refined / Origin x: -23.4021 Å / Origin y: 2.5709 Å / Origin z: 24.0531 Å
111213212223313233
T0.3396 Å2-0.1065 Å20.0631 Å2-0.321 Å20.0566 Å2--0.445 Å2
L0.4859 °2-0.2855 °20.1602 °2-0.6287 °20.467 °2--2.6049 °2
S0.061 Å °0.1377 Å °0.1807 Å °-0.107 Å °0.0883 Å °-0.0167 Å °-0.3757 Å °0.3538 Å °-0.1249 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 214
2X-RAY DIFFRACTION1allB7 - 214
3X-RAY DIFFRACTION1allC9 - 214
4X-RAY DIFFRACTION1allD9 - 214
5X-RAY DIFFRACTION1allE9 - 214
6X-RAY DIFFRACTION1allF9 - 214
7X-RAY DIFFRACTION1allB - F1 - 301
8X-RAY DIFFRACTION1allA - D1 - 401

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