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- PDB-4kbr: Crystal structure of mouse Ceramide-1-phosphate transfer protein ... -

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Basic information

Entry
Database: PDB / ID: 4kbr
TitleCrystal structure of mouse Ceramide-1-phosphate transfer protein (apo-form)
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


Glycosphingolipid metabolism / ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...Glycosphingolipid metabolism / ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / 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 / lipid binding / Golgi apparatus / membrane / 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
PHOSPHATE ION / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.547 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 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.3Apr 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
E: Glycolipid transfer protein domain-containing protein 1
F: Glycolipid transfer protein domain-containing protein 1
G: Glycolipid transfer protein domain-containing protein 1
H: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,73816
Polymers197,9798
Non-polymers7608
Water4,576254
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,7471
Non-polymers951
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)24,8422
Polymers24,7471
Non-polymers951
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)24,8422
Polymers24,7471
Non-polymers951
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)24,8422
Polymers24,7471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,7471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,7471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,7471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8422
Polymers24,7471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Glycolipid transfer protein domain-containing protein 1
C: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6854
Polymers49,4952
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-23 kcal/mol
Surface area18870 Å2
MethodPISA
10
B: Glycolipid transfer protein domain-containing protein 1
E: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6854
Polymers49,4952
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-22 kcal/mol
Surface area19200 Å2
MethodPISA
11
D: Glycolipid transfer protein domain-containing protein 1
hetero molecules

G: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6854
Polymers49,4952
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1440 Å2
ΔGint-22 kcal/mol
Surface area18740 Å2
MethodPISA
12
F: Glycolipid transfer protein domain-containing protein 1
hetero molecules

H: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6854
Polymers49,4952
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1300 Å2
ΔGint-20 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.997, 83.876, 268.721
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: 24747.330 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gltpd1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q8BS40
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 2 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 57653 / % possible obs: 93.5 % / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Χ2: 1.091 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.6410.60.59651590.891185.4
2.64-2.7510.40.47952390.972186.3
2.75-2.8710.30.34853580.924188.1
2.87-3.0210.20.24154520.987189.3
3.02-3.21100.17255841.062191.9
3.21-3.469.70.11258861.167195.6
3.46-3.819.60.08160571.185198.4
3.81-4.369.70.06961521.286199.7
4.36-5.499.90.06862441.404199.9
5.49-509.80.03265220.991199.8

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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
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human CPTP in complex with 2:0 C1P

Resolution: 2.547→39.507 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 2912 5.07 %Random
Rwork0.2006 ---
obs0.2042 57462 93.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.47 Å2 / Biso mean: 55.3094 Å2 / Biso min: 27.35 Å2
Refinement stepCycle: LAST / Resolution: 2.547→39.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12910 0 40 254 13204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913222
X-RAY DIFFRACTIONf_angle_d1.15117930
X-RAY DIFFRACTIONf_chiral_restr0.0532074
X-RAY DIFFRACTIONf_plane_restr0.0072243
X-RAY DIFFRACTIONf_dihedral_angle_d12.7024717
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5468-2.58850.35641390.23972215235482
2.5885-2.63310.39421240.25842378250286
2.6331-2.6810.35081100.24872368247886
2.681-2.73260.33571220.26762396251886
2.7326-2.78830.37641370.26692405254288
2.7883-2.84890.36441180.24912380249888
2.8489-2.91520.341320.2432460259289
2.9152-2.98810.32811240.24372481260590
2.9881-3.06880.34941230.25462483260690
3.0688-3.15910.31821430.25822530267391
3.1591-3.2610.31591500.26782598274894
3.261-3.37750.29951450.22792629277496
3.3775-3.51270.31211580.22012689284797
3.5127-3.67240.31881360.20442740287698
3.6724-3.86590.21851360.18762748288499
3.8659-4.10790.22661490.16927882937100
4.1079-4.42460.23461620.158427932955100
4.4246-4.86920.21711460.151728202966100
4.8692-5.57210.24561620.185428252987100
5.5721-7.01380.26771270.211328933020100
7.0138-39.51220.20621690.16012931310098
Refinement TLS params.Method: refined / Origin x: -27.1615 Å / Origin y: 27.2651 Å / Origin z: -33.5591 Å
111213212223313233
T0.366 Å2-0.0511 Å20.0047 Å2-0.3637 Å20.0244 Å2--0.3574 Å2
L-0.0647 °20.0254 °20.0019 °2--0.0113 °20.0177 °2--0.1727 °2
S0.0043 Å °0.0697 Å °-0.009 Å °0.0902 Å °-0.0178 Å °0.0128 Å °0.0149 Å °-0.0286 Å °0.0105 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 216
2X-RAY DIFFRACTION1allB8 - 216
3X-RAY DIFFRACTION1allC8 - 216
4X-RAY DIFFRACTION1allD8 - 216
5X-RAY DIFFRACTION1allE8 - 216
6X-RAY DIFFRACTION1allF8 - 216
7X-RAY DIFFRACTION1allG7 - 216
8X-RAY DIFFRACTION1allH8 - 216
9X-RAY DIFFRACTION1allB - G1 - 301
10X-RAY DIFFRACTION1allC - G1 - 429

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