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- PDB-2e3p: Crystal structure of CERT START domain in complex with C16-cearmi... -

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Basic information

Entry
Database: PDB / ID: 2e3p
TitleCrystal structure of CERT START domain in complex with C16-cearmide (P1)
ComponentsLipid-transfer protein CERT
KeywordsLIPID TRANSPORT / LIPID TRANSFER PROTEIN / CERT / CERAMIDE TRANSFER
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide metabolic process / intermembrane lipid transfer / ceramide binding / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide metabolic process / intermembrane lipid transfer / ceramide binding / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / muscle contraction / response to endoplasmic reticulum stress / mitochondrion organization / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain ...STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-16C / Ceramide transfer protein / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKudo, N. / Kumagai, K. / Wakatsuki, S. / Nishijima, M. / Hanada, K. / Kato, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.
Authors: Kudo, N. / Kumagai, K. / Tomishige, N. / Yamaji, T. / Wakatsuki, S. / Nishijima, M. / Hanada, K. / Kato, R.
History
DepositionNov 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid-transfer protein CERT
B: Lipid-transfer protein CERT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9394
Polymers57,8642
Non-polymers1,0762
Water7,044391
1
A: Lipid-transfer protein CERT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4702
Polymers28,9321
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipid-transfer protein CERT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4702
Polymers28,9321
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.976, 49.699, 62.365
Angle α, β, γ (deg.)77.72, 71.06, 82.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lipid-transfer protein CERT / Goodpasture-antigen binding protein / GPBP / CDNA FLJ34532 fis / clone HLUNG2008235 / highly ...Goodpasture-antigen binding protein / GPBP / CDNA FLJ34532 fis / clone HLUNG2008235 / highly similar to Homo sapiens goodpasture antigen-binding protein (COL4A3BP)mRNA


Mass: 28931.764 Da / Num. of mol.: 2 / Fragment: CERT START DOMAIN (RESIDUES 347-598)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CERT / Plasmid: pGEX-5X1 (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q53YV2, UniProt: Q9Y5P4*PLUS
#2: Chemical ChemComp-16C / N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE / C16-CERAMIDE / N-PALMITOYL-D-ERYTHRO-SPHINGOSINE / (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL / (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL


Mass: 537.901 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H67NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→58.03 Å / Num. obs: 92503 / % possible obs: 92.7 %
Reflection shellResolution: 1.4→1.45 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.588 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4762 5 %RANDOM
Rwork0.217 ---
obs0.219 90431 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.3 Å2-0.24 Å2
2---0.06 Å20.18 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 76 391 4377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224071
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9495528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08624.229201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90715724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8691530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21798
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22784
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2316
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.52432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26723927
X-RAY DIFFRACTIONr_scbond_it1.90431861
X-RAY DIFFRACTIONr_scangle_it2.9134.51601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 314 -
Rwork0.399 6150 -
obs--88.27 %

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