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- PDB-6if0: Crystal structure of CERT START domain in complex with compound D16 -

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Basic information

Entry
Database: PDB / ID: 6if0
TitleCrystal structure of CERT START domain in complex with compound D16
ComponentsLIPID-TRANSFER PROTEIN CERT
KeywordsLIPID TRANSPORT
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-A59 / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSuzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K.
CitationJournal: Commun Chem / Year: 2019
Title: Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT
Authors: Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Suzuki, M. / Kobayashi, S. / Hanada, K.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPID-TRANSFER PROTEIN CERT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4922
Polymers27,0571
Non-polymers4361
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11600 Å2
Unit cell
Length a, b, c (Å)59.825, 59.825, 152.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LIPID-TRANSFER PROTEIN CERT


Mass: 27056.781 Da / Num. of mol.: 1 / Fragment: UNP residues 364-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CERT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5P4
#2: Chemical ChemComp-A59 / 2-({4'-pentyl-3'-[(Z)-2-(pyridin-2-yl)ethenyl][1,1'-biphenyl]-4-yl}sulfonyl)ethan-1-ol


Mass: 435.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1M trisodium citrate/HCL buffer, pH 5.9 containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.3 Å / Num. obs: 26600 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 7.7 / Num. measured all: 171003 / Scaling rejects: 258
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.846.40.76815170.7340.3290.837100
9-42.35.30.0252830.9990.0110.02799.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
REFMAC5.8.0230phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.953 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.126 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1311 4.9 %RANDOM
Rwork0.1954 ---
obs0.1975 25203 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.35 Å2 / Biso mean: 26.973 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 31 189 2058
Biso mean--25.21 34.06 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121918
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6592607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.3622.308104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83215321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8331513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021439
LS refinement shellResolution: 1.8→1.863 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.326 133 -
Rwork0.336 2386 -
all-2519 -
obs--99.8 %

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