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- PDB-5zyl: Crystal structure of CERT START domain in complex with compound E25A -

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Basic information

Entry
Database: PDB / ID: 5zyl
TitleCrystal structure of CERT START domain in complex with compound E25A
ComponentsLIPID-TRANSFER PROTEIN CERT
KeywordsLIPID TRANSPORT / CERT / PH / START / COMPLEX
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / ceramide transport / ceramide metabolic process / ceramide binding / intermembrane lipid transfer / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / ceramide transport / ceramide metabolic process / ceramide binding / intermembrane lipid transfer / 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-9MC / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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
DepositionMay 25, 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)27,5963
Polymers27,0571
Non-polymers5402
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.006, 60.006, 153.455
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 / Ceramide transfer protein / hCERT / StAR-related lipid transfer protein 11


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 / Plasmid: pET28b-His-3C-CERT START / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5P4
#2: Chemical ChemComp-9MC / 2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol


Mass: 447.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTwo residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. ...Two residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. THIS SEQUENCE CORRESPONDS TO THE ISOFORM 2 FOUND IN UNP Q9Y5P4.

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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: 2.55 Å3/Da / Density % sol: 51.82 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Oct 3, 2017 / Details: detector name is RIGAKU HyPix-6000HE
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→30.69 Å / Num. obs: 26974 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.035 / Rrim(I) all: 0.111 / Net I/σ(I): 16.8 / Num. measured all: 263927 / Scaling rejects: 493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.846.10.7215710.7790.3030.784100
9-30.695.90.0342790.9990.0150.03797.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
REFMACphasing
RefinementResolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.719 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.123 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1346 5 %RANDOM
Rwork0.1744 ---
obs0.1769 25537 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.47 Å2 / Biso mean: 18.614 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 38 330 2257
Biso mean--15.98 29.36 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122015
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.6682743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1522.696115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6571514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021517
LS refinement shellResolution: 1.8→1.863 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.272 140 -
Rwork0.245 2442 -
all-2582 -
obs--99.96 %

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