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- PDB-5zyh: Crystal structure of CERT START domain in complex with compound E5 -

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Basic information

Entry
Database: PDB / ID: 5zyh
TitleCrystal structure of CERT START domain in complex with compound E5
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 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-9N0 / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.95 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)27,4922
Polymers27,0571
Non-polymers4361
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11650 Å2
Unit cell
Length a, b, c (Å)60.090, 60.090, 153.770
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 (E. coli) / References: UniProt: Q9Y5P4
#2: Chemical ChemComp-9N0 / 2-[4-[3-~{tert}-butyl-5-[(1~{R},2~{S})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol


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.: 108 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
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 FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2016
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→55.97 Å / Num. obs: 21424 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Net I/σ(I): 14.5 / Num. measured all: 81037 / Scaling rejects: 268
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-23.80.41414810.7990.2430.483100
8.94-55.973.10.0432800.970.0330.05599.2

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.5.32data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementResolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.329 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.157 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1074 5 %RANDOM
Rwork0.2121 ---
obs0.214 20280 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.78 Å2 / Biso mean: 31.547 Å2 / Biso min: 11.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 31 108 1974
Biso mean--46.36 34.36 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121915
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6622610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79322.381105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33915318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6191513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021431
LS refinement shellResolution: 1.95→2.018 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.367 117 -
Rwork0.295 1921 -
all-2038 -
obs--99.85 %

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