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- PDB-5zyi: Crystal structure of CERT START domain in complex with compound E16 -

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Basic information

Entry
Database: PDB / ID: 5zyi
TitleCrystal structure of CERT START domain in complex with compound E16
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-9ML / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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)27,5062
Polymers27,0571
Non-polymers4501
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11640 Å2
Unit cell
Length a, b, c (Å)60.100, 60.100, 153.460
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-9ML / 2-[4-[4-pentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol


Mass: 449.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
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: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 22, 2017
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 26872 / % possible obs: 99.5 % / Redundancy: 6.798 % / Biso Wilson estimate: 36.071 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Χ2: 0.982 / Net I/σ(I): 21.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.7790.9571.8119680.6931.037100
1.85-1.96.7920.7932.2818760.7890.85999
1.9-1.956.6860.4734.318100.890.51397.3
1.95-2.016.8750.3225.5818040.9430.349100
2.01-2.086.8260.2467.7117480.9570.267100
2.08-2.156.8970.1969.6116810.970.212100
2.15-2.236.920.16411.4416240.9840.17898.2
2.23-2.326.6460.13914.8515630.9860.15199.1
2.32-2.436.9910.10317.0515230.9930.111100
2.43-2.556.950.0919.4114480.9950.09899.9
2.55-2.686.950.0723.5813940.9970.076100
2.68-2.856.9440.06127.813280.9980.066100
2.85-3.046.9250.04435.5712490.9980.048100
3.04-3.296.90.04139.8511650.9990.044100
3.29-3.66.7840.03348.4610770.9990.03699.9
3.6-4.026.6210.02953.529990.9990.03299.8
4.02-4.656.6920.02556.78810.9990.027100
4.65-5.696.5230.02556.847570.9990.027100
5.69-8.056.3380.02555.16090.9990.027100
8.05-255.4920.01955.83680.9990.02196.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementResolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.086 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.148 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1181 5.1 %RANDOM
Rwork0.2138 ---
obs0.2158 21768 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.23 Å2 / Biso mean: 32.443 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 32 104 1970
Biso mean--27.47 35.46 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121941
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6642645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6635230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78721.852108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2781515
X-RAY DIFFRACTIONr_chiral_restr0.1090.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021456
LS refinement shellResolution: 1.9→1.966 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.428 128 -
Rwork0.387 2039 -
all-2167 -
obs--98.41 %

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