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- PDB-6j0o: Crystal structure of CERT START domain in complex with compound SC1 -

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Basic information

Entry
Database: PDB / ID: 6j0o
TitleCrystal structure of CERT START domain in complex with compound SC1
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-XAF / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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
DepositionDec 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)27,4943
Polymers27,0571
Non-polymers4372
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11680 Å2
Unit cell
Length a, b, c (Å)60.250, 60.250, 153.550
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
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-XAF / 2-[4-[2-fluoranyl-5-[3-(6-methylpyridin-2-yl)-1~{H}-pyrazol-4-yl]phenyl]phenyl]sulfonylethanol


Mass: 437.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20FN3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsUNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. ...UNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. However distances between this peak and surrounding H-bond donor/acceptor are too short. Therefore it is assigned to unknown atom, not to water oxygen.
Sequence detailsAuthors state that these amino residues are originated from protease site after N-terminal affinity tag.

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1M trisodium citrate/HCL buffer, pH5.9 containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 10, 2014
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→30.13 Å / Num. obs: 27078 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 16.4 / Num. measured all: 122989 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.50.442698115510.8970.230.52.699.3
9-30.133.80.01710172710.9990.010.0240.997.6

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Processing

Software
NameVersionClassification
MOSFLM7.0.9data reduction
Aimless0.2.8data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.617 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1244 4.6 %RANDOM
Rwork0.2015 ---
obs0.2035 25774 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.37 Å2 / Biso mean: 26.48 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 32 208 2065
Biso mean--28.29 35.13 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121904
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.662595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5585227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15122.157102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18515311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021469
LS refinement shellResolution: 1.8→1.863 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.288 129 -
Rwork0.26 2417 -
all-2546 -
obs--99.03 %

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