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Basic information

Entry
Database: PDB / ID: 4ews
TitleCrystal structure of cholesteryl ester transfer protein in complex with inhibitors
ComponentsCETP
KeywordsLIPID TRANSPORT/INHIBITOR / Cholestryl Ester Transfer Protein / high-density lipoprotein / low-density lipoprotein / Cholestryl Ester Transfer Protein-INHIBITOR complex / LIPID TRANSPORT-INHIBITOR complex
Function / homology
Function and homology information


triglyceride binding / positive regulation of phospholipid transport / triglyceride transport / LDL remodeling / positive regulation of cholesterol transport / regulation of cholesterol efflux / phospholipid transporter activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / phospholipid homeostasis ...triglyceride binding / positive regulation of phospholipid transport / triglyceride transport / LDL remodeling / positive regulation of cholesterol transport / regulation of cholesterol efflux / phospholipid transporter activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / phospholipid homeostasis / phosphatidylcholine binding / high-density lipoprotein particle remodeling / reverse cholesterol transport / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / low-density lipoprotein particle remodeling / triglyceride homeostasis / lipid transport / HDL remodeling / triglyceride metabolic process / cholesterol binding / lipid homeostasis / negative regulation of macrophage derived foam cell differentiation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol metabolic process / cholesterol homeostasis / vesicle / lipid binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cholesteryl ester transfer / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain / Bactericidal permeability-increasing protein; domain 1 ...Cholesteryl ester transfer / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
ethyl / CHOLESTERYL OLEATE / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / TRIETHYLENE GLYCOL / Cholesteryl ester transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.59 Å
AuthorsLiu, S. / Qiu, X.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Crystal structures of cholesteryl ester transfer protein in complex with inhibitors.
Authors: Liu, S. / Mistry, A. / Reynolds, J.M. / Lloyd, D.B. / Griffor, M.C. / Perry, D.A. / Ruggeri, R.B. / Clark, R.W. / Qiu, X.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Crystal structure of cholesteryl ester transfer protein reveals a long tunnel and four bound lipid molecules.
Authors: Qiu, X. / Mistry, A. / Ammirati, M.J. / Chrunyk, B.A. / Clark, R.W. / Cong, Y. / Culp, J.S. / Danley, D.E. / Freeman, T.B. / Geoghegan, K.F. / Griffor, M.C. / Hawrylik, S.J. / Hayward, C.M. ...Authors: Qiu, X. / Mistry, A. / Ammirati, M.J. / Chrunyk, B.A. / Clark, R.W. / Cong, Y. / Culp, J.S. / Danley, D.E. / Freeman, T.B. / Geoghegan, K.F. / Griffor, M.C. / Hawrylik, S.J. / Hayward, C.M. / Hensley, P. / Hoth, L.R. / Karam, G.A. / Lira, M.E. / Lloyd, D.B. / McGrath, K.M. / Stutzman-Engwall, K.J. / Subashi, A.K. / Subashi, T.A. / Thompson, J.F. / Wang, I.K. / Zhao, H. / Seddon, A.P.
History
DepositionApr 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CETP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8519
Polymers53,0981
Non-polymers3,7538
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.600, 69.323, 188.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein CETP


Mass: 53097.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): DG44 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P11597
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 88 molecules

#3: Chemical ChemComp-2OB / CHOLESTERYL OLEATE / (3BETA,9BETA,14BETA,17ALPHA)-CHOLEST-5-EN-3-YL (9Z)-OCTADEC-9-ENOATE


Mass: 651.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H78O2
#4: Chemical ChemComp-DLP / 1,2-DILINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DI-LINOLEOYL-3-SN-PHOSPHATIDYLCHOLINE


Mass: 782.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H80NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-0RP / ethyl (2R,4S)-4-{[3,5-bis(trifluoromethyl)benzyl](methoxycarbonyl)amino}-2-ethyl-6-(trifluoromethyl)-3,4-dihydroquinoline-1(2H )-carboxylate / Torcetrapib


Mass: 600.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F9N2O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mg/ml protein 1:1 mixing with 0.1M HEPES, pH=7.5, 0.2 M MgCl2 and 27-35% (W/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 22976 / Num. obs: 22976 / % possible obs: 79.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 53.22 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2OBD

2obd


Resolution: 2.59→28.75 Å / Cor.coef. Fo:Fc: 0.9404 / Cor.coef. Fo:Fc free: 0.9099 / SU R Cruickshank DPI: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1148 5 %RANDOM
Rwork0.2132 ---
obs0.2155 22976 78.93 %-
Displacement parametersBiso mean: 82.43 Å2
Baniso -1Baniso -2Baniso -3
1--6.3137 Å20 Å20 Å2
2---1.4299 Å20 Å2
3---7.7436 Å2
Refine analyzeLuzzati coordinate error obs: 0.531 Å
Refinement stepCycle: LAST / Resolution: 2.59→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 251 81 4044
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094139HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.265702HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1502SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes588HARMONIC5
X-RAY DIFFRACTIONt_it4139HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion20.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion551SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4663SEMIHARMONIC4
LS refinement shellResolution: 2.59→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3481 62 5.83 %
Rwork0.3265 1002 -
all0.3276 1064 -
obs--78.93 %
Refinement TLS params.Method: refined / Origin x: 14.7249 Å / Origin y: 4.3266 Å / Origin z: 39.0924 Å
111213212223313233
T0.082 Å2-0.0096 Å20.0314 Å2-0.436 Å2-0.0514 Å2---0.1544 Å2
L0.5925 °20.2674 °2-0.5153 °2-0.5416 °2-0.7196 °2--3.2256 °2
S0.0425 Å °-0.1094 Å °-0.0269 Å °-0.0107 Å °-0.0373 Å °-0.1462 Å °-0.0577 Å °0.4501 Å °-0.0052 Å °

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