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- PDB-4f2a: Crystal structure of cholestryl esters transfer protein in comple... -

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Basic information

Entry
Database: PDB / ID: 4f2a
TitleCrystal structure of cholestryl esters transfer protein in complex with inhibitors
ComponentsCholesteryl ester transfer protein
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 / regulation of cholesterol efflux / phospholipid transporter activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / phospholipid homeostasis / high-density lipoprotein particle remodeling ...triglyceride binding / positive regulation of phospholipid transport / triglyceride transport / LDL remodeling / regulation of cholesterol efflux / phospholipid transporter activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / phospholipid homeostasis / high-density lipoprotein particle remodeling / phosphatidylcholine binding / cholesterol transfer activity / reverse cholesterol transport / cholesterol transport / high-density lipoprotein particle / low-density lipoprotein particle remodeling / triglyceride homeostasis / HDL remodeling / positive regulation of cholesterol transport / triglyceride metabolic process / lipid transport / 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
Chem-0SF / CHOLESTERYL OLEATE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / TRIETHYLENE GLYCOL / Cholesteryl ester transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.11 Å
AuthorsLiu, S. / Qiu, X.
CitationJournal: 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.
History
DepositionMay 7, 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholesteryl ester transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6738
Polymers53,0981
Non-polymers3,5767
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.772, 69.915, 187.145
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 Cholesteryl ester transfer protein / Lipid transfer protein I


Mass: 53097.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETP / 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 , 5 types, 6 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-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / 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-0SF / (2R)-3-{[4-(4-chloro-3-ethylphenoxy)pyrimidin-2-yl][3-(1,1,2,2-tetrafluoroethoxy)benzyl]amino}-1,1,1-trifluoropropan-2-ol


Mass: 567.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21ClF7N3O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.97 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 16759 / Num. obs: 12770 / % possible obs: 76.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 45.83 Å2 / Rmerge(I) obs: 0.111

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.11→38.88 Å / Cor.coef. Fo:Fc: 0.9077 / Cor.coef. Fo:Fc free: 0.8523 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 614 4.82 %RANDOM
Rwork0.1828 ---
obs0.1855 12746 75.53 %-
Displacement parametersBiso mean: 102.06 Å2
Baniso -1Baniso -2Baniso -3
1--20.9719 Å20 Å20 Å2
2---18.576 Å20 Å2
3---39.5479 Å2
Refine analyzeLuzzati coordinate error obs: 0.736 Å
Refinement stepCycle: LAST / Resolution: 3.11→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 234 0 3946
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014079HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.355540HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1499SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes592HARMONIC5
X-RAY DIFFRACTIONt_it4079HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion23.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion550SEMIHARMONIC5
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_contact4619SEMIHARMONIC4
LS refinement shellResolution: 3.11→3.41 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 43 3.3 %
Rwork0.2467 1261 -
all0.248 1304 -
obs--75.53 %
Refinement TLS params.Method: refined / Origin x: -14.638 Å / Origin y: 4.1221 Å / Origin z: -39.1618 Å
111213212223313233
T-0.0202 Å20.0724 Å20.0287 Å2-0.1058 Å20.1036 Å2--0.074 Å2
L0.8626 °2-0.2622 °2-0.7761 °2-0.8601 °20.8209 °2--4.2696 °2
S0.0343 Å °0.0759 Å °-0.0948 Å °0.0343 Å °-0.0695 Å °0.1987 Å °-0.134 Å °-0.2909 Å °0.0351 Å °
Refinement TLS groupSelection details: { A|5 - A|476 }

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