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- PDB-2obd: Crystal Structure of Cholesteryl Ester Transfer Protein -

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Entry
Database: PDB / ID: 2obd
TitleCrystal Structure of Cholesteryl Ester Transfer Protein
ComponentsCholesteryl ester transfer protein
KeywordsLIPID TRANSPORT / cholesteryl ester / lipid transfer protein
Function / homology
Function and homology information


triglyceride binding / positive regulation of phospholipid transport / triglyceride transport / LDL remodeling / regulation of cholesterol efflux / positive regulation of cholesterol transport / very-low-density lipoprotein particle remodeling / phospholipid transporter activity / high-density lipoprotein particle remodeling / cholesterol transfer activity ...triglyceride binding / positive regulation of phospholipid transport / triglyceride transport / LDL remodeling / regulation of cholesterol efflux / positive regulation of cholesterol transport / very-low-density lipoprotein particle remodeling / phospholipid transporter activity / high-density lipoprotein particle remodeling / cholesterol transfer activity / reverse cholesterol transport / phosphatidylcholine metabolic process / phospholipid homeostasis / low-density lipoprotein particle remodeling / high-density lipoprotein particle / phosphatidylcholine binding / triglyceride homeostasis / cholesterol transport / HDL remodeling / triglyceride metabolic process / cholesterol binding / lipid transport / 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
CHOLESTERYL OLEATE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cholesteryl ester transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsQiu, X.
CitationJournal: 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
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 29, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.0Oct 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / database_PDB_caveat / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_list.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Revision 4.1Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholesteryl ester transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,48911
Polymers53,0981
Non-polymers4,39210
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.780, 70.320, 187.620
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 / Mutation: C1A, C131A, N88D, N240D, N341D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETP / Cell line (production host): Chinese Hamster Ovary DG44 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P11597
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 425 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: 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.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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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: 4.15 Å3/Da / Density % sol: 70.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ~30% PDE 400, 0.2M MgCl2, HEPES 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONESRF ID23-121
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 20, 2005
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 59800 / Num. obs: 52263 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.157 Å / Redundancy: 3 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.1 / % possible all: 50

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→46.88 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.674 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.219 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 2176 5.1 %RANDOM
Rwork0.21689 ---
all0.22 52263 --
obs0.22 40673 81.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--2.07 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 301 416 4465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224135
X-RAY DIFFRACTIONr_angle_refined_deg1.6352.0245572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90224.819166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72515678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7021513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022903
X-RAY DIFFRACTIONr_nbd_refined0.2090.21869
X-RAY DIFFRACTIONr_nbtor_refined0.320.22745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.219
X-RAY DIFFRACTIONr_mcbond_it0.6971.52431
X-RAY DIFFRACTIONr_mcangle_it1.22823855
X-RAY DIFFRACTIONr_scbond_it1.86231864
X-RAY DIFFRACTIONr_scangle_it3.0184.51717
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 70 -
Rwork0.3 1449 -
obs--39.96 %

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