[English] 日本語
Yorodumi
- PDB-2obd: Crystal Structure of Cholesteryl Ester Transfer Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 7 types, 425 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more