[English] 日本語
Yorodumi
- PDB-1eth: TRIACYLGLYCEROL LIPASE/COLIPASE COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eth
TitleTRIACYLGLYCEROL LIPASE/COLIPASE COMPLEX
Components
  • COLIPASE
  • TRIACYLGLYCEROL ACYL-HYDROLASE
KeywordsCOMPLEX (HYDROLASE/COFACTOR) / COMPLEX (HYDROLASE-COFACTOR) / LIPID DEGRADATION / COMPLEX (HYDROLASE-COFACTOR) complex
Function / homology
Function and homology information


Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / high-density lipoprotein particle remodeling / triacylglycerol lipase / triacylglycerol lipase activity ...Digestion of dietary lipid / Retinoid metabolism and transport / all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity / lipoprotein lipase activity / lipase binding / phospholipase A1 activity / triglyceride catabolic process / high-density lipoprotein particle remodeling / triacylglycerol lipase / triacylglycerol lipase activity / response to food / retinoid metabolic process / lipid catabolic process / digestion / cholesterol homeostasis / response to bacterium / enzyme activator activity / fatty acid biosynthetic process / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase ...Colipase / Colipase, N-terminal / Colipase, C-terminal / Colipase, conserved site / : / Colipase, N-terminal domain / Colipase, C-terminal domain / Colipase signature. / Colipase family profile. / Colipase / Pancreatic lipase / Lipase, subunit A / Lipase, subunit A / Lipase, LIPH-type / Lipase, N-terminal / Triacylglycerol lipase family / Lipase / Lipase / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipases, serine active site. / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Pancreatic triacylglycerol lipase / Colipase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHermoso, J. / Pignol, D. / Kerfelec, B. / Crenon, I. / Chapus, C. / Fontecilla-Camps, J.C.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Lipase activation by nonionic detergents. The crystal structure of the porcine lipase-colipase-tetraethylene glycol monooctyl ether complex.
Authors: Hermoso, J. / Pignol, D. / Kerfelec, B. / Crenon, I. / Chapus, C. / Fontecilla-Camps, J.C.
#1: Journal: Nature / Year: 1993
Title: Interfacial Activation of the Lipase-Procolipase Complex by Mixed Micelles Revealed by X-Ray Crystallography
Authors: Van Tilbeurgh, H. / Egloff, M.P. / Martinez, C. / Rugani, N. / Verger, R. / Cambillau, C.
#2: Journal: Nature / Year: 1992
Title: Structure of the Pancreatic Lipase-Procolipase Complex
Authors: Van Tilbeurgh, H. / Sarda, L. / Verger, R. / Cambillau, C.
History
DepositionSep 13, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
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 / database_PDB_caveat / 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_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIACYLGLYCEROL ACYL-HYDROLASE
B: COLIPASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
D: COLIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,74114
Polymers120,4574
Non-polymers3,28410
Water6,431357
1
A: TRIACYLGLYCEROL ACYL-HYDROLASE
B: COLIPASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,42113
Polymers110,1373
Non-polymers3,28410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRIACYLGLYCEROL ACYL-HYDROLASE
C: TRIACYLGLYCEROL ACYL-HYDROLASE
D: COLIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,42113
Polymers110,1373
Non-polymers3,28410
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)289.100, 289.100, 289.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein TRIACYLGLYCEROL ACYL-HYDROLASE / TRIACYLGLYCEROL LIPASE


Mass: 49908.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00591, triacylglycerol lipase
#2: Protein COLIPASE


Mass: 10319.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P02703

-
Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 365 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 61 %
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mllipase1drop0.01ml
210 mg/mlcolipase1drop0.007 ml
350 mMMES1reservoir
40.5 Mammonium sulfate1reservoir
515 mMTGME1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorDetector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→12.4 Å / Num. obs: 42501 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.13

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.8→6 Å / σ(F): 2 / Details: CRYST1 UNUSUAL UNIT-CELL DATA: PSEUDOSYMMETRY P 23
RfactorNum. reflection% reflection
Rfree0.29 -7 %
Rwork0.21 --
obs0.21 33758 -
Displacement parametersBiso mean: 19.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 216 357 8911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.62

+
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