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- PDB-8eoj: Microsomal triglyceride transfer protein -

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Basic information

Entry
Database: PDB / ID: 8eoj
TitleMicrosomal triglyceride transfer protein
Components
  • Microsomal triglyceride transfer protein large subunit
  • Protein disulfide-isomerase
KeywordsTRANSPORT PROTEIN / Microsomal triglyceride transfer protein / human liver / LIPID TRANSPORT / ISOMERASE
Function / homology
Function and homology information


plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / phosphatidylethanolamine transfer activity / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing ...plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / phosphatidylethanolamine transfer activity / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / triglyceride transport / phospholipid transfer activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / ceramide 1-phosphate transfer activity / very-low-density lipoprotein particle assembly / phospholipid transporter activity / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / lipoprotein metabolic process / Collagen biosynthesis and modifying enzymes / Chylomicron assembly / interleukin-23-mediated signaling pathway / lipid transporter activity / phospholipid transport / cholesterol transfer activity / Interleukin-23 signaling / low-density lipoprotein particle remodeling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / triglyceride metabolic process / lipoprotein transport / microvillus membrane / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / apolipoprotein binding / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / positive regulation of cell adhesion / cholesterol homeostasis / establishment of localization in cell / Post-translational protein phosphorylation / brush border membrane / Hedgehog ligand biogenesis / lipid metabolic process / response to calcium ion / circadian rhythm / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / basolateral plasma membrane / vesicle / positive regulation of viral entry into host cell / cytoskeleton / receptor complex / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / lipid binding / protein-containing complex binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Microsomal triglyceride transfer protein large subunit / MTP large subunit, lipid-binding domain / MTP large subunit, lipid-binding domain / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain ...Microsomal triglyceride transfer protein large subunit / MTP large subunit, lipid-binding domain / MTP large subunit, lipid-binding domain / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Protein disulfide-isomerase / Microsomal triglyceride transfer protein large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsZhang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2023
Title: High-resolution structural-omics of human liver enzymes.
Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu /
Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
History
DepositionOct 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein disulfide-isomerase
B: Microsomal triglyceride transfer protein large subunit


Theoretical massNumber of molelcules
Total (without water)156,6642
Polymers156,6642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein disulfide-isomerase / PDI / Cellular thyroid hormone-binding protein / Prolyl 4-hydroxylase subunit beta / p55


Mass: 57190.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P07237, protein disulfide-isomerase
#2: Protein Microsomal triglyceride transfer protein large subunit


Mass: 99474.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55157

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Microsomal triglyceride transfer protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3291 nm / Nominal defocus min: 170 nm
Image recordingElectron dose: 41.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 487553
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249877 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 72.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029474
ELECTRON MICROSCOPYf_angle_d0.51312780
ELECTRON MICROSCOPYf_dihedral_angle_d11.3183461
ELECTRON MICROSCOPYf_chiral_restr0.0421482
ELECTRON MICROSCOPYf_plane_restr0.0041629

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