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- EMDB-28377: Microsomal triglyceride transfer protein -

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Basic information

Entry
Database: EMDB / ID: EMD-28377
TitleMicrosomal triglyceride transfer protein
Map dataMicrosomal triglyceride transfer protein
Sample
  • Complex: Microsomal triglyceride transfer protein
    • Protein or peptide: Protein disulfide-isomerase
    • Protein or peptide: Microsomal triglyceride transfer protein large subunit
KeywordsMicrosomal triglyceride transfer protein / human liver / LIPID TRANSPORT / ISOMERASE / TRANSPORT PROTEIN
Function / homology
Function and homology information


plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / triglyceride transport / phospholipid transfer activity ...plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / triglyceride transport / phospholipid transfer activity / phosphatidylethanolamine transfer activity / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / ceramide 1-phosphate transfer activity / phospholipid transporter activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / very-low-density lipoprotein particle assembly / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Chylomicron assembly / lipid transporter activity / lipoprotein metabolic process / cholesterol transfer activity / phospholipid transport / Interleukin-23 signaling / low-density lipoprotein particle remodeling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / lipoprotein transport / triglyceride metabolic process / microvillus membrane / protein disulfide isomerase activity / Insulin processing / Detoxification of Reactive Oxygen Species / apolipoprotein binding / protein secretion / protein-disulfide reductase activity / positive regulation of cell adhesion / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / cholesterol homeostasis / establishment of localization in cell / brush border membrane / Hedgehog ligand biogenesis / Post-translational protein phosphorylation / 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 / receptor complex / cytoskeleton / protein heterodimerization activity / external side of plasma membrane / endoplasmic reticulum lumen / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsZhang Z
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28377.png

Downloads & links

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Map

FileDownload / File: emd_28377.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMicrosomal triglyceride transfer protein
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2886956 - 0.9311967
Average (Standard dev.)-0.0004139445 (±0.016373353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Microsomal triglyceride transfer protein

Fileemd_28377_additional_1.map
AnnotationMicrosomal triglyceride transfer protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Microsomal triglyceride transfer protein

Fileemd_28377_half_map_1.map
AnnotationMicrosomal triglyceride transfer protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Microsomal triglyceride transfer protein

Fileemd_28377_half_map_2.map
AnnotationMicrosomal triglyceride transfer protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microsomal triglyceride transfer protein

EntireName: Microsomal triglyceride transfer protein
Components
  • Complex: Microsomal triglyceride transfer protein
    • Protein or peptide: Protein disulfide-isomerase
    • Protein or peptide: Microsomal triglyceride transfer protein large subunit

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Supramolecule #1: Microsomal triglyceride transfer protein

SupramoleculeName: Microsomal triglyceride transfer protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein disulfide-isomerase

MacromoleculeName: Protein disulfide-isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein disulfide-isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.190137 KDa
SequenceString: MLRRALLCLA VAALVRADAP EEEDHVLVLR KSNFAEALAA HKYLLVEFYA PWCGHCKALA PEYAKAAGKL KAEGSEIRLA KVDATEESD LAQQYGVRGY PTIKFFRNGD TASPKEYTAG READDIVNWL KKRTGPAATT LPDGAAAESL VESSEVAVIG F FKDVESDS ...String:
MLRRALLCLA VAALVRADAP EEEDHVLVLR KSNFAEALAA HKYLLVEFYA PWCGHCKALA PEYAKAAGKL KAEGSEIRLA KVDATEESD LAQQYGVRGY PTIKFFRNGD TASPKEYTAG READDIVNWL KKRTGPAATT LPDGAAAESL VESSEVAVIG F FKDVESDS AKQFLQAAEA IDDIPFGITS NSDVFSKYQL DKDGVVLFKK FDEGRNNFEG EVTKENLLDF IKHNQLPLVI EF TEQTAPK IFGGEIKTHI LLFLPKSVSD YDGKLSNFKT AAESFKGKIL FIFIDSDHTD NQRILEFFGL KKEECPAVRL ITL EEEMTK YKPESEELTA ERITEFCHRF LEGKIKPHLM SQELPEDWDK QPVKVLVGKN FEDVAFDEKK NVFVEFYAPW CGHC KQLAP IWDKLGETYK DHENIVIAKM DSTANEVEAV KVHSFPTLKF FPASADRTVI DYNGERTLDG FKKFLESGGQ DGAGD DDDL EDLEEAEEPD MEEDDDQKAV KDEL

UniProtKB: Protein disulfide-isomerase

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Macromolecule #2: Microsomal triglyceride transfer protein large subunit

MacromoleculeName: Microsomal triglyceride transfer protein large subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.474102 KDa
SequenceString: MILLAVLFLC FISSYSASVK GHTTGLSLNN DRLYKLTYST EVLLDRGKGK LQDSVGYRIS SNVDVALLWR NPDGDDDQLI QITMKDVNV ENVNQQRGEK SIFKGKSPSK IMGKENLEAL QRPTLLHLIH GKVKEFYSYQ NEAVAIENIK RGLASLFQTQ L SSGTTNEV ...String:
MILLAVLFLC FISSYSASVK GHTTGLSLNN DRLYKLTYST EVLLDRGKGK LQDSVGYRIS SNVDVALLWR NPDGDDDQLI QITMKDVNV ENVNQQRGEK SIFKGKSPSK IMGKENLEAL QRPTLLHLIH GKVKEFYSYQ NEAVAIENIK RGLASLFQTQ L SSGTTNEV DISGNCKVTY QAHQDKVIKI KALDSCKIAR SGFTTPNQVL GVSSKATSVT TYKIEDSFVI AVLAEETHNF GL NFLQTIK GKIVSKQKLE LKTTEAGPRL MSGKQAAAII KAVDSKYTAI PIVGQVFQSH CKGCPSLSEL WRSTRKYLQP DNL SKAEAV RNFLAFIQHL RTAKKEEILQ ILKMENKEVL PQLVDAVTSA QTSDSLEAIL DFLDFKSDSS IILQERFLYA CGFA SHPNE ELLRALISKF KGSIGSSDIR ETVMIITGTL VRKLCQNEGC KLKAVVEAKK LILGGLEKAE KKEDTRMYLL ALKNA LLPE GIPSLLKYAE AGEGPISHLA TTALQRYDLP FITDEVKKTL NRIYHQNRKV HEKTVRTAAA AIILNNNPSY MDVKNI LLS IGELPQEMNK YMLAIVQDIL RFEMPASKIV RRVLKEMVAH NYDRFSRSGS SSAYTGYIER SPRSASTYSL DILYSGS GI LRRSNLNIFQ YIGKAGLHGS QVVIEAQGLE ALIAATPDEG EENLDSYAGM SAILFDVQLR PVTFFNGYSD LMSKMLSA S GDPISVVKGL ILLIDHSQEL QLQSGLKANI EVQGGLAIDI SGAMEFSLWY RESKTRVKNR VTVVITTDIT VDSSFVKAG LETSTETEAG LEFISTVQFS QYPFLVCMQM DKDEAPFRQF EKKYERLSTG RGYVSQKRKE SVLAGCEFPL HQENSEMCKV VFAPQPDST SSGWF

UniProtKB: Microsomal triglyceride transfer protein large subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.291 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 81000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 487553
Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249877
FSC plot (resolution estimation)

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