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- PDB-6i7s: Microsomal triglyceride transfer protein -

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Basic information

Entry
Database: PDB / ID: 6i7s
TitleMicrosomal triglyceride transfer protein
Components
  • Microsomal triglyceride transfer protein large subunit
  • Protein disulfide-isomerase
KeywordsLIPID TRANSPORT / Lipid transfer / protein complex / protein disulfide isomerase
Function / homology
Function and homology information


plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / triglyceride transport / phosphatidylcholine transfer activity / procollagen-proline 4-dioxygenase complex / insulin processing / phosphatidylethanolamine transfer activity ...plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / triglyceride transport / phosphatidylcholine transfer activity / procollagen-proline 4-dioxygenase complex / insulin processing / phosphatidylethanolamine transfer activity / VLDL assembly / thiol oxidase activity / phospholipid transfer activity / procollagen-proline 4-dioxygenase activity / LDL remodeling / ceramide 1-phosphate transfer activity / protein disulfide-isomerase / very-low-density lipoprotein particle assembly / endoplasmic reticulum chaperone complex / phospholipid transporter activity / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / phospholipid transport / interleukin-23-mediated signaling pathway / cholesterol transfer activity / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / low-density lipoprotein particle remodeling / Interleukin-12 signaling / cellular response to interleukin-7 / lipoprotein transport / triglyceride metabolic process / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / microvillus membrane / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / protein secretion / apolipoprotein binding / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of T cell migration / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / response to endoplasmic reticulum stress / cholesterol homeostasis / Hedgehog ligand biogenesis / Post-translational protein phosphorylation / establishment of localization in cell / brush border membrane / response to calcium ion / circadian rhythm / lipid metabolic process / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / protein folding / lamellipodium / actin binding / vesicle / basolateral plasma membrane / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / receptor complex / endoplasmic reticulum lumen / protein heterodimerization activity / external side of plasma membrane / focal adhesion / lipid binding / protein-containing complex binding / enzyme binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Lipovitellin-phosvitin complex; beta-sheet shell regions / Lipovitellin; beta-sheet shell regions, chain A / 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 ...Lipovitellin-phosvitin complex; beta-sheet shell regions / Lipovitellin; beta-sheet shell regions, chain A / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Protein disulfide-isomerase / Microsomal triglyceride transfer protein large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBiterova, E. / Isupov, M.N. / Keegan, R.M. / Lebedev, A.A. / Ruddock, L.W.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland266457 Finland
Academy of Finland272573 Finland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The crystal structure of human microsomal triglyceride transfer protein.
Authors: Biterova, E.I. / Isupov, M.N. / Keegan, R.M. / Lebedev, A.A. / Sohail, A.A. / Liaqat, I. / Alanen, H.I. / Ruddock, L.W.
History
DepositionNov 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase
B: Protein disulfide-isomerase
G: Microsomal triglyceride transfer protein large subunit
H: Microsomal triglyceride transfer protein large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,64855
Polymers308,2024
Non-polymers5,44651
Water3,999222
1
A: Protein disulfide-isomerase
G: Microsomal triglyceride transfer protein large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,37926
Polymers154,1012
Non-polymers2,27824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-80 kcal/mol
Surface area60810 Å2
MethodPISA
2
B: Protein disulfide-isomerase
H: Microsomal triglyceride transfer protein large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,26829
Polymers154,1012
Non-polymers3,16827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-39 kcal/mol
Surface area61020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.537, 105.595, 112.269
Angle α, β, γ (deg.)89.810, 76.950, 74.240
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12G
22H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA20 - 4784 - 462
21PROPROALAALABB20 - 4784 - 462
12GLYGLYPROPROGC21 - 88411 - 874
22GLYGLYPROPROHD21 - 88411 - 874

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABGH

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


Mass: 55495.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P07237, protein disulfide-isomerase
#2: Protein Microsomal triglyceride transfer protein large subunit


Mass: 98604.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTTP, MTP / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P55157

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Non-polymers , 9 types, 273 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 8.25, 0.2 M Li2SO4, 32% v/v PEG 400, 2% Polypropylene glycol P425

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.5→49.35 Å / Num. obs: 108279 / % possible obs: 93.8 % / Redundancy: 1.694 % / Biso Wilson estimate: 71.063 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.086 / Χ2: 1.086 / Net I/σ(I): 8.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.651.7221.2020.63168790.2761.790.7
2.65-2.831.7150.6521.16167000.5720.92295.2
2.83-3.061.6540.3432.09154690.8160.48594.7
3.06-3.351.6650.164.3143490.9480.22795.5
3.35-3.741.7380.0838.52129090.9860.11795.1
3.74-4.321.6830.04414.44112170.9950.06393.3
4.32-5.281.6330.02721.994050.9980.03893
5.28-7.421.740.02723.0773080.9970.03893.3
7.42-49.351.7030.01636.3740430.9990.02391.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LSH, 4EKZ

1lsh

4ekz


Resolution: 2.5→49.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.305 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 5414 5 %RANDOM
Rwork0.2045 ---
obs0.2071 102860 93.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.52 Å2 / Biso mean: 72.488 Å2 / Biso min: 25.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20.63 Å2-2.06 Å2
2---0.52 Å2-1.77 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 2.5→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20821 0 342 222 21385
Biso mean--86.51 55.64 -
Num. residues----2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01221585
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.63529000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21452656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37723.391065
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.137153926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.18415106
X-RAY DIFFRACTIONr_chiral_restr0.1050.22798
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215933
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A14142
12B14142
21G26114
22H26114
LS refinement shellResolution: 2.499→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 378 -
Rwork0.423 7180 -
all-7558 -
obs--88.68 %

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