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- PDB-6eny: Structure of the human PLC editing module -

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Basic information

Entry
Database: PDB / ID: 6eny
TitleStructure of the human PLC editing module
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Calreticulin
  • HLA class I histocompatibility antigen, A-3 alpha chain
  • Protein disulfide-isomerase A3
  • Tapasin
KeywordsIMMUNE SYSTEM / adaptive immunity / antigen processing / chaperone / MHC class I
Function / homologyThioredoxin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / MHC_I C-terminus / Calreticulin family / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like superfamily / Thioredoxin-like superfamily / Immunoglobulin-like domain superfamily / Calreticulin/calnexin, conserved site / Thioredoxin, conserved site ...Thioredoxin-like domain / Concanavalin A-like lectin/glucanase domain superfamily / MHC_I C-terminus / Calreticulin family / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like superfamily / Thioredoxin-like superfamily / Immunoglobulin-like domain superfamily / Calreticulin/calnexin, conserved site / Thioredoxin, conserved site / Beta-2-Microglobulin / Immunoglobulin-like fold / Thioredoxin domain / MHC classes I/II-like antigen recognition protein / Endoplasmic reticulum targeting sequence. / MHC class I-like antigen recognition-like / MHC class I, alpha chain, C-terminal / Calreticulin / Calreticulin/calnexin, P domain superfamily / Tapasin / Immunoglobulin-like domain / Protein disulphide isomerase / Disulphide isomerase / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Calreticulin/calnexin / MHC class I alpha chain, alpha1 alpha2 domains / Immunoglobulin C1-set domain / Thioredoxin / Thioredoxin family active site. / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Amyloid fiber formation / Interferon alpha/beta signaling / Calnexin/calreticulin cycle / E3 ubiquitin ligases ubiquitinate target proteins / Interferon gamma signaling / Immunoglobulins and major histocompatibility complex proteins signature. / ATF6 (ATF6-alpha) activates chaperone genes / Scavenging by Class F Receptors / Scavenging by Class A Receptors / DAP12 signaling / Neutrophil degranulation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Thioredoxin domain profile. / Assembly of Viral Components at the Budding Site / Calreticulin family signature 2. / Calreticulin family repeated motif signature. / Ig-like domain profile. / Calreticulin family signature 1. / ER-Phagosome pathway / Nef mediated downregulation of MHC class I complex cell surface expression / Endosomal/Vacuolar pathway / peptide antigen stabilization / peptide antigen-transporting ATPase activity / TAP1 binding / TAP2 binding / peptide antigen assembly with MHC class I protein complex / vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane / sequestering of calcium ion / MHC class I peptide loading complex / negative regulation of trophoblast cell migration / glucocorticoid receptor signaling pathway / ATF6-mediated unfolded protein response / complement component C1q binding / endoplasmic reticulum quality control compartment / regulation of meiotic nuclear division / positive regulation of dendritic cell chemotaxis / phospholipase C activity / protein disulfide-isomerase / sarcoplasmic reticulum lumen / negative regulation of retinoic acid receptor signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / peptide disulfide oxidoreductase activity / protein folding in endoplasmic reticulum / hormone binding / disulfide oxidoreductase activity / regulation of protein complex stability / cardiac muscle cell differentiation / positive regulation of extrinsic apoptotic signaling pathway / protein maturation by protein folding / cellular response to lithium ion / protein export from nucleus / protein disulfide isomerase activity / cortical actin cytoskeleton organization / MHC class I protein binding / retrograde vesicle-mediated transport, Golgi to ER / response to testosterone / protein binding involved in protein folding / smooth endoplasmic reticulum / protein localization to nucleus / cellular senescence / positive regulation of phagocytosis / polysome / negative regulation of neuron differentiation / response to endoplasmic reticulum stress / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of cell cycle arrest / phagocytic vesicle / cellular calcium ion homeostasis
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsTrowitzsch, S. / Januliene, D. / Blees, A. / Moeller, A. / Tampe, R.
CitationJournal: Nature / Year: 2017
Title: Structure of the human MHC-I peptide-loading complex.
Authors: Andreas Blees / Dovile Januliene / Tommy Hofmann / Nicole Koller / Carla Schmidt / Simon Trowitzsch / Arne Moeller / Robert Tampé
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 7, 2017 / Release: Nov 29, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 29, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
B: Beta-2-microglobulin
C: Tapasin
D: Protein disulfide-isomerase A3
F: HLA class I histocompatibility antigen, A-3 alpha chain
G: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,88411
Polyers196,7215
Non-polymers1,1636
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, gel filtration, native gel electrophoresis, mass spectrometry, microscopy
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 5 types, 5 molecules BCDFG

#1: Protein/peptide Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P61769
#2: Protein/peptide Tapasin / / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 45761.184 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O15533
#3: Protein/peptide Protein disulfide-isomerase A3 / 58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / Endoplasmic reticulum resident protein 57 / ERp57 / Endoplasmic reticulum resident protein 60 / ERp60


Mass: 54341.102 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P30101, protein disulfide-isomerase
#4: Protein/peptide HLA class I histocompatibility antigen, A-3 alpha chain / MHC class I antigen A*3


Mass: 38363.535 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P04439
#5: Protein/peptide Calreticulin / / CRP55 / Calregulin / Endoplasmic reticulum resident protein 60 / ERp60 / HACBP / grp60


Mass: 46507.145 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P27797

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Non-polymers , 3 types, 6 molecules

#6: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#7: Chemical ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6
#8: Chemical ChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Glucose

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Protein Complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Gautomatchparticle selection
3EPUimage acquisition
5GctfCTF correction
8Cootmodel fitting
9Flex-EMmodel fitting
11RELION2.1initial Euler assignment
14FREALIGNX3D reconstruction
15PHENIXmodel refinement
CTF correctionDetails: CTF correction was performed internally in Relion and Frealign
Type: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 141078 / Symmetry type: POINT
Least-squares processHighest resolution: 5.8 Å

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