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- EMDB-3906: Cryo-EM density map of the human PLC editing module -

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Basic information

Entry
Database: EMDB / ID: 3906
TitleCryo-EM density map of the human PLC editing module
Map dataCryoEM map of a protein complex
SampleProtein Complex
  • Beta-2-microglobulinBeta-2 microglobulin
  • Tapasin
  • Protein disulfide-isomerase A3
  • HLA class I histocompatibility antigen, A-3 alpha chain
  • Calreticulin
  • (ligand) x 3
Function / homologyImmunoglobulin-like fold / MHC class I-like antigen recognition-like superfamily / Immunoglobulins and major histocompatibility complex proteins signature. / Thioredoxin family active site. / Endoplasmic reticulum targeting sequence. / Immunoglobulin C1-set domain / Disulphide isomerase / MHC_I C-terminus / Calreticulin family / Protein disulphide isomerase ...Immunoglobulin-like fold / MHC class I-like antigen recognition-like superfamily / Immunoglobulins and major histocompatibility complex proteins signature. / Thioredoxin family active site. / Endoplasmic reticulum targeting sequence. / Immunoglobulin C1-set domain / Disulphide isomerase / MHC_I C-terminus / Calreticulin family / Protein disulphide isomerase / Class I Histocompatibility antigen, domains alpha 1 and 2 / Thioredoxin / Thioredoxin-like superfamily / Calreticulin family signature 2. / Immunoglobulin-like domain superfamily / Immunoglobulin-like domain / Tapasin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Thioredoxin, conserved site / Beta-2-Microglobulin / Calreticulin / Thioredoxin domain / Concanavalin A-like lectin/glucanase domain superfamily / MHC classes I/II-like antigen recognition protein / Calreticulin family signature 1. / Calreticulin family repeated motif signature. / MHC class I, alpha chain, C-terminal / Ig-like domain profile. / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / MHC class I alpha chain, alpha1 alpha2 domains / Amyloid fiber formation / Interferon alpha/beta signaling / Calnexin/calreticulin cycle / E3 ubiquitin ligases ubiquitinate target proteins / Interferon gamma signaling / Neutrophil degranulation / ATF6 (ATF6-alpha) activates chaperone genes / Calreticulin/calnexin / Scavenging by Class F Receptors / Scavenging by Class A Receptors / DAP12 signaling / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Immunoglobulin/major histocompatibility complex, conserved site / Assembly of Viral Components at the Budding Site / Immunoglobulin C1-set / Nef mediated downregulation of MHC class I complex cell surface expression / Endosomal/Vacuolar pathway / ER-Phagosome pathway / Thioredoxin domain profile. / MHC class I-like antigen recognition-like / TAP complex binding / peptide antigen stabilization / peptide antigen-transporting ATPase activity / TAP1 binding / TAP2 binding / peptide antigen assembly with MHC class I protein complex / sequestering of calcium ion / vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane / negative regulation of trophoblast cell migration / MHC class I peptide loading complex / glucocorticoid receptor signaling pathway / ATF6-mediated unfolded protein response / complement component C1q binding / endoplasmic reticulum quality control compartment / regulation of meiotic nuclear division / phospholipase C activity / positive regulation of dendritic cell chemotaxis / 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 endoplasmic reticulum / response to testosterone / smooth endoplasmic reticulum / protein folding chaperone / protein localization to nucleus / cellular senescence / positive regulation of phagocytosis / negative regulation of cell cycle arrest / polysome / phagocytic vesicle / negative regulation of neuron differentiation / response to endoplasmic reticulum stress / positive regulation of substrate adhesion-dependent cell spreading / cellular calcium ion homeostasis
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsJanuliene D / Blees A / Trowitzsch S / Tampe R / Moeller A
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 ReportPDB-ID: 6eny

SummaryFull reportAbout validation report
DateDeposition: Oct 7, 2017 / Header (metadata) release: Nov 29, 2017 / Map release: Nov 29, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6eny
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3906.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.08 Å/pix.
= 215.4 Å
200 pix
1.08 Å/pix.
= 215.4 Å
200 pix
1.08 Å/pix.
= 215.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density
Contour Level:0.032 (by author), 0.032 (movie #1):
Minimum - Maximum-0.022047075 - 0.06878314
Average (Standard dev.)0.0014957641 (0.0058695944)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 215.40001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z215.400215.400215.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0220.0690.001

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Supplemental data

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Sample components

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Entire Protein Complex

EntireName: Protein Complex / Number of components: 9

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Component #1: protein, Protein Complex

ProteinName: Protein Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Beta-2-microglobulin

ProteinName: Beta-2-microglobulinBeta-2 microglobulin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.74816 kDa
SourceSpecies: Human (human)

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Component #3: protein, Tapasin

ProteinName: Tapasin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.761184 kDa
SourceSpecies: Human (human)

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Component #4: protein, Protein disulfide-isomerase A3

ProteinName: Protein disulfide-isomerase A3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.341102 kDa
SourceSpecies: Human (human)

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Component #5: protein, HLA class I histocompatibility antigen, A-3 alpha chain

ProteinName: HLA class I histocompatibility antigen, A-3 alpha chain
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.363535 kDa
SourceSpecies: Human (human)

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Component #6: protein, Calreticulin

ProteinName: Calreticulin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.507145 kDa
SourceSpecies: Human (human)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #9: ligand, BETA-D-GLUCOSE

LigandName: BETA-D-GLUCOSEGlucose / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 55 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 141078
3D reconstructionSoftware: FREALIGN
CTF correction: CTF correction was performed internally in Relion and Frealign
Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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