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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: EMD-3906
TitleCryo-EM density map of the human PLC editing module
Map dataCryoEM map of a protein complex
Sample
  • Complex: Protein Complex
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tapasin
    • Protein or peptide: Protein disulfide-isomerase A3
    • Protein or peptide: HLA class I histocompatibility antigen, A-3 alpha chain
    • Protein or peptide: Calreticulin
Keywordsadaptive immunity / antigen processing / chaperone / MHC class I / IMMUNE SYSTEM
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / response to biphenyl / MHC class I protein complex binding / TAP2 binding / TAP1 binding / cytolytic granule / positive regulation of dendritic cell chemotaxis ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / response to biphenyl / MHC class I protein complex binding / TAP2 binding / TAP1 binding / cytolytic granule / positive regulation of dendritic cell chemotaxis / protein disulfide-isomerase / ATF6 (ATF6-alpha) activates chaperone genes / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / nuclear receptor-mediated glucocorticoid signaling pathway / cellular response to electrical stimulus / complement component C1q complex binding / response to peptide / regulation of meiotic nuclear division / negative regulation of retinoic acid receptor signaling pathway / sequestering of calcium ion / endoplasmic reticulum quality control compartment / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / response to glycoside / disulfide oxidoreductase activity / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of protein complex stability / nuclear export signal receptor activity / cardiac muscle cell differentiation / phospholipase C activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / cortical actin cytoskeleton organization / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Scavenging by Class A Receptors / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / nuclear androgen receptor binding / Scavenging by Class F Receptors / CD8 receptor binding / cellular response to lithium ion / protein disulfide isomerase activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / MHC class I protein binding / response to testosterone / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / molecular sequestering activity / protection from natural killer cell mediated cytotoxicity / protein-disulfide reductase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / negative regulation of neuron differentiation / protein localization to nucleus / smooth endoplasmic reticulum / detection of bacterium / T cell receptor binding / positive regulation of phagocytosis / phagocytic vesicle / extrinsic apoptotic signaling pathway / positive regulation of cell cycle / ERAD pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / endoplasmic reticulum-Golgi intermediate compartment membrane / endocytic vesicle lumen / protein folding chaperone / protein maturation / peptide binding / response to endoplasmic reticulum stress / protein export from nucleus / : / : / acrosomal vesicle / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / 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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tapasin / HLA class I histocompatibility antigen, A alpha chain / Calreticulin / Protein disulfide-isomerase A3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsJanuliene D / Blees A / Trowitzsch S / Tampe R / Moeller A
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationSFB 807 Germany
German Research FoundationGRK 1986 Germany
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 /
Abstract: The peptide-loading complex (PLC) is a transient, multisubunit membrane complex in the endoplasmic reticulum that is essential for establishing a hierarchical immune response. The PLC coordinates ...The peptide-loading complex (PLC) is a transient, multisubunit membrane complex in the endoplasmic reticulum that is essential for establishing a hierarchical immune response. The PLC coordinates peptide translocation into the endoplasmic reticulum with loading and editing of major histocompatibility complex class I (MHC-I) molecules. After final proofreading in the PLC, stable peptide-MHC-I complexes are released to the cell surface to evoke a T-cell response against infected or malignant cells. Sampling of different MHC-I allomorphs requires the precise coordination of seven different subunits in a single macromolecular assembly, including the transporter associated with antigen processing (TAP1 and TAP2, jointly referred to as TAP), the oxidoreductase ERp57, the MHC-I heterodimer, and the chaperones tapasin and calreticulin. The molecular organization of and mechanistic events that take place in the PLC are unknown owing to the heterogeneous composition and intrinsically dynamic nature of the complex. Here, we isolate human PLC from Burkitt's lymphoma cells using an engineered viral inhibitor as bait and determine the structure of native PLC by electron cryo-microscopy. Two endoplasmic reticulum-resident editing modules composed of tapasin, calreticulin, ERp57, and MHC-I are centred around TAP in a pseudo-symmetric orientation. A multivalent chaperone network within and across the editing modules establishes the proofreading function at two lateral binding platforms for MHC-I molecules. The lectin-like domain of calreticulin senses the MHC-I glycan, whereas the P domain reaches over the MHC-I peptide-binding pocket towards ERp57. This arrangement allows tapasin to facilitate peptide editing by clamping MHC-I. The translocation pathway of TAP opens out into a large endoplasmic reticulum lumenal cavity, confined by the membrane entry points of tapasin and MHC-I. Two lateral windows channel the antigenic peptides to MHC-I. Structures of PLC captured at distinct assembly states provide mechanistic insight into the recruitment and release of MHC-I. Our work defines the molecular symbiosis of an ABC transporter and an endoplasmic reticulum chaperone network in MHC-I assembly and provides insight into the onset of the adaptive immune response.
History
DepositionOct 7, 2017-
Header (metadata) releaseNov 29, 2017-
Map releaseNov 29, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3906.png

Downloads & links

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Map

FileDownload / File: emd_3906.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of a protein complex
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.022047075 - 0.06878314
Average (Standard dev.)0.0014957641 (±0.0058695944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 215.40001 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Protein Complex
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tapasin
    • Protein or peptide: Protein disulfide-isomerase A3
    • Protein or peptide: HLA class I histocompatibility antigen, A-3 alpha chain
    • Protein or peptide: Calreticulin

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Supramolecule #1: Protein Complex

SupramoleculeName: Protein Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.74816 KDa
SequenceString:
IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

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Macromolecule #2: Tapasin

MacromoleculeName: Tapasin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.761184 KDa
SequenceString: GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL DPELYLSVHD PAGALQAAFR RYPRGAPAPH CEMSRFVPLP ASAKWASGL TPAQNCPRAL DGAWLMVSIS SPVLSLSSLL RPQPEPQQEP VLITMATVVL TVLTHTPAPR VRLGQDALLD L SFAYMPPT ...String:
GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL DPELYLSVHD PAGALQAAFR RYPRGAPAPH CEMSRFVPLP ASAKWASGL TPAQNCPRAL DGAWLMVSIS SPVLSLSSLL RPQPEPQQEP VLITMATVVL TVLTHTPAPR VRLGQDALLD L SFAYMPPT SEAASSLAPG PPPFGLEWRR QHLGKGHLLL AATPGLNGQM PAAQEGAVAF AAWDDDEPWG PWTGNGTFWL PR VQPFQEG TYLATIHLPY LQGQVTLELA VYKPPKVSLM PATLARAAPG EAPPELLCLV SHFYPSGGLE VEWELRGGPG GRS QKAEGQ RWLSALRHHS DGSVSLSGHL QPPPVTTEQH GARYACRIHH PSLPASGRSA EVTLEVAGLS GPSLEDSVGL FLSA FLLLG LFKALGWAAV YLSTCKDSKK KAE

UniProtKB: Tapasin

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Macromolecule #3: Protein disulfide-isomerase A3

MacromoleculeName: Protein disulfide-isomerase A3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein disulfide-isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.341102 KDa
SequenceString: SDVLELTDDN FESRISDTGS AGLMLVEFFA PWCGHCKRLA PEYEAAATRL KGIVPLAKVD CTANTNTCNK YGVSGYPTLK IFRDGEEAG AYDGPRTADG IVSHLKKQAG PASVPLRTEE EFKKFISDKD ASIVGFFDDS FSEAHSEFLK AASNLRDNYR F AHTNVESL ...String:
SDVLELTDDN FESRISDTGS AGLMLVEFFA PWCGHCKRLA PEYEAAATRL KGIVPLAKVD CTANTNTCNK YGVSGYPTLK IFRDGEEAG AYDGPRTADG IVSHLKKQAG PASVPLRTEE EFKKFISDKD ASIVGFFDDS FSEAHSEFLK AASNLRDNYR F AHTNVESL VNEYDDNGEG IILFRPSHLT NKFEDKTVAY TEQKMTSGKI KKFIQENIFG ICPHMTEDNK DLIQGKDLLI AY YDVDYEK NAKGSNYWRN RVMMVAKKFL DAGHKLNFAV ASRKTFSHEL SDFGLESTAG EIPVVAIRTA KGEKFVMQEE FSR DGKALE RFLQDYFDGN LKRYLKSEPI PESNDGPVKV VVAENFDEIV NNENKDVLIE FYAPWCGHCK NLEPKYKELG EKLS KDPNI VIAKMDATAN DVPSPYEVRG FPTIYFSPAN KKLNPKKYEG GRELSDFISY LQREATNPPV IQEEKPKKKK KAQED L

UniProtKB: Protein disulfide-isomerase A3

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Macromolecule #4: HLA class I histocompatibility antigen, A-3 alpha chain

MacromoleculeName: HLA class I histocompatibility antigen, A-3 alpha chain
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.363535 KDa
SequenceString: GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DQETRNVKAQ SQTDRVDLGT LRGYYNQSE AGSHTIQIMY GCDVGSDGRF LRGYRQDAYD GKDYIALNED LRSWTAADMA AQITKRKWEA AHEAEQLRAY L DGTCVEWL ...String:
GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DQETRNVKAQ SQTDRVDLGT LRGYYNQSE AGSHTIQIMY GCDVGSDGRF LRGYRQDAYD GKDYIALNED LRSWTAADMA AQITKRKWEA AHEAEQLRAY L DGTCVEWL RRYLENGKET LQRTDPPKTH MTHHPISDHE ATLRCWALGF YPAEITLTWQ RDGEDQTQDT ELVETRPAGD GT FQKWAAV VVPSGEEQRY TCHVQHEGLP KPLTLRWELS SQPTIPIVGI IAGLVLLGAV ITGAVVAAVM WRRKSSDRKG GSY TQAASS DSAQGSDVSL TACKV

UniProtKB: HLA class I histocompatibility antigen, A alpha chain

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Macromolecule #5: Calreticulin

MacromoleculeName: Calreticulin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.507145 KDa
SequenceString: EPAVYFKEQF LDGDGWTSRW IESKHKSDFG KFVLSSGKFY GDEEKDKGLQ TSQDARFYAL SASFEPFSNK GQTLVVQFTV KHEQNIDCG GGYVKLFPNS LDQTDMHGDS EYNIMFGPDI CGPGTKKVHV IFNYKGKNVL INKDIRSKDD EFTHLYTLIV R PDNTYEVK ...String:
EPAVYFKEQF LDGDGWTSRW IESKHKSDFG KFVLSSGKFY GDEEKDKGLQ TSQDARFYAL SASFEPFSNK GQTLVVQFTV KHEQNIDCG GGYVKLFPNS LDQTDMHGDS EYNIMFGPDI CGPGTKKVHV IFNYKGKNVL INKDIRSKDD EFTHLYTLIV R PDNTYEVK IDNSQVESGS LEDDWDFLPP KKIKDPDASK PEDWDERAKI DDPTDSKPED WDKPEHIPDP DAKKPEDWDE EM DGEWEPP VIQNPEYKGE WKPRQIDNPD YKGTWIHPEI DNPEYSPDPS IYAYDNFGVL GLDLWQVKSG TIFDNFLITN DEA YAEEFG NETWGVTKAA EKQMKDKQDE EQRLKEEEED KKRKEEEEAE DKEDDEDKDE DEEDEEDKEE DEEEDVPGQA KDEL

UniProtKB: Calreticulin

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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

Concentration2 mg/mL
BufferpH: 7.5
GridModel: C-flat-2/2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Selected particles from the best 2D class averages were subjected to 3D-classification in Relion, using a low-pass filtered global average as a starting model. The best map was then used as ...Details: Selected particles from the best 2D class averages were subjected to 3D-classification in Relion, using a low-pass filtered global average as a starting model. The best map was then used as an initial model for subsequent 3D classification.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. X) / Number images used: 141078
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION

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