[English] 日本語
Yorodumi
- EMDB-55111: Structure of a disulfide-bridged complex between HLA-A*02:01-K127... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55111
TitleStructure of a disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
Map data
Sample
  • Complex: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tapasin
    • Protein or peptide: Protein disulfide-isomerase A3
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9
KeywordsMHC-I / ERp57 / Tapasin / IMMUNE SYSTEM / ANTIGEN PROCESSING / PEPTIDE PROOFREADING / CHAPERONES
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / TAP2 binding / regulation of protein complex stability ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / TAP2 binding / regulation of protein complex stability / TAP1 binding / C-type glycerophospholipase activity / antigen processing and presentation of peptide antigen via MHC class I / TAP complex binding / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein disulfide isomerase activity / lncRNA binding / protein-disulfide reductase activity / MHC class I protein binding / phagocytic vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / Maturation of DENV proteins / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / negative regulation of neurogenesis / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / specific granule lumen / peptide antigen binding / phagocytic vesicle membrane / regulation of gene expression / positive regulation of T cell activation / Interferon gamma signaling / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / tertiary granule lumen / Modulation by Mtb of host immune system / melanosome / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / protein folding / ER-Phagosome pathway / protein-containing complex assembly / early endosome membrane / amyloid fibril formation / protein homotetramerization / molecular adaptor activity / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / cysteine-type endopeptidase activity / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin family active site. / Thioredoxin, conserved site / : / Thioredoxin domain profile. ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin family active site. / Thioredoxin, conserved 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 / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tapasin / Protein disulfide-isomerase A3 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMitlehner A / Loll B / Hilal T
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1325/20-1 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Dynamic states of an MHC class I molecule during peptide exchange.
Authors: Alexandra Mitlehner / Aldo S Pasos-Trejo / Moritz Becker / Huan Lan / Lennard Berg / Tarek Hilal / Bernhard Loll / Benno Kuropka / Cecilia Clementi / Christian Freund /
Abstract: Antigens of intracellular origin are processed then presented by proteins of the highly polymorphic major histocompatibility complex I (MHCI), thereby enabling T cell activation during an immune ...Antigens of intracellular origin are processed then presented by proteins of the highly polymorphic major histocompatibility complex I (MHCI), thereby enabling T cell activation during an immune response. In particular, the peptide-exchange catalyst tapasin (Tsn) plays a critical role in shaping the pool of peptide antigens that ultimately reach the cell surface. Here, using disulfide bond engineering in conjunction with cryogenic electron microscopy (cryoEM) and molecular dynamics simulations, we provide evidence for partial collapse of the antigen binding groove during the peptide exchange process. An intermediate is formed that is characterized by interactions between the peptide's N-terminus and conserved tyrosine side chains in MHCI. Unfolding of the MHCI α1-helix in the Tsn-bound state is contrasted by a stable α2-helix that is kept in its native-like major conformation by the support of the large interface it entertains with the exchange catalyst. Helical disorder propensities and backbone flexibilities of the α1-helix are predicted to have increased during evolution, suggesting that the dynamic features introduced by polymorphic variation may have contributed to shaping the pool of antigens presented to T cells.
History
DepositionSep 23, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55111.png

Downloads & links

-
Map

FileDownload / File: emd_55111.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.0 - 1.5654447
Average (Standard dev.)0.0059443107 (±0.043367717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 235.87201 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_55111_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55111_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp5...

EntireName: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
Components
  • Complex: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tapasin
    • Protein or peptide: Protein disulfide-isomerase A3
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9

-
Supramolecule #1: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp5...

SupramoleculeName: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
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: 11.750199 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
IQRCPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

-
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: 42.746488 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPAVIECWFV EDASGCGLAK RPGALLLRQG PGEPPPRPDL DPELYLSVHD PAGALQAAFR RYPRGAPAPH CEMSRFVPLP ASAKWASGL TPAQNCPRAL DGAWLMVSIS SPVLSLSSLL RPQPEPQQEP VLITMATVVL TVLTHTPAPR VRLGQDALLD L SFAYMPPT ...String:
GPAVIECWFV EDASGCGLAK 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 SHFYPSCGLE VEWELRGGPG GRS QKAEGQ RWLSALRHHS DGSVSLSGHL QPPPVTTEQH GARYACRIHH PSLPASGRSA EVTLEVAGLS GPSLEDHHHH HH

UniProtKB: Tapasin

-
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: 54.309035 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDVLELTDDN FESRISDTGS AGLMLVEFFA PWCGHCKRLA PEYEAAATRL KGIVPLAKVD ATANTNTCNK YGVSGYPTLK IFRDGEEAG AYDGPRTADG IVSHLKKQAG PASVPLRTEE EFKKFISDKD ASIVGFFDDS FSEAHSEFLK AASNLRDNYR F AHTNVESL ...String:
SDVLELTDDN FESRISDTGS AGLMLVEFFA PWCGHCKRLA PEYEAAATRL KGIVPLAKVD ATANTNTCNK 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

-
Macromolecule #4: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.291734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGCYNQSE AGSHTVQRMY GCDVGSDWRF LRGYHQYAYD GKDYIALNED LRSWTAADMA AQTTKHKWEA AHVAEQLRAY L EGTCVEWL ...String:
GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGCYNQSE AGSHTVQRMY GCDVGSDWRF LRGYHQYAYD GKDYIALNED LRSWTAADMA AQTTKHKWEA AHVAEQLRAY L EGTCVEWL RRYLENGKET LQRTDAPKTH MTHHAVSDHE ATLRCWALSF YPAEITLTWQ RDGEDQTQDT ELVETRPAGD GT FQKWAAV VVPSGQEQRY TCHVQHEGLP KPLTLRWEPG SGGSGGSAGG GLNDIFEAQK IEWH

UniProtKB: MHC class I antigen

-
Macromolecule #5: LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9

MacromoleculeName: LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 823.056 Da
SequenceString:
KILGFV(NFA)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
0.15 %C14H28O6n-octylglucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5958 / Average exposure time: 40.57 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2281616
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 172457
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more