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- PDB-9sqn: Structure of a disulfide-bridged complex between HLA-A*02:01-K127... -

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Basic information

Entry
Database: PDB / ID: 9sqn
TitleStructure of a disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 1
Components
  • Beta-2-microglobulin
  • LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9
  • MHC class I antigen
  • Protein disulfide-isomerase A3
  • Tapasin
KeywordsIMMUNE SYSTEM / MHC-I / ERp57 / Tapasin / ANTIGEN PROCESSING / PEPTIDE PROOFREADING / CHAPERONES
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / 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 ...MHC class Ib protein complex assembly / peptide antigen stabilization / 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 / TAP complex binding / protein disulfide isomerase activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / lncRNA binding / protein-disulfide reductase activity / MHC class I protein binding / antigen processing and presentation of peptide antigen via MHC class I / phagocytic vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / response to endoplasmic reticulum stress / 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 / Maturation of DENV proteins / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / : / positive regulation of cellular senescence / melanosome / regulation of gene expression / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / protein-containing complex assembly / protein folding / early endosome membrane / amyloid fibril formation / molecular adaptor activity / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / cysteine-type endopeptidase activity / 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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMitlehner, A. / Loll, B. / Hilal, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1325/20-1 Germany
CitationJournal: To Be Published
Title: Dynamic states of an MHC class I molecule upon peptide release
Authors: Mitlehner, A. / Pasos-Trejo, A.S. / Becker, M. / Hilal, T. / Loll, B. / Kuropka, B. / Clementi, C. / Freund, C.
History
DepositionSep 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta-2-microglobulin
D: Tapasin
E: Protein disulfide-isomerase A3
A: MHC class I antigen
C: LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8306
Polymers143,9205
Non-polymers9111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules BDEA

#1: Protein Beta-2-microglobulin


Mass: 11750.199 Da / Num. of mol.: 1 / Mutation: T5C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Protein Tapasin / TPN / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 42746.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15533
#3: Protein Protein disulfide-isomerase A3 / 58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / ...58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / Endoplasmic reticulum resident protein 57 / ER protein 57 / ERp57 / Endoplasmic reticulum resident protein 60 / ER protein 60 / ERp60


Mass: 54309.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA3, ERP57, ERP60, GRP58 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30101, protein disulfide-isomerase
#4: Protein MHC class I antigen


Mass: 34291.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9TQB6

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Protein/peptide / Sugars , 2 types, 2 molecules C

#5: Protein/peptide LYS-ILE-LEU-GLY-PHE-VAL-NFA, pKV9


Mass: 822.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 4
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
30.15 %n-octylglucosideC14H28O61
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40.57 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5958

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.0particle selection
4cryoSPARC4.5.0CTF correction
9cryoSPARC4.5.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11cryoSPARC4.6.0classification
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2281616
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202843 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 139
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 139.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002310057
ELECTRON MICROSCOPYf_angle_d0.610513665
ELECTRON MICROSCOPYf_chiral_restr0.03991452
ELECTRON MICROSCOPYf_plane_restr0.00331794
ELECTRON MICROSCOPYf_dihedral_angle_d4.50871413

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