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

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Basic information

Entry
Database: PDB / ID: 9sqp
TitleStructure of a disulfide-bridged complex between HLA-A*02:01-K127N/Y84C and ERp57/tapasin-K16C - State 3
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 / 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)
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: 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, 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
Revision 1.1Sep 23, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)144,9926
Polymers143,9205
Non-polymers1,0731
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 / Mutation: K16C, G304C
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 / Mutation: C60A
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 / Mutation: Y84C, K127N
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) / References: protein disulfide-isomerase
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+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: 235772 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingB value: 152
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 179.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239811
ELECTRON MICROSCOPYf_angle_d0.613332
ELECTRON MICROSCOPYf_chiral_restr0.04111423
ELECTRON MICROSCOPYf_plane_restr0.00341748
ELECTRON MICROSCOPYf_dihedral_angle_d4.10541373

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