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- EMDB-53331: Editing Module 2 of the Peptide-Loading Complex Arrested by HCMV US6 -

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Basic information

Entry
Database: EMDB / ID: EMD-53331
TitleEditing Module 2 of the Peptide-Loading Complex Arrested by HCMV US6
Map dataEditing module 2 of the Human Peptide-Loading Complex Arrested by US6
Sample
  • Complex: Human peptide loading complex arrested by HCMV US6
Keywordsantigen processing / adaptive immunity / cryo-EM / ER chaperones / MHC class I / transporter associated with antigen processing / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsStolz M / Susac L / Trowitzsch S / Tampe R
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)789121European Union
European Research Council (ERC)101141396European Union
German Research Foundation (DFG)TA157/12-1 Germany
German Research Foundation (DFG)CRC1507/P18 Germany
Other privateUR013222
Citation
Journal: Sci Adv / Year: 2026
Title: Architectural principles of transporter-chaperone coupling within the native MHC I peptide-loading complex.
Authors: Milena Stolz / Lukas Sušac / Amin Fahim / Rieke Keller / Lisa Saggau / Filippo Mancia / Simon Trowitzsch / Robert Tampé /
Abstract: Adaptive immunity depends on major histocompatibility complex class I (MHC I) presentation of peptides, a process orchestrated by the peptide-loading complex (PLC) in the endoplasmic reticulum (ER). ...Adaptive immunity depends on major histocompatibility complex class I (MHC I) presentation of peptides, a process orchestrated by the peptide-loading complex (PLC) in the endoplasmic reticulum (ER). The PLC ensures precise peptide selection and loading and is a major target of viral immune evasion, notably by human cytomegalovirus (HCMV). Here, we report the 2.59- to 2.88-Å cryo-electron microscopy structure of native human PLC bound to the HCMV immune evasin US6. US6 inhibits the transporter associated with antigen processing 1/2 (TAP1/2) by laterally attaching its transmembrane helix to TAP2 using a disulfide-rich domain to mimic a translocating peptide. This domain blocks the ER-lumenal exit and locks TAP in an outward-facing conformation with closed nucleotide-binding domains and asymmetric adenosine 5'-triphosphate/adenosine 5'-diphosphate occlusion. The structure also reveals how TAP's amino-terminal transmembrane domains scaffold the MHC I chaperone tapasin. These findings elucidate the mechanism of US6-mediated immune evasion and highlight potential targets for therapeutic modulation of immune presentation in infection and cancer.
#1: Journal: Nat Commun / Year: 2026
Title: Single-molecule dynamics reveal ATP binding alone powers substrate translocation by an ABC transporter
Authors: Nocker C / Pecak M / Nocker T / Fahim A / Susac L / Tampe R
History
DepositionApr 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53331.png

Downloads & links

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Map

FileDownload / File: emd_53331.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEditing module 2 of the Human Peptide-Loading Complex Arrested by US6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.60115325 - 0.812205
Average (Standard dev.)0.00003379218 (±0.0139718065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Editing module 2 of the Human Peptide-Loading Complex...

Fileemd_53331_additional_1.map
AnnotationEditing module 2 of the Human Peptide-Loading Complex Arrested by US6 (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM2 Tsn-MHCI-b2m-half-map-A

Fileemd_53331_half_map_1.map
AnnotationEM2_Tsn-MHCI-b2m-half-map-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM2 Tsn-MHCI-b2m-half-map-B

Fileemd_53331_half_map_2.map
AnnotationEM2_Tsn-MHCI-b2m-half-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human peptide loading complex arrested by HCMV US6

EntireName: Human peptide loading complex arrested by HCMV US6
Components
  • Complex: Human peptide loading complex arrested by HCMV US6

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Supramolecule #1: Human peptide loading complex arrested by HCMV US6

SupramoleculeName: Human peptide loading complex arrested by HCMV US6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 570 KDa

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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

Concentration3.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S-NaOHHEPES-sodium hydroxide
150.0 mMNaClsodium chloride
10.0 mMMgCl2magnesium chloride
0.05 %C56H92O25glycodiosgenin
2.5 mMC10H16N2O3Sbiotin

Details: 20 mM HEPES-NaOH pH 6.5, 150 mM NaCl, 10 mM MgCl2, 2.5 mM biotin, 0.05% (w/v) glycodiosgenin
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 25454 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 726723
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 269213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.9.8.95)

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