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- PDB-9z0e: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound... -

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Basic information

Entry
Database: PDB / ID: 9z0e
TitleStructure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
Components
  • ERAD-associated E3 ubiquitin-protein ligase HRD1
  • ERAD-associated E3 ubiquitin-protein ligase component HRD3
KeywordsMEMBRANE PROTEIN / Hrd1 ubiquitin ligase / Hrd3 / MSP1D1 nanodisc
Function / homology
Function and homology information


Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / endoplasmic reticulum unfolded protein response / protein autoubiquitination ...Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / endoplasmic reticulum unfolded protein response / protein autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / identical protein binding
Similarity search - Function
: / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ERAD-associated E3 ubiquitin-protein ligase component HRD3 / ERAD-associated E3 ubiquitin-protein ligase HRD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPisa, R. / Rapoport, T.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GMO52586 United States
Howard Hughes Medical Institute (HHMI) United States
American Heart Association833683/2021 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99GM154114 United States
CitationJournal: bioarchive / Year: 2025
Title: Lipid bilayer thinning near a ubiquitin ligase selects ER membrane proteins for degradation
Authors: Pisa, R. / Rapoport, T.A.
History
DepositionOct 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
B: ERAD-associated E3 ubiquitin-protein ligase HRD1
C: ERAD-associated E3 ubiquitin-protein ligase HRD1
A: ERAD-associated E3 ubiquitin-protein ligase component HRD3


Theoretical massNumber of molelcules
Total (without water)174,0453
Polymers174,0453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Coomassie stained SDS-PAGE Western blot
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ERAD-associated E3 ubiquitin-protein ligase HRD1 / HMG-CoA reductase degradation protein 1 / RING-type E3 ubiquitin transferase HRD1


Mass: 40129.148 Da / Num. of mol.: 2 / Mutation: I91C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRD1, DER3, YOL013C / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q08109, RING-type E3 ubiquitin transferase
#2: Protein ERAD-associated E3 ubiquitin-protein ligase component HRD3 / HMG-CoA reductase degradation protein 3


Mass: 93787.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRD3, YLR207W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05787
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: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4101
Details: ---------Data Collection Parameters------------ Voltage 300kv Cs 0.01 mm ac 0.07 Magnification 81kx Physical pixel size 0.857 A Total dose 55 e/A2 50 frames per movie Dose per frame 1.1 e/A2 ...Details: ---------Data Collection Parameters------------ Voltage 300kv Cs 0.01 mm ac 0.07 Magnification 81kx Physical pixel size 0.857 A Total dose 55 e/A2 50 frames per movie Dose per frame 1.1 e/A2 Data collection strategy 3 by 3 + 3 shots per hole Defocus range -0.8um ~ -2.0um Energy filter slit width 10eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2SerialEMimage acquisition
7Coot0.9model fitting
9PHENIX1.21.2_5419model refinement
13cryoSPARC4.73D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126359 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6VJY

6vjy


Accession code: 6VJY / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 228.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00299840
ELECTRON MICROSCOPYf_angle_d0.72613321
ELECTRON MICROSCOPYf_chiral_restr0.04171492
ELECTRON MICROSCOPYf_plane_restr0.0031644
ELECTRON MICROSCOPYf_dihedral_angle_d4.54871280

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