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- EMDB-73699: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-73699
TitleStructure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
Map dataStructure of a disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3
Sample
  • Complex: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
    • Protein or peptide: ERAD-associated E3 ubiquitin-protein ligase HRD1
    • Protein or peptide: 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPisa R / Rapoport TA
Funding support United States, 4 items
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 TA
History
DepositionOct 31, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73699.png

Downloads & links

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Map

FileDownload / File: emd_73699.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3
Voxel sizeX=Y=Z: 0.857 Å
Density
Contour LevelBy AUTHOR: 0.0995
Minimum - Maximum-0.13183819 - 0.3777245
Average (Standard dev.)0.00040885323 (±0.01203619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 287.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_73699_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_73699_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound...

EntireName: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
Components
  • Complex: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
    • Protein or peptide: ERAD-associated E3 ubiquitin-protein ligase HRD1
    • Protein or peptide: ERAD-associated E3 ubiquitin-protein ligase component HRD3

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Supramolecule #1: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound...

SupramoleculeName: Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ERAD-associated E3 ubiquitin-protein ligase HRD1

MacromoleculeName: ERAD-associated E3 ubiquitin-protein ligase HRD1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 40.129148 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVPENRRKQL AIFVVVTYLL TFYCVYSATK TSVSFLQVTL KLNEGFNLMV LSIFILLNST LLWQLLTKLL FGELRLIEHE HIFERLPFT ICNTLFMSSL FHERYFFTVA FFGLLLLYLK VFHWILKDRL EALLQSINDS TTMKTLIFSR FSFNLVLLAV V DYQIITRC ...String:
MVPENRRKQL AIFVVVTYLL TFYCVYSATK TSVSFLQVTL KLNEGFNLMV LSIFILLNST LLWQLLTKLL FGELRLIEHE HIFERLPFT ICNTLFMSSL FHERYFFTVA FFGLLLLYLK VFHWILKDRL EALLQSINDS TTMKTLIFSR FSFNLVLLAV V DYQIITRC ISSIYTNQKS DIESTSLYLI QVMEFTMLLI DLLNLFLQTC LNFWEFYRSQ QSLSNENNHI VHGDPTDENT VE SDQSQPV LNDDDDDDDD DRQFTGLEGK FMYEKAIDVF TRFLKTALHL SMLIPFRMPM MLLKDVVWDI LALYQSGTSL WKI WRNNKQ GSGGASGGSG DYKDDDDK

UniProtKB: ERAD-associated E3 ubiquitin-protein ligase HRD1

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Macromolecule #2: ERAD-associated E3 ubiquitin-protein ligase component HRD3

MacromoleculeName: ERAD-associated E3 ubiquitin-protein ligase component HRD3
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 93.787172 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MITLLLYLCV ICNAIVLIRA DSIADPWPEA RHLLNTIAKS RDPMKEAAME PNADEFVGFY VPMDYSPRNE EKNYQSIWQN EITDSQRHI YELLVQSSEQ FNNSEATYTL SQIHLWSQYN FPHNMTLAHK YLEKFNDLTH FTNHSAIFDL AVMYATGGCA S GNDQTVIP ...String:
MITLLLYLCV ICNAIVLIRA DSIADPWPEA RHLLNTIAKS RDPMKEAAME PNADEFVGFY VPMDYSPRNE EKNYQSIWQN EITDSQRHI YELLVQSSEQ FNNSEATYTL SQIHLWSQYN FPHNMTLAHK YLEKFNDLTH FTNHSAIFDL AVMYATGGCA S GNDQTVIP QDSAKALLYY QRAAQLGNLK AKQVLAYKYY SGFNVPRNFH KSLVLYRDIA EQLRKSYSRD EWDIVFPYWE SY NVRISDF ESGLLGKGLN SVPSSTVRKR TTRPDIGSPF IAQVNGVQMT LQIEPMGRFA FNGNDGNING DEDDEDASER RII RIYYAA LNDYKGTYSQ SRNCERAKNL LELTYKEFQP HVDNLDPLQV FYYVRCLQLL GHMYFTGEGS SKPNIHMAEE ILTT SLEIS RRAQGPIGRA CIDLGLINQY ITNNISQAIS YYMKAMKTQA NNGIVEFQLS KLATSFPEEK IGDPFNLMET AYLNG FIPA IYEFAVMIES GMNSKSSVEN TAYLFKTFVD KNEAIMAPKL RTAFAALIND RSEVALWAYS QLAEQGYETA QVSAAY LMY QLPYEFEDPP RTTDQRKTLA ISYYTRAFKQ GNIDAGVVAG DIYFQMQNYS KAMALYQGAA LKYSIQAIWN LGYMHEH GL GVNRDFHLAK RYYDQVSEHD HRFYLASKLS VLKLHLKSWL TWITREKVNY WKPSSPLNPN EDTQHSKTSW YKQLTKIL Q RMRHKEDSDK AAEDSHKHRT VVQNGANHRG DDQEEASEIL GFQMEDGGGE NLYFQSGGGM DERTTGWRGG HVVEGLAGE LEQLRARLEH HPQGQREP

UniProtKB: ERAD-associated E3 ubiquitin-protein ligase component HRD3

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4101 / Average electron dose: 55.0 e/Å2
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 126359
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6vjy


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9z0e:
Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc

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