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- EMDB-63459: Cryo-EM structure of HRD1-SEL1LX3-XTP3B complex in C2 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-63459
TitleCryo-EM structure of HRD1-SEL1LX3-XTP3B complex in C2 symmetry
Map data
Sample
  • Complex: Cryo-EM structure of human complex E
    • Protein or peptide: E3 ubiquitin-protein ligase synoviolin
    • Protein or peptide: Protein sel-1 homolog 1
    • Protein or peptide: Endoplasmic reticulum lectin 1
    • Protein or peptide: ALA-ASN-ALA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsE3 Ligase / ANTIBIOTIC
Function / homology
Function and homology information


negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / Pre-NOTCH Processing in Golgi / XBP1(S) activates chaperone genes / immature B cell differentiation / Derlin-1 retrotranslocation complex / triglyceride metabolic process ...negative regulation of retrograde protein transport, ER to cytosol / Hrd1p ubiquitin ligase complex / endoplasmic reticulum mannose trimming / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / Pre-NOTCH Processing in Golgi / XBP1(S) activates chaperone genes / immature B cell differentiation / Derlin-1 retrotranslocation complex / triglyceride metabolic process / retrograde protein transport, ER to cytosol / ubiquitin-specific protease binding / smooth endoplasmic reticulum / protein secretion / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / Notch signaling pathway / ERAD pathway / endomembrane system / ER Quality Control Compartment (ERQC) / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / RING-type E3 ubiquitin transferase / ABC-family proteins mediated transport / ubiquitin protein ligase activity / unfolded protein binding / protein-folding chaperone binding / ATPase binding / ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / nucleoplasm / membrane
Similarity search - Function
Protein OS9-like domain / Protein OS-9-like / Glucosidase II beta subunit-like protein / : / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Mannose-6-phosphate receptor binding domain superfamily / MRH domain ...Protein OS9-like domain / Protein OS-9-like / Glucosidase II beta subunit-like protein / : / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Ring finger domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / 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
E3 ubiquitin-protein ligase synoviolin / Endoplasmic reticulum lectin 1 / Protein sel-1 homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQian HW / Liu GY
Funding support1 items
OrganizationGrant numberCountry
Other privateKY9100000034
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the human HRD1 ubiquitin ligase complex.
Authors: Liling Guo / Guoyun Liu / Jingjing He / Xiaoxiao Jia / Yonglin He / Zhenhua Wang / Hongwu Qian /
Abstract: In the endoplasmic reticulum (ER), defective proteins are cleaned via the ER-associated protein degradation (ERAD) pathway. The HRD1 ubiquitin ligase complex, with HRD1, SEL1L, XTP3B or OS9 and ...In the endoplasmic reticulum (ER), defective proteins are cleaned via the ER-associated protein degradation (ERAD) pathway. The HRD1 ubiquitin ligase complex, with HRD1, SEL1L, XTP3B or OS9 and Derlin family proteins as the core components, plays essential roles in the recognition, retrotranslocation, and ubiquitination of luminal ERAD substrates. However, the molecular basis is unclear. Here, we determine the cryo-EM structure of the human HRD1-SEL1L-XTP3B complex at 3.3 Å resolution. HRD1 is a dimer, but only one protomer carries the SEL1L-XTP3B complex, forming a 2:1:1 complex. Careful inspection of the EM map reveals a trimmed N-glycan sandwiched by XTP3B and SEL1L, and SEL1L may also contribute to the recognition of the trimmed glycan. The complex undergoes dramatic conformational changes when coexpressed with Derlin proteins. The HRD1 dimer is broken, and two HRD1-SEL1L-XTP3B (1:1:1) units are joined together by a four-helix bundle formed by two SEL1L molecules. The four-helix bundle also touches the micelle, resulting in a bent transmembrane region. These findings indicate that Derlins engagement may induce local curvature in the ER membrane. Cell-based functional assays are conducted to verify the structural observations. Our work provides a structural basis for further mechanistic elucidation of mammalian HRD1 complex-mediated ERAD.
History
DepositionFeb 17, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63459.png

Downloads & links

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Map

FileDownload / File: emd_63459.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.104
Minimum - Maximum-2.40794 - 3.305411
Average (Standard dev.)0.001675061 (±0.046137247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63459_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63459_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human complex E

EntireName: Cryo-EM structure of human complex E
Components
  • Complex: Cryo-EM structure of human complex E
    • Protein or peptide: E3 ubiquitin-protein ligase synoviolin
    • Protein or peptide: Protein sel-1 homolog 1
    • Protein or peptide: Endoplasmic reticulum lectin 1
    • Protein or peptide: ALA-ASN-ALA
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of human complex E

SupramoleculeName: Cryo-EM structure of human complex E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase synoviolin

MacromoleculeName: E3 ubiquitin-protein ligase synoviolin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.744586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFRTAVMMAA SLALTGAVVA HAYYLKHQFY PTVVYLTKSS PSMAVLYIQA FVLVFLLGKV MGKVFFGQLR AAEMEHLLER SWYAVTETC LAFTVFRDDF SPRFVALFTL LLFLKCFHWL AEDRVDFMER SPNISWLFHC RIVSLMFLLG ILDFLFVSHA Y HSILTRGA ...String:
MFRTAVMMAA SLALTGAVVA HAYYLKHQFY PTVVYLTKSS PSMAVLYIQA FVLVFLLGKV MGKVFFGQLR AAEMEHLLER SWYAVTETC LAFTVFRDDF SPRFVALFTL LLFLKCFHWL AEDRVDFMER SPNISWLFHC RIVSLMFLLG ILDFLFVSHA Y HSILTRGA SVQLVFGFEY AILMTMVLTI FIKYVLHSVD LQSENPWDNK AVYMLYTELF TGFIKVLLYM AFMTIMIKVH TF PLFAIRP MYLAMRQFKK AVTDAIMSRR AIRNMNTLYP DATPEELQAM DNVCIICREE MVTGAKRLPC NHIFHTSCLR SWF QRQQTC PTCRMDVLRA SLPAQSPPPP EPADQGPPPA PHPPPLLPQP PNFPQGLLPP FPPGMFPLWP PMGPFPPVPP PPSS GEAVA PPSTSAAALS RPSGAATTTA AGTSATAASA TASGPGSGSA PEAGPAPGFP FPPPWMGMPL PPPFAFPPMP VPPAG FAGL TPEELRALEG HERQHLEARL QSLRNIHTLL DAAMLQINQY LTVLASLGPP RPATSVNSTE ETATTVVAAA SSTSIP SSE ATTPTPGASP PAPEMERPPA PESVGTEEMP EDGEPDAAEL RRRRLQKLES PVAH

UniProtKB: E3 ubiquitin-protein ligase synoviolin

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Macromolecule #2: Protein sel-1 homolog 1

MacromoleculeName: Protein sel-1 homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.848484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVRIGLTLL LCAVLLSLAS ASSDEEGSQD ESLDSKTTLT SDESVKDHTT AGRVVAGQIF LDSEESELES SIQEEEDSLK SQEGESVTE DISFLESPNP ENKDYEEPKK VRKPALTAIE GTAHGEPCHF PFLFLDKEYD ECTSDGREDG RLWCATTYDY K ADEKWGFC ...String:
MRVRIGLTLL LCAVLLSLAS ASSDEEGSQD ESLDSKTTLT SDESVKDHTT AGRVVAGQIF LDSEESELES SIQEEEDSLK SQEGESVTE DISFLESPNP ENKDYEEPKK VRKPALTAIE GTAHGEPCHF PFLFLDKEYD ECTSDGREDG RLWCATTYDY K ADEKWGFC ETEEEAAKRR QMQEAEMMYQ TGMKILNGSN KKSQKREAYR YLQKAASMNH TKALERVSYA LLFGDYLPQN IQ AAREMFE KLTEEGSPKG QTALGFLYAS GLGVNSSQAK ALVYYTFGAL GGNLIAHMVL GYRYWAGIGV LQSCESALTH YRL VANHVA SDISLTGGSV VQRIRLPDEV ENPGMNSGML EEDLIQYYQF LAEKGDVQAQ VGLGQLHLHG GRGVEQNHQR AFDY FNLAA NAGNSHAMAF LGKMYSEGSD IVPQSNETAL HYFKKAADMG NPVGQSGLGM AYLYGRGVQV NYDLALKYFQ KAAEQ GWVD GQLQLGSMYY NGIGVKRDYK QALKYFNLAS QGGHILAFYN LAQMHASGTG VMRSCHTAVE LFKNVCERGR WSERLM TAY NSYKDGDYNA AVIQYLLLAE QGYEVAQSNA AFILDQREAS IVGENETYPR ALLHWNRAAS QGYTVARIKL GDYHFYG FG TDVDYETAFI HYRLASEQQH SAQAMFNLGY MHEKGLGIKQ DIHLAKRFYD MAAEASPDAQ VPVFLALCKL GVVYFLQY I RETNIRDMFT QLDMDQLLGP EWDLYLMTII ALLLGTVIAY RQRQHQDMPA PRPPGPRPAP PQQEGPPEQQ PPQ

UniProtKB: Protein sel-1 homolog 1

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Macromolecule #3: Endoplasmic reticulum lectin 1

MacromoleculeName: Endoplasmic reticulum lectin 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.931109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGGGGVRS LVPGGPVLLV LCGLLEASGG GRALPQLSDD IPFRVNWPGT EFSLPTTGVL YKEDNYVIMT TAHKEKYKCI LPLVTSGDE EEEKDYKGPN PRELLEPLFK QSSCSYRIES YWTYEVCHGK HIRQYHEEKE TGQKINIHEY YLGNMLAKNL L FEKEREAE ...String:
MEEGGGGVRS LVPGGPVLLV LCGLLEASGG GRALPQLSDD IPFRVNWPGT EFSLPTTGVL YKEDNYVIMT TAHKEKYKCI LPLVTSGDE EEEKDYKGPN PRELLEPLFK QSSCSYRIES YWTYEVCHGK HIRQYHEEKE TGQKINIHEY YLGNMLAKNL L FEKEREAE EKEKSNEIPT KNIEGQMTPY YPVGMGNGTP CSLKQNRPRS STVMYICHPE SKHEILSVAE VTTCEYEVVI LT PLLCSHP KYRFRASPVN DIFCQSLPGS PFKPLTLRQL EQQEEILRVP FRRNKEEDLQ STKEERFPAI HKSIAIGSQP VLT VGTTHI SKLTDDQLIK EFLSGSYCFR GGVGWWKYEF CYGKHVHQYH EDKDSGKTSV VVGTWNQEEH IEWAKKNTAR AYHL QDDGT QTVRMVSHFY GNGDICDITD KPRQVTVKLK CKESDSPHAV TVYMLEPHSC QYILGVESPV ICKILDTADE NGLLS LPN

UniProtKB: Endoplasmic reticulum lectin 1

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Macromolecule #4: ALA-ASN-ALA

MacromoleculeName: ALA-ASN-ALA / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 274.274 Da
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ANA

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 341051
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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