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- PDB-9uav: Cryo-EM structure of HRD1-SEL1L-XTP3B (state D2) complex -

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Basic information

Entry
Database: PDB / ID: 9uav
TitleCryo-EM structure of HRD1-SEL1L-XTP3B (state D2) complex
Components
  • ALA-ASN-ALA
  • E3 ubiquitin-protein ligase synoviolin
  • Endoplasmic reticulum lectin 1
  • Protein sel-1 homolog 1
KeywordsALLERGEN / ERAD
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 / ER Quality Control Compartment (ERQC) / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / Notch signaling pathway / endomembrane system / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / ABC-family proteins mediated transport / RING-type E3 ubiquitin transferase / 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 ubiquitination / protein stabilization / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQian, H.W. / Liu, G.Y.
Funding support1items
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
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Sep 10, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase synoviolin
B: E3 ubiquitin-protein ligase synoviolin
C: Protein sel-1 homolog 1
D: Protein sel-1 homolog 1
E: Endoplasmic reticulum lectin 1
F: Endoplasmic reticulum lectin 1
G: ALA-ASN-ALA
H: ALA-ASN-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,92216
Polymers243,1258
Non-polymers3,7978
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 6 molecules ABCDEF

#1: Protein E3 ubiquitin-protein ligase synoviolin / RING-type E3 ubiquitin transferase synoviolin / Synovial apoptosis inhibitor 1


Mass: 30930.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYVN1, HRD1, KIAA1810 / Production host: Homo sapiens (human)
References: UniProt: Q86TM6, RING-type E3 ubiquitin transferase
#2: Protein Protein sel-1 homolog 1 / Suppressor of lin-12-like protein 1 / Sel-1L


Mass: 61371.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEL1L, TSA305, UNQ128/PRO1063 / Production host: Homo sapiens (human) / References: UniProt: Q9UBV2
#3: Protein Endoplasmic reticulum lectin 1 / ER lectin / Erlectin / XTP3-transactivated gene B protein


Mass: 28985.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERLEC1, C2orf30, XTP3TPB, UNQ1878/PRO4321 / Production host: Homo sapiens (human) / References: UniProt: Q96DZ1

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Protein/peptide , 1 types, 2 molecules GH

#4: Protein/peptide ALA-ASN-ALA


Mass: 274.274 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 8 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-4]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: Cryo-EM structure of human complex F / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1905 / Symmetry type: POINT
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00713046
ELECTRON MICROSCOPYf_angle_d1.09317824
ELECTRON MICROSCOPYf_dihedral_angle_d8.3862160
ELECTRON MICROSCOPYf_chiral_restr0.0582140
ELECTRON MICROSCOPYf_plane_restr0.0082336

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