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- PDB-8kev: Cryo-EM structure of HRD1-SEL1L-XTP3B (state D1) complex -

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Basic information

Entry
Database: PDB / ID: 8kev
TitleCryo-EM structure of HRD1-SEL1L-XTP3B (state D1) 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 / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / Notch signaling pathway / ERAD pathway / ER Quality Control Compartment (ERQC) / endomembrane system / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQian, H.W. / He, J.J.
Funding support1items
OrganizationGrant numberCountry
Other privateKY9100000034
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the human HRD1 ubiquitin ligase complex
Authors: Guo, L. / Liu, G. / He, J. / Jia, X. / He, Y. / Wang, Z. / Qian, H.
History
DepositionAug 13, 2023Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)427,39416
Polymers423,5978
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 DCEFAB

#1: Protein Protein sel-1 homolog 1 / Suppressor of lin-12-like protein 1 / Sel-1L


Mass: 88848.484 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: 54931.109 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
#4: Protein E3 ubiquitin-protein ligase synoviolin / RING-type E3 ubiquitin transferase synoviolin / Synovial apoptosis inhibitor 1


Mass: 67744.586 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

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Protein/peptide , 1 types, 2 molecules GH

#2: 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-ROHGlycam 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
[][D-1-deoxy-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
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 HRD1-SEL1L-XTP3B (state D1) complex
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
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 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134367 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613218
ELECTRON MICROSCOPYf_angle_d1.08918068
ELECTRON MICROSCOPYf_dihedral_angle_d9.3962196
ELECTRON MICROSCOPYf_chiral_restr0.0552174
ELECTRON MICROSCOPYf_plane_restr0.0092372

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