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- PDB-8ket: Cryo-EM structure of HRD1-SEL1LFL-XTP3B complex -

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Basic information

Entry
Database: PDB / ID: 8ket
TitleCryo-EM structure of HRD1-SEL1LFL-XTP3B complex
Components
  • ANA
  • E3 ubiquitin-protein ligase synoviolin
  • Endoplasmic reticulum lectin 1
  • Protein sel-1 homolog 1
KeywordsALLERGEN / ERAD / protein degradation
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 / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol ...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 / immature B cell differentiation / XBP1(S) activates chaperone genes / Derlin-1 retrotranslocation complex / retrograde protein transport, ER to cytosol / triglyceride metabolic process / ubiquitin-specific protease binding / protein secretion / smooth endoplasmic reticulum / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / ERAD pathway / Notch signaling 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 / 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: 3.3 Å
AuthorsQian, H.W. / He, J.J.
Funding support1items
OrganizationGrant numberCountry
Other privateKY9100000034
CitationJournal: To Be Published
Title: Cryo-EM structure of human complex A
Authors: Qian, H.W. / He, J.J.
History
DepositionAug 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
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Description: Chirality error / Provider: author / Type: Coordinate replacement
Revision 2.0Mar 5, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
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Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
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Item: _em_admin.last_update / _em_admin.title / _em_entity_assembly.name

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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
F: Endoplasmic reticulum lectin 1
H: ANA
C: Protein sel-1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,98510
Polymers251,8665
Non-polymers2,1205
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, 4 molecules ABFC

#1: Protein E3 ubiquitin-protein ligase synoviolin


Mass: 67744.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYVN1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q86TM6
#2: Protein Endoplasmic reticulum lectin 1


Mass: 54931.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERLEC1 / Production host: Homo sapiens (human) / References: UniProt: Q96DZ1
#4: Protein Protein sel-1 homolog 1 / Suppressor of lin-12-like protein 1 / Sel-1L


Mass: 61170.957 Da / Num. of mol.: 1
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

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Protein/peptide , 1 types, 1 molecules H

#3: Protein/peptide ANA


Mass: 274.274 Da / Num. of mol.: 1
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, 5 molecules

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


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpa1-6[DManpb1-4]DManpa1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3-2-3-2/a3-b1_b4-c1_c4-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][b-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.: 4 / 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 HRD1-SEL1LFL-XTP3B 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
SpecimenConc.: 12 mg/ml / Embedding 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: 2000 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

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215524 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048512
ELECTRON MICROSCOPYf_angle_d0.6211685
ELECTRON MICROSCOPYf_dihedral_angle_d9.8541480
ELECTRON MICROSCOPYf_chiral_restr0.0451447
ELECTRON MICROSCOPYf_plane_restr0.0061568

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