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- PDB-8zpw: Cryo-EM structure of the yeast Htm1/Pdi1 complex at a resolution ... -

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Basic information

Entry
Database: PDB / ID: 8zpw
TitleCryo-EM structure of the yeast Htm1/Pdi1 complex at a resolution of 3.0 angstrom
Components
  • ER degradation-enhancing alpha-mannosidase-like protein 1
  • Protein disulfide-isomerase
KeywordsPEPTIDE BINDING PROTEIN / complex / carbohydrate cleavage / peptide binding
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / Calnexin/calreticulin cycle / : / ubiquitin-dependent glycoprotein ERAD pathway / alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / protein disulfide-isomerase / endoplasmic reticulum quality control compartment / positive regulation of endoplasmic reticulum unfolded protein response ...mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / Calnexin/calreticulin cycle / : / ubiquitin-dependent glycoprotein ERAD pathway / alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / protein disulfide-isomerase / endoplasmic reticulum quality control compartment / positive regulation of endoplasmic reticulum unfolded protein response / protein glycosylation / protein disulfide isomerase activity / protein-disulfide reductase activity / endoplasmic reticulum unfolded protein response / response to endoplasmic reticulum stress / unfolded protein binding / protein folding / carbohydrate binding / carbohydrate metabolic process / endoplasmic reticulum lumen / calcium ion binding / endoplasmic reticulum / membrane
Similarity search - Function
ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Protein disulphide isomerase / Thioredoxin-like domain / Endoplasmic reticulum targeting sequence. / Thioredoxin / Six-hairpin glycosidase-like superfamily / Thioredoxin, conserved site ...ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Protein disulphide isomerase / Thioredoxin-like domain / Endoplasmic reticulum targeting sequence. / Thioredoxin / Six-hairpin glycosidase-like superfamily / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Protein disulfide-isomerase / ER degradation-enhancing alpha-mannosidase-like protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWu, X.W. / Zhao, D. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM052586 United States
CitationJournal: bioRxiv / Year: 2024
Title: Initiation of ERAD by the bifunctional complex of Mnl1 mannosidase and protein disulfide isomerase.
Authors: Dan Zhao / Xudong Wu / Tom A Rapoport /
Abstract: Misfolded glycoproteins in the endoplasmic reticulum (ER) lumen are translocated into the cytosol and degraded by the proteasome, a conserved process called ER-associated protein degradation (ERAD). ...Misfolded glycoproteins in the endoplasmic reticulum (ER) lumen are translocated into the cytosol and degraded by the proteasome, a conserved process called ER-associated protein degradation (ERAD). In , the glycan of these proteins is trimmed by the luminal mannosidase Mnl1 (Htm1) to generate a signal that triggers degradation. Curiously, Mnl1 is permanently associated with protein disulfide isomerase (Pdi1). Here, we have used cryo-electron microscopy, biochemical, and experiments to clarify how this complex initiates ERAD. The Mnl1-Pdi1 complex first de-mannosylates misfolded, globular proteins that are recognized through a C-terminal domain (CTD) of Mnl1; Pdi1 causes the CTD to ignore completely unfolded polypeptides. The disulfides of these globular proteins are then reduced by the Pdi1 component of the complex, generating unfolded polypeptides that can be translocated across the membrane. Mnl1 blocks the canonical oxidative function of Pdi1, but allows it to function as the elusive disulfide reductase in ERAD.
History
DepositionMay 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ER degradation-enhancing alpha-mannosidase-like protein 1
B: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3206
Polymers149,6162
Non-polymers7044
Water00
1


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

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Components

#1: Protein ER degradation-enhancing alpha-mannosidase-like protein 1


Mass: 91336.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MNL1, HTM1, YHR204W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38888, alpha-mannosidase
#2: Protein Protein disulfide-isomerase / PDI / Thioredoxin-related glycoprotein 1


Mass: 58279.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PDI1, MFP1, TRG1, YCL043C, YCL313, YCL43C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17967, protein disulfide-isomerase
#3: 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.: 3 / 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: A complex of yeast Htm1/Pdi1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313324 / Symmetry type: POINT

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