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Yorodumi- EMDB-8642: Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8642 | |||||||||
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Title | Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3 | |||||||||
Map data | CryoEM map of Hrd3 filtering to 3.9A and applied with -180 b-factor | |||||||||
Sample |
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Function / homology | Function and homology information Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / ubiquitin-dependent glycoprotein ERAD pathway / Hrd1p ubiquitin ligase ERAD-L complex / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / : / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Mi W / Schoebel S / Stein A / Rapoport TA / Liao M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2017 Title: Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Authors: Stefan Schoebel / Wei Mi / Alexander Stein / Sergey Ovchinnikov / Ryan Pavlovicz / Frank DiMaio / David Baker / Melissa G Chambers / Huayou Su / Dongsheng Li / Tom A Rapoport / Maofu Liao / Abstract: Misfolded endoplasmic reticulum proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the membrane, and degraded by the proteasome-a ...Misfolded endoplasmic reticulum proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the membrane, and degraded by the proteasome-a pathway termed endoplasmic reticulum-associated protein degradation (ERAD). Proteins with misfolded domains in the endoplasmic reticulum lumen or membrane are discarded through the ERAD-L and ERAD-M pathways, respectively. In Saccharomyces cerevisiae, both pathways require the ubiquitin ligase Hrd1, a multi-spanning membrane protein with a cytosolic RING finger domain. Hrd1 is the crucial membrane component for retro-translocation, but it is unclear whether it forms a protein-conducting channel. Here we present a cryo-electron microscopy structure of S. cerevisiae Hrd1 in complex with its endoplasmic reticulum luminal binding partner, Hrd3. Hrd1 forms a dimer within the membrane with one or two Hrd3 molecules associated at its luminal side. Each Hrd1 molecule has eight transmembrane segments, five of which form an aqueous cavity extending from the cytosol almost to the endoplasmic reticulum lumen, while a segment of the neighbouring Hrd1 molecule forms a lateral seal. The aqueous cavity and lateral gate are reminiscent of features of protein-conducting conduits that facilitate polypeptide movement in the opposite direction-from the cytosol into or across membranes. Our results suggest that Hrd1 forms a retro-translocation channel for the movement of misfolded polypeptides through the endoplasmic reticulum membrane. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8642.map.gz | 25 MB | EMDB map data format | |
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Header (meta data) | emd-8642-v30.xml emd-8642.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8642_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_8642.png | 46.2 KB | ||
Others | emd_8642_additional.map.gz | 20.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8642 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8642 | HTTPS FTP |
-Related structure data
Related structure data | 5v7vMC 8637C 8638C 8639C 5v6pC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8642.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of Hrd3 filtering to 3.9A and applied with -180 b-factor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: CryoEM map of Hrd3 without filtering or amplitude modification
File | emd_8642_additional.map | ||||||||||||
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Annotation | CryoEM map of Hrd3 without filtering or amplitude modification | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hrd1/Hrd3 complex
Entire | Name: Hrd1/Hrd3 complex |
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Components |
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-Supramolecule #1: Hrd1/Hrd3 complex
Supramolecule | Name: Hrd1/Hrd3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: ERAD-associated E3 ubiquitin-protein ligase component HRD3
Macromolecule | Name: ERAD-associated E3 ubiquitin-protein ligase component HRD3 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 93.759156 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MITLLLYLCV ICNAIVLIRA DSIADPWPEA RHLLNTIAKS RDPMKEAAME PNADEFVGFY VPMDYSPRNE EKNYQSIWQN EITDSQRHI YELLVQSSEQ FNNSEATYTL SQIHLWSQYN FPHNMTLAHK YLEKFNDLTH FTNHSAIFDL AVMYATGGCA S GNDQTVIP ...String: MITLLLYLCV ICNAIVLIRA DSIADPWPEA RHLLNTIAKS RDPMKEAAME PNADEFVGFY VPMDYSPRNE EKNYQSIWQN EITDSQRHI YELLVQSSEQ FNNSEATYTL SQIHLWSQYN FPHNMTLAHK YLEKFNDLTH FTNHSAIFDL AVMYATGGCA S GNDQTVIP QDSAKALLYY QRAAQLGNLK AKQVLAYKYY SGFNVPRNFH KSLVLYRDIA EQLRKSYSRD EWDIVFPYWE SY NVRISDF ESGLLGKGLN SVPSSTVRKR TTRPDIGSPF IAQVNGVQMT LQIEPMGRFA FNGNDGNING DEDDEDASER RII RIYYAA LNDYKGTYSQ SRNCERAKNL LELTYKEFQP HVDNLDPLQV FYYVRCLQLL GHMYFTGEGS SKPNIHMAEE ILTT SLEIS RRAQGPIGRA CIDLGLINQY ITNNISQAIS YYMKAMKTQA NNGIVEFQLS KLATSFPEEK IGDPFNLMET AYLNG FIPA IYEFAVMIES GMNSKSSVEN TAYLFKTFVD KNEAIMAPKL RTAFAALIND RSEVALWAYS QLAEQGYETA QVSAAY LMY QLPYEFEDPP RTTDQRKTLA ISYYTRAFKQ GNIDAGVVAG DIYFQMQNYS KAMALYQGAA LKYSIQAIWN LGYMHEH GL GVNRDFHLAK RYYDQVSEHD HRFYLASKLS VLKLHLKSWL TWITREKVNY WKPSSPLNPN EDTQHSKTSW YKQLTKIL Q RMRHKEDSDK AAEDSHKHRT VVQNGANHRG DDQEEASEIL GFQMEDGGGE NLYFQSGGGM DEKTTGWRGG HVVEGLAGE LEQLRARLEH HPQGQREP |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 82.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |