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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21224 | |||||||||
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Title | CryoEM map of Hrd3/Yos9 complex | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wu X / Rapoport TA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Authors: Xudong Wu / Marc Siggel / Sergey Ovchinnikov / Wei Mi / Vladimir Svetlov / Evgeny Nudler / Maofu Liao / Gerhard Hummer / Tom A Rapoport / ![]() ![]() Abstract: Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD- ...Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo-electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two "half-channels" with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
Images | ![]() | 104.6 KB | ||
Others | ![]() | 2.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vk3MC ![]() 6vjyC ![]() 6vjzC ![]() 6vk0C ![]() 6vk1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: unsharpened map
File | emd_21224_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : a complex of Hrd1/Hrd3/Yos9
Entire | Name: a complex of Hrd1/Hrd3/Yos9 |
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Components |
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-Supramolecule #1: a complex of Hrd1/Hrd3/Yos9
Supramolecule | Name: a complex of Hrd1/Hrd3/Yos9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Hrd3
Macromolecule | Name: Hrd3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 84.328023 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 TTR(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) DASERRIIRI YYAAL NDYK GTYSQSRNCE RAKNLLELTY KEFQPHVDNL DPLQVFYYVR CLQLLGHMYF TGEGSSKPNI HMAEEILTTS LEISRR AQG PIGRACIDLG LINQYITNNI SQAISYYMKA MKTQANNGIV EFQLSKLATS FPEEKIGDPF NLMETAYLNG FIPAIYE FA VMIESGMNSK SSVENTAYLF KTFVDKNEAI MAPKLRTAFA ALINDRSEVA LWAYSQLAEQ GYETAQVSAA YLMYQLPY E FEDPPRTTDQ RKTLAISYYT RAFKQGNIDA GVVAGDIYFQ MQNYSKAMAL YQGAALKYSI QAIWNLGYMH EHGLGVNRD FHLAKRYYDQ VSEHDHRFYL ASKLSVLKLH LKSWLTWITR EKVNYWKPSS PLNPNEDTQH SKTSWYKQLT KILQRMRHKE DSDKAAEDS HKHRTVVQNG ANHRGDDQEE ASEILGFQME D |
-Macromolecule #2: Protein OS-9 homolog
Macromolecule | Name: Protein OS-9 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 61.311285 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MQAKIIYALS AISALIPLGS SLLAPIEDPI VSNKYLISYI DEDDWSDRIL QNQSVMNSGY IVNMGDDLEC FIQNASTQLN DVLEDSNEH SNSEKTALLT KTLNQGVKTI FDKLNERCIF YQAGFWIYEY CPGIEFVQFH GRVNTKTGEI VNRDESLVYR L GKPKANVE ...String: MQAKIIYALS AISALIPLGS SLLAPIEDPI VSNKYLISYI DEDDWSDRIL QNQSVMNSGY IVNMGDDLEC FIQNASTQLN DVLEDSNEH SNSEKTALLT KTLNQGVKTI FDKLNERCIF YQAGFWIYEY CPGIEFVQFH GRVNTKTGEI VNRDESLVYR L GKPKANVE EREFELLYDD VGYYISEIIG SGDICDVTGA ERMVEIQYVC GGSNSGPSTI QWVRETKICV YEAQVTIPEL CN LELLAKN EDQKNASPIL CRMPAKSKIG SNSIDLITKY EPIFLGSGIY FLRPFNTDER DKLMVTDNAM SNWDEITETY YQK FGNAIN KMLSLRLVSL PNGHILQPGD SCVWLAEVVD MKDRFQTTLS LNILNSQRAE IFFNKTFTFN EDNGNFLSYK IGDH GESTE LGQITHSNKA DINTAEIRSD EYLINTDNEL FLRISKEIAE VKELLNEIVS PHEMEVIFEN MRNQPNNDFE LALMN KLKS SLNDDNKVEQ INNARMDDDE STSHTTRDIG EAGSQTTGNT ESEVTNVAAG VFIEHDEL |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.9 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: Gctf |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 99298 |