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Yorodumi- EMDB-49171: Structure of a GRP94 folding intermediate engaged with a CCDC134-... -
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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon | |||||||||
Map data | Whole particle (RTC) map after focused refinement on the 60S subunit | |||||||||
Sample |
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Keywords | Ribosome / Membrane protein / Translocon / Transport / N-Glycosylation | |||||||||
| Function / homology | Function and homology informationpositive regulation of MyD88-dependent toll-like receptor signaling pathway / : / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development ...positive regulation of MyD88-dependent toll-like receptor signaling pathway / : / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development / ATF6 (ATF6-alpha) activates chaperone genes / endoplasmic reticulum Sec complex / pronephric nephron development / endoplasmic reticulum chaperone complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / sequestering of calcium ion / cotranslational protein targeting to membrane / plasma membrane organization / endoplasmic reticulum quality control compartment / Ssh1 translocon complex / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / positive regulation of growth hormone secretion / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / oligosaccharyltransferase complex / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of organ growth / ventricular system development / : / : / SRP-dependent cotranslational protein targeting to membrane, translocation / XBP1(S) activates chaperone genes / translation at presynapse / signal sequence binding / exit from mitosis / SRP-dependent cotranslational protein targeting to membrane / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / optic nerve development / regulation of translation involved in cellular response to UV / protein N-linked glycosylation / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / post-translational protein targeting to membrane, translocation / ribosomal protein import into nucleus / endoplasmic reticulum organization / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / retinal ganglion cell axon guidance / Trafficking and processing of endosomal TLR / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / epithelial cell apoptotic process / embryonic hemopoiesis / insulin secretion / middle ear morphogenesis / Scavenging by Class A Receptors / epidermal growth factor binding / retrograde protein transport, ER to cytosol / azurophil granule membrane / low-density lipoprotein particle receptor binding / cytoplasmic side of rough endoplasmic reticulum membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein phosphatase inhibitor activity / negative regulation of ubiquitin protein ligase activity / sperm plasma membrane / homeostatic process / : / macrophage chemotaxis / cellular response to ATP / lung morphogenesis / male meiosis I / positive regulation of natural killer cell proliferation / smooth endoplasmic reticulum / Protein hydroxylation / Peptide chain elongation / Advanced glycosylation endproduct receptor signaling / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to actinomycin D / Eukaryotic Translation Termination / blastocyst development / ubiquitin ligase inhibitor activity / regulation of ossification / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / protein transmembrane transporter activity / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Yamsek M / Jha R / Keenan RJ | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2024 Title: Regulated N-glycosylation controls chaperone function and receptor trafficking. Authors: Mengxiao Ma / Ramin Dubey / Annie Jen / Ganesh V Pusapati / Bharti Singal / Evgenia Shishkova / Katherine A Overmyer / Valérie Cormier-Daire / Juliette Fedry / L Aravind / Joshua J Coon / Rajat Rohatgi / ![]() Abstract: One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a ...One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCDC134, an ER luminal protein. During its translocation into the ER, an N-terminal peptide in HSP90B1 templates the assembly of a translocon complex containing CCDC134 and OST-A that protects HSP90B1 during folding, preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT and IGF1R signaling and causes the bone developmental disorder osteogenesis imperfecta. Thus, N-glycosylation can be regulated by specificity factors in the ER to control cell surface receptor signaling and tissue development. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_49171.map.gz | 340.4 MB | EMDB map data format | |
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| Header (meta data) | emd-49171-v30.xml emd-49171.xml | 99.1 KB 99.1 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_49171_fsc.xml | 16.9 KB | Display | FSC data file |
| Images | emd_49171.png | 121.2 KB | ||
| Masks | emd_49171_msk_1.map | 421.9 MB | Mask map | |
| Filedesc metadata | emd-49171.cif.gz | 21 KB | ||
| Others | emd_49171_half_map_1.map.gz emd_49171_half_map_2.map.gz | 341.1 MB 341.1 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-49171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-49171 | HTTPS FTP |
-Validation report
| Summary document | emd_49171_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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| Full document | emd_49171_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | emd_49171_validation.xml.gz | 24.5 KB | Display | |
| Data in CIF | emd_49171_validation.cif.gz | 33 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-49171 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-49171 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9n9jMC ![]() 9ygyC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_49171.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Whole particle (RTC) map after focused refinement on the 60S subunit | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.40243 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_49171_msk_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: Half-map 1
| File | emd_49171_half_map_1.map | ||||||||||||
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| Annotation | Half-map 1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map 2
| File | emd_49171_half_map_2.map | ||||||||||||
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| Annotation | Half-map 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Nascent GRP94 folding intermediate bound to a ribosome-translocon...
+Supramolecule #1: Nascent GRP94 folding intermediate bound to a ribosome-translocon...
+Macromolecule #1: Translocon-associated protein subunit alpha
+Macromolecule #2: Translocon-associated protein subunit beta
+Macromolecule #3: Translocon-associated protein subunit gamma
+Macromolecule #4: Translocon-associated protein subunit delta
+Macromolecule #5: Peptidyl-prolyl cis-trans isomerase FKBP11
+Macromolecule #6: Coiled-coil domain-containing protein 134
+Macromolecule #7: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #8: Protein transport protein Sec61 subunit beta
+Macromolecule #9: Protein transport protein Sec61 subunit gamma
+Macromolecule #10: Stress-associated endoplasmic reticulum protein 1
+Macromolecule #11: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #12: Oligosaccharyltransferase complex subunit OSTC
+Macromolecule #13: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #14: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #18: 60S ribosomal protein L8
+Macromolecule #19: 60S ribosomal protein L3
+Macromolecule #20: Large ribosomal subunit protein uL4
+Macromolecule #21: Large ribosomal subunit protein uL18
+Macromolecule #22: Large ribosomal subunit protein eL6
+Macromolecule #23: 60S ribosomal protein L7
+Macromolecule #24: Large ribosomal subunit protein eL8
+Macromolecule #25: Large ribosomal subunit protein uL6
+Macromolecule #26: Ribosomal protein uL16-like
+Macromolecule #27: Large ribosomal subunit protein eL13
+Macromolecule #28: Large ribosomal subunit protein eL14
+Macromolecule #29: Large ribosomal subunit protein eL15
+Macromolecule #30: Large ribosomal subunit protein uL13
+Macromolecule #31: Large ribosomal subunit protein uL22
+Macromolecule #32: Large ribosomal subunit protein eL18
+Macromolecule #33: Large ribosomal subunit protein eL19
+Macromolecule #34: Large ribosomal subunit protein eL20
+Macromolecule #35: Large ribosomal subunit protein eL21
+Macromolecule #36: Large ribosomal subunit protein eL22
+Macromolecule #37: Large ribosomal subunit protein uL14
+Macromolecule #38: Large ribosomal subunit protein eL24
+Macromolecule #39: Large ribosomal subunit protein uL23
+Macromolecule #40: Large ribosomal subunit protein uL24
+Macromolecule #41: Large ribosomal subunit protein eL27
+Macromolecule #42: 60S ribosomal protein L27a
+Macromolecule #43: 60S ribosomal protein L29
+Macromolecule #44: Large ribosomal subunit protein eL30
+Macromolecule #45: Large ribosomal subunit protein eL31
+Macromolecule #46: Large ribosomal subunit protein eL32
+Macromolecule #47: Large ribosomal subunit protein eL33
+Macromolecule #48: Large ribosomal subunit protein eL34
+Macromolecule #49: Large ribosomal subunit protein uL29
+Macromolecule #50: Large ribosomal subunit protein eL36
+Macromolecule #51: Large ribosomal subunit protein eL37
+Macromolecule #52: Large ribosomal subunit protein eL38
+Macromolecule #53: Large ribosomal subunit protein eL39
+Macromolecule #54: Ubiquitin-60S ribosomal protein L40
+Macromolecule #55: Small ribosomal subunit protein eS32
+Macromolecule #56: Large ribosomal subunit protein eL42
+Macromolecule #57: Large ribosomal subunit protein eL43
+Macromolecule #58: 60S ribosomal protein L28
+Macromolecule #59: 60S acidic ribosomal protein P0
+Macromolecule #60: 60S ribosomal protein L12
+Macromolecule #61: 60S ribosomal protein L10a
+Macromolecule #62: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #63: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #64: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...
+Macromolecule #65: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #66: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #69: Endoplasmin
+Macromolecule #70: Large ribosomal subunit protein uL5
+Macromolecule #15: 28S ribosomal RNA
+Macromolecule #16: 5S ribosomal RNA
+Macromolecule #17: 5.8S ribosomal RNA
+Macromolecule #67: tRNA
+Macromolecule #68: tRNA
+Macromolecule #75: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...
+Macromolecule #76: MAGNESIUM ION
+Macromolecule #77: ZINC ION
+Macromolecule #78: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 0.056 mg/mL | |||||||||||||||||||||
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| Buffer | pH: 7.4 Component:
Details: HEPES buffer was adjusted to pH 7.4 with potassium hydroxide. | |||||||||||||||||||||
| Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. | |||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Three microliters of affinity-purified RTCs were applied to the grid, incubated for 60 seconds, blotted for 7 seconds, drained for 0.5 seconds, and frozen in liquid nitrogen-cooled ethane.. | |||||||||||||||||||||
| Details | Native ribosome-translocon complexes isolated from HEK293 microsomes by affinity purification via a Flag-tag on FKBP11 |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6569 / Average electron dose: 60.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 53000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Details | Tightly restrained real-space refinement in Coot and Phenix |
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| Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
| Output model | ![]() PDB-9n9j: |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
Citation














































Z (Sec.)
Y (Row.)
X (Col.)














































FIELD EMISSION GUN

