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Yorodumi- EMDB-4729: Structure of XBP1u-paused ribosome nascent chain complex (post-state) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4729 | |||||||||
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Title | Structure of XBP1u-paused ribosome nascent chain complex (post-state) | |||||||||
Map data | XBP1u-nascent chain mediated ribosomal pausing. Post state paused XBP1u-RNC | |||||||||
Sample |
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Function / homology | Function and homology information ATF6-mediated unfolded protein response / positive regulation of protein acetylation / response to insulin-like growth factor stimulus / positive regulation of vascular wound healing / organelle organization / positive regulation of plasma cell differentiation / positive regulation of lactation / IRE1alpha activates chaperones / sterol homeostasis / ATF6 (ATF6-alpha) activates chaperone genes ...ATF6-mediated unfolded protein response / positive regulation of protein acetylation / response to insulin-like growth factor stimulus / positive regulation of vascular wound healing / organelle organization / positive regulation of plasma cell differentiation / positive regulation of lactation / IRE1alpha activates chaperones / sterol homeostasis / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of ERAD pathway / : / positive regulation of phospholipid biosynthetic process / negative regulation of myotube differentiation / intracellular triglyceride homeostasis / cellular response to fructose stimulus / XBP1(S) activates chaperone genes / negative regulation of endoplasmic reticulum unfolded protein response / cellular response to laminar fluid shear stress / cellular response to nutrient / cellular response to fluid shear stress / positive regulation of endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of vascular associated smooth muscle cell migration / endothelial cell proliferation / positive regulation of hepatocyte proliferation / ERAD pathway / muscle organ development / positive regulation of T cell differentiation / cellular response to peptide hormone stimulus / positive regulation of B cell differentiation / IRE1-mediated unfolded protein response / positive regulation of immunoglobulin production / neuron development / positive regulation of TOR signaling / rough endoplasmic reticulum / positive regulation of fat cell differentiation / fatty acid homeostasis / cellular response to vascular endothelial growth factor stimulus / cellular response to glucose starvation / adipose tissue development / cis-regulatory region sequence-specific DNA binding / vascular endothelial growth factor receptor signaling pathway / positive regulation of autophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to interleukin-4 / DNA-(apurinic or apyrimidinic site) lyase / response to endoplasmic reticulum stress / cytosolic ribosome / cholesterol homeostasis / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear estrogen receptor binding / regulation of cell growth / cellular response to glucose stimulus / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein destabilization / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / chromatin DNA binding / autophagy / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / protein transport / ribosome biogenesis / cellular response to oxidative stress / 5S rRNA binding / ubiquitin-dependent protein catabolic process / angiogenesis / cellular response to lipopolysaccharide / protease binding / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / ribosome / structural constituent of ribosome / positive regulation of cell migration / immune response / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / nucleolus Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) / Rabbit (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Shanmuganathan V / Cheng J / Berninghausen O / Beckmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Elife / Year: 2019 Title: Structural and mutational analysis of the ribosome-arresting human XBP1u. Authors: Vivekanandan Shanmuganathan / Nina Schiller / Anastasia Magoulopoulou / Jingdong Cheng / Katharina Braunger / Florian Cymer / Otto Berninghausen / Birgitta Beatrix / Kenji Kohno / Gunnar von ...Authors: Vivekanandan Shanmuganathan / Nina Schiller / Anastasia Magoulopoulou / Jingdong Cheng / Katharina Braunger / Florian Cymer / Otto Berninghausen / Birgitta Beatrix / Kenji Kohno / Gunnar von Heijne / Roland Beckmann / Abstract: XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM ...XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel. | |||||||||
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_4729.map.gz | 138.1 MB | EMDB map data format | |
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Header (meta data) | emd-4729-v30.xml emd-4729.xml | 103.2 KB 103.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4729_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_4729.png | 277.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4729 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4729 | HTTPS FTP |
-Related structure data
Related structure data | 6r5qMC 4735C 4737C 4745C 6r6gC 6r6pC 6r7qC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4729.map.gz / Format: CCP4 / Size: 236.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | XBP1u-nascent chain mediated ribosomal pausing. Post state paused XBP1u-RNC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Structure of XBP1u-paused ribosome nascent chain complex (post-state).
+Supramolecule #1: Structure of XBP1u-paused ribosome nascent chain complex (post-state).
+Supramolecule #2: ribosome
+Supramolecule #3: tRNA
+Supramolecule #4: X-box-binding protein 1
+Supramolecule #5: mRNA
+Macromolecule #1: E-tRNA
+Macromolecule #3: P-tRNA
+Macromolecule #4: 28S ribosomal RNA
+Macromolecule #5: 5S rRNA
+Macromolecule #6: 5.8S ribosomal RNA
+Macromolecule #51: 18S ribosomal RNA
+Macromolecule #82: mRNA
+Macromolecule #2: X-box-binding protein 1
+Macromolecule #7: uL2
+Macromolecule #8: uL3
+Macromolecule #9: uL4
+Macromolecule #10: 60S ribosomal protein L5
+Macromolecule #11: 60S ribosomal protein L6
+Macromolecule #12: uL30
+Macromolecule #13: eL8
+Macromolecule #14: uL6
+Macromolecule #15: Ribosomal protein L10 (Predicted)
+Macromolecule #16: Ribosomal protein L11
+Macromolecule #17: 60S ribosomal protein L13
+Macromolecule #18: Ribosomal protein L14
+Macromolecule #19: Ribosomal protein L15
+Macromolecule #20: uL13
+Macromolecule #21: uL22
+Macromolecule #22: eL18
+Macromolecule #23: eL19
+Macromolecule #24: eL20
+Macromolecule #25: eL21
+Macromolecule #26: eL22
+Macromolecule #27: eL14
+Macromolecule #28: Ribosomal protein L24
+Macromolecule #29: uL23
+Macromolecule #30: Ribosomal protein L26
+Macromolecule #31: 60S ribosomal protein L27
+Macromolecule #32: uL15
+Macromolecule #33: eL29
+Macromolecule #34: eL30
+Macromolecule #35: eL31
+Macromolecule #36: eL32
+Macromolecule #37: eL33
+Macromolecule #38: eL34
+Macromolecule #39: uL29
+Macromolecule #40: 60S ribosomal protein L36
+Macromolecule #41: Ribosomal protein L37
+Macromolecule #42: eL38
+Macromolecule #43: eL39
+Macromolecule #44: eL40
+Macromolecule #45: 60s ribosomal protein l41
+Macromolecule #46: eL42
+Macromolecule #47: ribosomal protein eL43
+Macromolecule #48: eL28
+Macromolecule #49: 60S acidic ribosomal protein P0
+Macromolecule #50: uL11
+Macromolecule #52: uS2
+Macromolecule #53: 40S ribosomal protein S3a
+Macromolecule #54: uS5
+Macromolecule #55: Ribosomal protein S3
+Macromolecule #56: 40S ribosomal protein S4
+Macromolecule #57: Ribosomal protein S5
+Macromolecule #58: 40S ribosomal protein S6
+Macromolecule #59: 40S ribosomal protein S7
+Macromolecule #60: 40S ribosomal protein S8
+Macromolecule #61: Ribosomal protein S9 (Predicted)
+Macromolecule #62: eS10
+Macromolecule #63: Ribosomal protein S11
+Macromolecule #64: 40S ribosomal protein S12
+Macromolecule #65: ribosomal protein uS15
+Macromolecule #66: uS11
+Macromolecule #67: uS17
+Macromolecule #68: Ribosomal protein S16
+Macromolecule #69: eS17
+Macromolecule #70: uS13
+Macromolecule #71: eS19
+Macromolecule #72: uS10
+Macromolecule #73: eS21
+Macromolecule #74: Ribosomal protein S15a
+Macromolecule #75: Ribosomal protein S23
+Macromolecule #76: eS24
+Macromolecule #77: ribosomal protein eS25
+Macromolecule #78: eS26
+Macromolecule #79: 40S ribosomal protein S27
+Macromolecule #80: Ribosomal protein S28
+Macromolecule #81: uS14
+Macromolecule #83: eS31
+Macromolecule #84: ribosomal protein RACK1
+Macromolecule #85: 40S ribosomal protein S30
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6r5q: |