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Yorodumi- EMDB-4737: Structure of XBP1u-paused ribosome nascent chain complex (rotated... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4737 | |||||||||
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Title | Structure of XBP1u-paused ribosome nascent chain complex (rotated state) | |||||||||
Map data | Structure of XBP1u-paused ribosome nascent chain complex (rotated state) | |||||||||
Sample |
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Keywords | translational pausing / XBP1 / UPR / RIBOSOME | |||||||||
Function / homology | Function and homology information ATF6-mediated unfolded protein response / organelle organization / positive regulation of protein acetylation / response to insulin-like growth factor stimulus / positive regulation of vascular wound healing / positive regulation of lactation / sterol homeostasis / IRE1alpha activates chaperones / positive regulation of plasma cell differentiation / ATF6 (ATF6-alpha) activates chaperone genes ...ATF6-mediated unfolded protein response / organelle organization / positive regulation of protein acetylation / response to insulin-like growth factor stimulus / positive regulation of vascular wound healing / positive regulation of lactation / sterol homeostasis / IRE1alpha activates chaperones / positive regulation of plasma cell differentiation / 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 / negative regulation of SMAD protein signal transduction / XBP1(S) activates chaperone genes / cellular response to laminar fluid shear stress / cellular response to nutrient / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of endothelial cell apoptotic process / cellular response to fluid shear stress / 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 / positive regulation of hepatocyte proliferation / endothelial cell proliferation / cellular response to peptide hormone stimulus / regulation of G1 to G0 transition / muscle organ development / positive regulation of T cell differentiation / exit from mitosis / positive regulation of immunoglobulin production / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / positive regulation of B cell differentiation / positive regulation of fat cell differentiation / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / IRE1-mediated unfolded protein response / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / positive regulation of TOR signaling / 90S preribosome / cellular response to vascular endothelial growth factor stimulus / neuron development / T cell proliferation involved in immune response / fatty acid homeostasis / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding / adipose tissue development / erythrocyte development / vascular endothelial growth factor receptor signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / translation regulator activity / cellular response to actinomycin D / positive regulation of autophagy / ribosomal small subunit export from nucleus / cellular response to glucose starvation / ERAD pathway / cytosolic ribosome / endoplasmic reticulum unfolded protein response / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / phosphatidylinositol 3-kinase/protein kinase B signal transduction / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to endoplasmic reticulum stress / rescue of stalled ribosome / cellular response to amino acid stimulus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / liver development / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / cholesterol homeostasis / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / regulation of cell growth / nuclear estrogen receptor binding / cellular response to glucose stimulus / protein kinase C binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein destabilization Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Shanmuganathan V / Cheng J | |||||||||
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_4737.map.gz | 24.4 MB | EMDB map data format | |
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Header (meta data) | emd-4737-v30.xml emd-4737.xml | 109.8 KB 109.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4737_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_4737.png | 232.3 KB | ||
Filedesc metadata | emd-4737.cif.gz | 19.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4737 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4737 | HTTPS FTP |
-Validation report
Summary document | emd_4737_validation.pdf.gz | 285.9 KB | Display | EMDB validaton report |
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Full document | emd_4737_full_validation.pdf.gz | 285 KB | Display | |
Data in XML | emd_4737_validation.xml.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4737 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4737 | HTTPS FTP |
-Related structure data
Related structure data | 6r6pMC 4729C 4735C 4745C 6r5qC 6r6gC 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_4737.map.gz / Format: CCP4 / Size: 236.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of XBP1u-paused ribosome nascent chain complex (rotated state) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 (rotated...
+Supramolecule #1: Structure of XBP1u-paused ribosome nascent chain complex (rotated...
+Supramolecule #2: Structure of XBP1u-paused ribosome nascent chain complex (rotated...
+Supramolecule #3: A/P- and P/E- site tRNA
+Supramolecule #4: X-box-binding protein 1
+Supramolecule #5: mRNA
+Macromolecule #1: 28S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #49: A/P-tRNA
+Macromolecule #50: P/E-tRNA
+Macromolecule #51: 18S rRNA
+Macromolecule #85: mRNA
+Macromolecule #4: uL2
+Macromolecule #5: uL3
+Macromolecule #6: uL4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: uL30
+Macromolecule #10: eL8
+Macromolecule #11: uL6
+Macromolecule #12: Ribosomal protein L10 (Predicted)
+Macromolecule #13: uL5
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: Ribosomal protein L14
+Macromolecule #16: Ribosomal protein L15
+Macromolecule #17: uL13
+Macromolecule #18: uL22
+Macromolecule #19: eL18
+Macromolecule #20: eL19
+Macromolecule #21: eL20
+Macromolecule #22: eL21
+Macromolecule #23: Ribosomal protein L22
+Macromolecule #24: uL14
+Macromolecule #25: Ribosomal protein L24
+Macromolecule #26: uL23
+Macromolecule #27: Ribosomal protein L26
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: uL15
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: eL30
+Macromolecule #32: eL31
+Macromolecule #33: eL32
+Macromolecule #34: eL33
+Macromolecule #35: eL34
+Macromolecule #36: uL29
+Macromolecule #37: 60S ribosomal protein L36
+Macromolecule #38: Ribosomal protein L37
+Macromolecule #39: eL38
+Macromolecule #40: ribosomal protein eL39
+Macromolecule #41: eL40
+Macromolecule #42: 60s ribosomal protein l41
+Macromolecule #43: eL42
+Macromolecule #44: ribosomal protein eL43
+Macromolecule #45: eL28
+Macromolecule #46: 60S acidic ribosomal protein P0
+Macromolecule #47: Ribosomal protein L12
+Macromolecule #48: X-box-binding protein 1
+Macromolecule #52: uS2
+Macromolecule #53: 40S ribosomal protein S3a
+Macromolecule #54: uS5
+Macromolecule #55: 40S ribosomal protein S4
+Macromolecule #56: 40S ribosomal protein S6
+Macromolecule #57: 40S ribosomal protein S7
+Macromolecule #58: 40S ribosomal protein S8
+Macromolecule #59: Ribosomal protein S9 (Predicted)
+Macromolecule #60: Ribosomal protein S11
+Macromolecule #61: ribosomal protein uS15
+Macromolecule #62: uS11
+Macromolecule #63: Ribosomal protein S16
+Macromolecule #64: eS17
+Macromolecule #65: eS21
+Macromolecule #66: Ribosomal protein S15a
+Macromolecule #67: Ribosomal protein S23
+Macromolecule #68: eS24
+Macromolecule #69: eS26
+Macromolecule #70: 40S ribosomal protein S27
+Macromolecule #71: 40S ribosomal protein S30
+Macromolecule #72: Ribosomal protein S3
+Macromolecule #73: Ribosomal protein S5
+Macromolecule #74: eS10
+Macromolecule #75: 40S ribosomal protein S12
+Macromolecule #76: uS14
+Macromolecule #77: uS13
+Macromolecule #78: eS19
+Macromolecule #79: uS10
+Macromolecule #80: ribosomal protein eS25
+Macromolecule #81: Ribosomal protein S28
+Macromolecule #82: S29
+Macromolecule #83: eS31
+Macromolecule #84: ribosomal protein RACK1
+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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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
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-6r6p: |