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- PDB-6r5q: Structure of XBP1u-paused ribosome nascent chain complex (post-state) -

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Entry
Database: PDB / ID: 6r5q
TitleStructure of XBP1u-paused ribosome nascent chain complex (post-state)
Components
  • (40S ribosomal protein ...) x 8
  • (60S ribosomal protein ...) x 6
  • (Ribosomal protein ...) x 19
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • E-tRNA
  • P-tRNA
  • X-box-binding protein 1
  • eL14
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL42
  • eL8
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS26
  • eS31
  • mRNAMessenger RNA
  • uL11
  • uL13
  • uL15
  • uL2
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS13
  • uS14
  • uS17
  • uS2
  • uS5
KeywordsRIBOSOME / translational pausing / XBP1 / UPR
Function / homology
Function and homology information


positive regulation of plasma cell differentiation / epithelial cell maturation involved in salivary gland development / positive regulation of histone methylation / positive regulation of vascular wound healing / sterol homeostasis / organelle organization / negative regulation of pathway-restricted SMAD protein phosphorylation / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / response to insulin-like growth factor stimulus / positive regulation of immunoglobulin production ...positive regulation of plasma cell differentiation / epithelial cell maturation involved in salivary gland development / positive regulation of histone methylation / positive regulation of vascular wound healing / sterol homeostasis / organelle organization / negative regulation of pathway-restricted SMAD protein phosphorylation / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / response to insulin-like growth factor stimulus / positive regulation of immunoglobulin production / positive regulation of protein acetylation / ATF6-mediated unfolded protein response / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / positive regulation of lactation / negative regulation of myotube differentiation / cellular response to fructose stimulus / cellular triglyceride homeostasis / positive regulation of immunoglobulin secretion / cellular response to nutrient / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of endoplasmic reticulum unfolded protein response / endothelial cell proliferation / cellular response to laminar fluid shear stress / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of T cell differentiation / positive regulation of TOR signaling / positive regulation of endothelial cell apoptotic process / positive regulation of MHC class II biosynthetic process / cytosolic ribosome / positive regulation of B cell differentiation / exocrine pancreas development / positive regulation of hepatocyte proliferation / muscle organ development / positive regulation of vascular associated smooth muscle cell migration / positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress / adipose tissue development / neuron development / integral component of endoplasmic reticulum membrane / TOR signaling / go:2000778: / cellular response to peptide hormone stimulus / cis-regulatory region sequence-specific DNA binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / IRE1-mediated unfolded protein response / cellular response to glucose starvation / positive regulation of fat cell differentiation / phosphatidylinositol 3-kinase signaling / cellular response to interleukin-4 / endoplasmic reticulum unfolded protein response / positive regulation of autophagy / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / fatty acid homeostasis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cellular response to leukemia inhibitory factor / response to endoplasmic reticulum stress / positive regulation of vascular associated smooth muscle cell proliferation / polysomal ribosome / regulation of autophagy / cellular response to vascular endothelial growth factor stimulus / regulation of cell growth / cellular response to amino acid stimulus / DNA-(apurinic or apyrimidinic site) endonuclease activity / negative regulation of ERK1 and ERK2 cascade / positive regulation of translation / cholesterol homeostasis / mRNA 5'-UTR binding / cellular response to glucose stimulus / cytoplasmic ribonucleoprotein granule / protein destabilization / positive regulation of protein-containing complex assembly / fatty acid biosynthetic process / rRNA processing / chromatin DNA binding / cytoplasmic translation / cellular response to fluid shear stress / cellular response to gamma radiation / ribosome biogenesis / estrogen receptor binding / liver development / protein transport / autophagy / positive regulation of protein import into nucleus / negative regulation of transforming growth factor beta receptor signaling pathway / large ribosomal subunit / cell body / cellular response to insulin stimulus / regulation of protein stability / cytosolic large ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / transcription by RNA polymerase II / vascular endothelial growth factor receptor signaling pathway / cellular response to oxidative stress / positive regulation of angiogenesis / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / small ribosomal subunit
Ribosomal protein S7p/S5e / Ribosomal protein L23 / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site ...Ribosomal protein S7p/S5e / Ribosomal protein L23 / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S17, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L18e/L15P / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L18e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S14, conserved site / 50S ribosomal protein L30e-like / Translation protein SH3-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein L37ae/L37e / TRASH domain / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation protein, beta-barrel domain superfamily / Ribosomal protein L34Ae / Ribosomal protein L30, N-terminal / Ribosomal protein L41 / Ribosomal protein S30 / Ribosomal protein S12/S23 / Ribosomal protein L7, eukaryotic / Ribosomal protein L24/L26, conserved site / KOW / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L30, conserved site / WD40-repeat-containing domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / K homology domain-like, alpha/beta / Ribosomal protein L2, domain 3 / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup
60s ribosomal protein l41 / Ribosomal_L28e domain-containing protein / Ribosomal protein L37 / Ribosomal protein L14 / X-box-binding protein 1 / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L10 (Predicted) / Ribosomal protein S9 (Predicted) / Ribosomal_L18e/L15P domain-containing protein ...60s ribosomal protein l41 / Ribosomal_L28e domain-containing protein / Ribosomal protein L37 / Ribosomal protein L14 / X-box-binding protein 1 / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L10 (Predicted) / Ribosomal protein S9 (Predicted) / Ribosomal_L18e/L15P domain-containing protein / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L5 / Uncharacterized protein / Uncharacterized protein / Ribos_L4_asso_C domain-containing protein / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L7a / 40S ribosomal protein S3a / Ribosomal protein L26 / Ribosomal_S13_N domain-containing protein / Uncharacterized protein / Ribosomal protein L15 / 60S ribosomal protein L6 / Ubiquitin-like domain-containing protein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S12 / Uncharacterized protein / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S15 / S10_plectin domain-containing protein / 40S ribosomal protein S27 / 60S ribosomal protein L27 / Ribosomal_L18e/L15P domain-containing protein / Uncharacterized protein / RPL17-C18orf32 readthrough / Uncharacterized protein / Elongin A / Uncharacterized protein / 60S ribosomal protein L36 / Uncharacterized protein / Zinc finger protein 34 / Ribosomal protein S11 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S3 / Uncharacterized protein / 40S ribosomal protein S6 / Uncharacterized protein / 40S ribosomal protein S4 / 40S ribosomal protein S8 / Ribosomal protein S28 / Uncharacterized protein / Ribosomal protein S5 / Ribosomal protein L30 / 40S ribosomal protein S25 / 40S ribosomal protein S30 / 60S acidic ribosomal protein P0
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (baker's yeast)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsShanmuganathan, V. / Cheng, J. / Berninghausen, O. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK1721 Germany
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / pdbx_struct_conn_angle ...em_image_scans / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn

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Structure visualization

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Assembly

Deposited unit
3: E-tRNA
1: X-box-binding protein 1
2: P-tRNA
5: 28S ribosomal RNA
7: 5S rRNA
8: 5.8S ribosomal RNA
A: uL2
B: uL3
C: uL4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: uL30
G: eL8
H: uL6
I: Ribosomal protein L10 (Predicted)
J: Ribosomal protein L11
L: 60S ribosomal protein L13
M: Ribosomal protein L14
N: Ribosomal protein L15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: eL14
W: Ribosomal protein L24
X: uL23
Y: Ribosomal protein L26
Z: 60S ribosomal protein L27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: eL38
l: eL39
m: eL40
n: 60s ribosomal protein l41
o: eL42
p: ribosomal protein eL43
r: eL28
s: 60S acidic ribosomal protein P0
t: uL11
K: 18S ribosomal RNA
q: uS2
u: 40S ribosomal protein S3a
v: uS5
w: Ribosomal protein S3
x: 40S ribosomal protein S4
y: Ribosomal protein S5
z: 40S ribosomal protein S6
BB: 40S ribosomal protein S7
CC: 40S ribosomal protein S8
DD: Ribosomal protein S9 (Predicted)
SS: eS10
EE: Ribosomal protein S11
RR: 40S ribosomal protein S12
QQ: ribosomal protein uS15
MM: uS11
WW: uS17
UU: Ribosomal protein S16
KK: eS17
II: uS13
PP: eS19
GG: uS10
HH: eS21
TT: Ribosomal protein S15a
VV: Ribosomal protein S23
NN: eS24
OO: ribosomal protein eS25
LL: eS26
JJ: 40S ribosomal protein S27
FF: Ribosomal protein S28
9: uS14
4: mRNA
0: eS31
6: ribosomal protein RACK1
AA: 40S ribosomal protein S30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,192,867390
Polymers3,185,20885
Non-polymers7,660305
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 7 types, 7 molecules 32578K4

#1: RNA chain E-tRNA


Mass: 24148.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#3: RNA chain P-tRNA


Mass: 24414.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#4: RNA chain 28S ribosomal RNA / /


Mass: 1148115.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: RNA chain 5S rRNA / 5S ribosomal RNA / 5S ribosomal RNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#6: RNA chain 5.8S ribosomal RNA / /


Mass: 48545.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#51: RNA chain 18S ribosomal RNA / /


Mass: 548040.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#82: RNA chain mRNA / Messenger RNA / Messenger RNA


Mass: 1877.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein/peptide , 2 types, 2 molecules 1l

#2: Protein/peptide X-box-binding protein 1 / XBP-1 / Tax-responsive element-binding protein 5 / TREB-5


Mass: 2895.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XBP1, TREB5, XBP2 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P17861
#43: Protein/peptide eL39


Mass: 6324.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1

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Protein , 43 types, 43 molecules ABCFGHOPQRSTUVXabcdefghkmorstq...

#7: Protein uL2


Mass: 26998.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#8: Protein uL3


Mass: 45119.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#9: Protein uL4


Mass: 41101.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#12: Protein uL30


Mass: 26658.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#13: Protein eL8


Mass: 26695.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#14: Protein uL6


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#20: Protein uL13


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: Protein uL22


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6, UniProt: G1SCJ6*PLUS
#22: Protein eL18


Mass: 21568.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX70
#23: Protein eL19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein eL21 / /


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#26: Protein eL22


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein eL14


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#29: Protein uL23


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#32: Protein uL15


Mass: 16489.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#33: Protein eL29


Mass: 12093.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#34: Protein eL30


Mass: 10914.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#35: Protein eL31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#36: Protein eL32 / CD59 / CD59


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#37: Protein eL33


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#38: Protein eL34 / /


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#39: Protein uL29


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#42: Protein eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein eL40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: Protein eL42


Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T040
#48: Protein eL28


Mass: 14220.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#49: Protein 60S acidic ribosomal protein P0


Mass: 21521.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U6N2
#50: Protein uL11


Mass: 16561.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#52: Protein uS2


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein uS5


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein eS10


Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#66: Protein uS11


Mass: 14431.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#67: Protein uS17


Mass: 14246.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#69: Protein eS17


Mass: 15250.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#70: Protein uS13


Mass: 16898.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZI5, UniProt: G1TPG3*PLUS
#71: Protein eS19


Mass: 15611.003 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#72: Protein uS10


Mass: 11395.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: Protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein eS24


Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: Protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#83: Protein eS31


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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60S ribosomal protein ... , 6 types, 6 molecules DELZin

#10: Protein 60S ribosomal protein L5 / /


Mass: 34077.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#11: Protein 60S ribosomal protein L6 / /


Mass: 28818.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#17: Protein 60S ribosomal protein L13 / /


Mass: 24200.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV0
#31: Protein 60S ribosomal protein L27 / /


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#40: Protein 60S ribosomal protein L36 / /


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#45: Protein/peptide 60s ribosomal protein l41 / / eL41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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Ribosomal protein ... , 19 types, 19 molecules IJMNWYjpwyDDEEQQUUTTVVOOFF6

#15: Protein Ribosomal protein L10 (Predicted) / Ribosome / Ribosome


Mass: 23736.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#16: Protein Ribosomal protein L11 / /


Mass: 19399.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#18: Protein Ribosomal protein L14 / /


Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#19: Protein Ribosomal protein L15 / /


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#28: Protein Ribosomal protein L24 / /


Mass: 14131.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#30: Protein Ribosomal protein L26 / /


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#41: Protein Ribosomal protein L37 / /


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#47: Protein ribosomal protein eL43 / /


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#55: Protein Ribosomal protein S3 / /


Mass: 25215.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#57: Protein Ribosomal protein S5 / /


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#61: Protein Ribosomal protein S9 (Predicted) / Ribosome / Ribosome


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#63: Protein Ribosomal protein S11 / /


Mass: 17586.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#65: Protein ribosomal protein uS15 / /


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#68: Protein Ribosomal protein S16 / /


Mass: 16032.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#74: Protein Ribosomal protein S15a / Ribosome / Ribosome


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#75: Protein Ribosomal protein S23 / /


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#77: Protein ribosomal protein eS25 / /


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#80: Protein Ribosomal protein S28 / /


Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#84: Protein ribosomal protein RACK1 / /


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

+
40S ribosomal protein ... , 8 types, 8 molecules uxzBBCCRRJJAA

#53: Protein 40S ribosomal protein S3a / /


Mass: 24759.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#56: Protein 40S ribosomal protein S4 / /


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#58: Protein 40S ribosomal protein S6 / /


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#59: Protein 40S ribosomal protein S7 / /


Mass: 21629.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#60: Protein 40S ribosomal protein S8 / /


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#64: Protein 40S ribosomal protein S12 / /


Mass: 13048.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#79: Protein 40S ribosomal protein S27 / /


Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#85: Protein 40S ribosomal protein S30 / /


Mass: 6317.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2

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Non-polymers , 2 types, 305 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 299 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of XBP1u-paused ribosome nascent chain complex (post-state).RIBOSOME1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 850MULTIPLE SOURCES
2ribosomeCOMPLEX4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 83, 84, 851NATURAL
3tRNATransfer RNACOMPLEX1, 31NATURAL
4X-box-binding protein 1COMPLEX21RECOMBINANT
5mRNAMessenger RNACOMPLEX821RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Saccharomyces cerevisiae (baker's yeast)4932
34Homo sapiens (human)9606
45Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
14Oryctolagus cuniculus (rabbit)9986
25synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameCategory
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223773 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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