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- PDB-6r6g: Structure of XBP1u-paused ribosome nascent chain complex with SRP. -

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Basic information

Entry
Database: PDB / ID: 6r6g
TitleStructure of XBP1u-paused ribosome nascent chain complex with SRP.
Components
  • (40S ribosomal protein ...) x 12
  • (60S ribosomal protein ...) x 11
  • (Ribosomal protein ...) x 20
  • (Signal recognition particle ...) x 5
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • 7S RNA
  • E-tRNA
  • P-tRNA
  • Signal sequence (HR2)
  • X-box-binding protein 1
  • eL14
  • eL18
  • eL20
  • eL21
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL39
  • eL42
  • eL8
  • eS10
  • eS17
  • eS19
  • eS31
  • mRNAMessenger RNA
  • uL11
  • uL15
  • uL2
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS13
  • uS14
  • uS19
  • uS2
  • uS5
KeywordsRIBOSOME / translational pausing / XBP1 / UPR / cotranslational targeting / SRP.
Function / homology
Function and homology information


epithelial cell maturation involved in salivary gland development / positive regulation of plasma cell differentiation / positive regulation of vascular wound healing / positive regulation of histone methylation / negative regulation of pathway-restricted SMAD protein phosphorylation / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / endoplasmic reticulum signal peptide binding / positive regulation of phospholipid biosynthetic process / sterol homeostasis ...epithelial cell maturation involved in salivary gland development / positive regulation of plasma cell differentiation / positive regulation of vascular wound healing / positive regulation of histone methylation / negative regulation of pathway-restricted SMAD protein phosphorylation / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / endoplasmic reticulum signal peptide binding / positive regulation of phospholipid biosynthetic process / sterol homeostasis / response to insulin-like growth factor stimulus / positive regulation of immunoglobulin production / granulocyte differentiation / organelle organization / positive regulation of protein acetylation / ATF6-mediated unfolded protein response / signal recognition particle, endoplasmic reticulum targeting / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / negative regulation of translational elongation / positive regulation of lactation / signal recognition particle binding / optic nerve development / negative regulation of myotube differentiation / protein targeting to ER / cellular response to fructose stimulus / cellular triglyceride homeostasis / SRP-dependent cotranslational protein targeting to membrane, translocation / positive regulation of immunoglobulin secretion / exit from mitosis / cellular response to nutrient / endothelial cell proliferation / retinal ganglion cell axon guidance / 7S RNA binding / cellular response to laminar fluid shear stress / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / 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 endothelial cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of MHC class II biosynthetic process / positive regulation of T cell differentiation / positive regulation of TOR signaling / positive regulation of B cell differentiation / positive regulation of hepatocyte proliferation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / exocrine pancreas development / cytosolic ribosome / positive regulation of vascular associated smooth muscle cell migration / muscle organ development / 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 / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to peptide hormone stimulus / TOR signaling / cis-regulatory region sequence-specific DNA binding / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / IRE1-mediated unfolded protein response / ribosomal large subunit biogenesis / cellular response to glucose starvation / positive regulation of fat cell differentiation / phosphatidylinositol 3-kinase signaling / endoplasmic reticulum unfolded protein response / ribosomal small subunit biogenesis / fatty acid homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of autophagy / cellular response to leukemia inhibitory factor / positive regulation of vascular associated smooth muscle cell proliferation / response to endoplasmic reticulum stress / mitotic cell cycle checkpoint / cellular response to interleukin-4 / positive regulation of interleukin-6 production / sequence-specific double-stranded DNA binding / retina development in camera-type eye / regulation of autophagy / cellular response to vascular endothelial growth factor stimulus / polysomal ribosome / cellular response to amino acid stimulus / neutrophil chemotaxis / regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / rough endoplasmic reticulum / cholesterol homeostasis / cellular response to glucose stimulus / protein destabilization / positive regulation of translation / cytoplasmic ribonucleoprotein granule / chromatin DNA binding / fatty acid biosynthetic process / mRNA 5'-UTR binding / GDP binding / cellular response to fluid shear stress / transcription by RNA polymerase II
Ribosomal protein S7p/S5e / Ubiquitin domain / 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 S7p/S5e / Ubiquitin domain / 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 L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin conserved site / Ribosomal protein L11, 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 S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L15e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Signal recognition particle subunit SRP68 / 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 S19, superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Signal recognition particle, SRP54 subunit / 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 L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L27e, conserved site / Ribosomal L28e/Mak16 / KOW / K homology domain superfamily, prokaryotic type / Signal recognition particle, SRP9/SRP14 subunit / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily / Signal recognition particle, SRP9 subunit / Ribosomal protein L34Ae / Ribosomal protein L41 / Ribosomal protein S30 / Signal recognition particle, SRP54 subunit, eukaryotic / Ribosomal protein S12/S23 / Ribosomal protein L7, eukaryotic / Ribosomal protein L24/L26, conserved site / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein S13-like, H2TH / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L6, N-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal / Plectin/S10, N-terminal / Ribosomal protein S25 / Basic-leucine zipper domain / S15/NS1, RNA-binding / TRASH domain / Ribosomal protein L22/L17, conserved site / Ribosomal protein L2, domain 3 / Ribosomal protein L21e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / WD40-repeat-containing domain / Ribosomal protein L10e/L16
40S ribosomal protein S7 / 40S ribosomal protein S13 / Ribosomal protein L26 / 40S ribosomal protein S3a / 60S ribosomal protein L7a / Uncharacterized protein / 60S ribosomal protein L9 / 60S ribosomal protein L12 / 60S ribosomal protein L4 / 60S ribosomal protein L9 ...40S ribosomal protein S7 / 40S ribosomal protein S13 / Ribosomal protein L26 / 40S ribosomal protein S3a / 60S ribosomal protein L7a / Uncharacterized protein / 60S ribosomal protein L9 / 60S ribosomal protein L12 / 60S ribosomal protein L4 / 60S ribosomal protein L9 / Uncharacterized protein / Ribosomal_L18_c domain-containing protein / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 60S ribosomal protein L27a / 60S ribosomal protein L6 / 60S ribosomal protein L23 / Ribosomal_L23eN domain-containing protein / 60S ribosomal protein L41 / Ribosomal protein L10 / 40S ribosomal protein S9 / Signal recognition particle 9 kDa protein / 60S ribosomal protein L17 / Ribosomal protein L24 / 60S ribosomal protein L35a / 40S ribosomal protein S27a / 40S ribosomal protein S12 / 60S ribosomal protein L29 / Uncharacterized protein / 60S ribosomal protein L31 / 60S ribosomal protein L21 / 60S ribosomal protein L35 / WD_REPEATS_REGION domain-containing protein / Ribosomal protein L15 / 40S ribosomal protein S30 / Ribosomal_L18e/L15P domain-containing protein / Signal recognition particle 14 kDa protein / 60S ribosomal protein L17 / Ribosomal protein L37 / 60S ribosomal protein L14 / Signal recognition particle subunit SRP68 / Signal recognition particle 54 kDa protein / X-box-binding protein 1 / Signal recognition particle 19 / 60S ribosomal protein L11 / 60S ribosomal protein L34 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / 60S acidic ribosomal protein P0 / 40S ribosomal protein S15 / 40S ribosomal protein S27 / 60S ribosomal protein L27 / Uncharacterized protein / 40S ribosomal protein S17 / 40S ribosomal protein S25 / 40S ribosomal protein S6 / 60S ribosomal protein L30 / Ribosomal protein S5 / 40S ribosomal protein S15a / 40S ribosomal protein S28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / Uncharacterized protein / 40S ribosomal protein S19 / 60S ribosomal protein L36 / 40S ribosomal protein S3 / 40S ribosomal protein S18 / Uncharacterized protein / S10_plectin domain-containing protein / 40S ribosomal protein S11 / 60S ribosomal protein L8 / Uncharacterized protein / Uncharacterized protein
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (baker's yeast)
Canis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShanmuganathan, V. / Cheng, J. / Braunger, K. / Berninghausen, O. / Beatrix, B. / 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 27, 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
0: eS31
1: X-box-binding protein 1
2: P-tRNA
3: E-tRNA
4: mRNA
5: 28S ribosomal RNA
6: ribosomal protein RACK1
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
9: uS14
A: uL2
AA: 40S ribosomal protein S30
B: uL3
BB: 40S ribosomal protein S7
C: uL4
CC: 40S ribosomal protein S8
DD: Ribosomal protein S9 (Predicted)
D: 60S ribosomal protein L5
EE: Ribosomal protein S11
E: 60S ribosomal protein L6
FF: Ribosomal protein S28
F: uL30
GG: Ribosomal protein S20
G: eL8
H: uL6
HH: 40S ribosomal protein S21
I: Ribosomal protein L10 (Predicted)
II: uS13
JJ: 40S ribosomal protein S27
J: Ribosomal protein L11
K: 18S ribosomal RNA
KK: eS17
L: 60S ribosomal protein L13
LL: 40S ribosomal protein S26
M: Ribosomal protein L14
MM: 40S ribosomal protein S14
N: Ribosomal protein L15
NN: 40S ribosomal protein S24
O: 60S ribosomal protein L13a
OO: ribosomal protein eS25
P: uL22
PP: eS19
Q: eL18
QQ: ribosomal protein uS15
R: 60S ribosomal protein L19
RR: 40S ribosomal protein S12
S: eL20
SS: eS10
T: eL21
TT: Ribosomal protein S15a
UU: Ribosomal protein S16
U: 60S ribosomal protein L22
VV: Ribosomal protein S23
V: eL14
W: Ribosomal protein L24
WW: uS19
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: 60S ribosomal protein L38
l: eL39
m: 60S ribosomal protein L40
n: 60s ribosomal protein l41
o: eL42
p: ribosomal protein eL43
q: uS2
r: eL28
s: 60S acidic ribosomal protein P0
t: uL11
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
AB: Signal recognition particle 54 kDa protein
AF: 7S RNA
AC: Signal recognition particle subunit SRP19
AI: Signal recognition particle subunit SRP68
AD: Signal recognition particle 9 kDa protein
AE: Signal recognition particle 14 kDa protein
AG: Signal sequence (HR2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,366,389396
Polymers3,358,79492
Non-polymers7,594304
Water0
1


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

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Components

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Protein , 33 types, 33 molecules 09ABCFGHIIKKPPPQSSSTVWWXabcdefghoqr...

#1: 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
#10: 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
#11: 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
#13: 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
#15: 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
#22: 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
#24: Protein eL8


Mass: 27351.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#25: 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
#28: 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
#32: 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
#41: 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
#42: 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
#43: 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
#47: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: 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
#49: 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
#54: 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
#56: Protein uS19


Mass: 14246.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#57: 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
#60: 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
#61: Protein eL29


Mass: 13401.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#62: 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
#63: 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
#64: Protein eL32 / CD59


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUN8
#65: 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
#66: 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
#67: 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
#74: 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
#76: Protein uS2


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#77: 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
#78: 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
#79: 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
#81: Protein uS5


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

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Protein/peptide , 3 types, 3 molecules 1lAG

#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
#71: 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
#92: Protein/peptide Signal sequence (HR2)


Mass: 1375.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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RNA chain , 8 types, 8 molecules 234578KAF

#3: RNA chain P-tRNA


Mass: 24108.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#4: 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)
#5: RNA chain mRNA / Messenger RNA


Mass: 1877.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: RNA chain 28S ribosomal RNA /


Mass: 1148420.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#8: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: 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)
#31: 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)
#87: RNA chain 7S RNA


Mass: 66779.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)

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Ribosomal protein ... , 20 types, 20 molecules 6DDEEFFGGIJMNOOQQTTUUVVWYjpwy

#7: 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
#17: Protein Ribosomal protein S9 (Predicted) / Ribosome


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#19: 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
#21: 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
#23: Protein Ribosomal protein S20 / / uS10


Mass: 11395.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein Ribosomal protein L10 (Predicted) / Ribosome


Mass: 24511.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#30: 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
#35: 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
#37: 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
#40: 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
#44: 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
#50: Protein Ribosomal protein S15a / Ribosome


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#51: 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
#53: 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
#55: 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
#58: 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
#69: 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
#75: 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
#82: 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
#84: 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

+
40S ribosomal protein ... , 12 types, 12 molecules AABBCCHHJJLLMMNNRRuxz

#12: 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
#14: 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
#16: 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
#26: Protein 40S ribosomal protein S21 / / eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#29: 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
#34: Protein 40S ribosomal protein S26 / / eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#36: Protein 40S ribosomal protein S14 / / uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein 40S ribosomal protein S24 / / eS24


Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#46: 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
#80: 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
#83: 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
#85: 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

+
60S ribosomal protein ... , 11 types, 11 molecules DELORUZikmn

#18: 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
#20: 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
#33: 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
#39: Protein 60S ribosomal protein L13a / / uL13


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#45: Protein 60S ribosomal protein L19 / / eL19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein 60S ribosomal protein L22 / / eL22


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: 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
#68: 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
#70: Protein 60S ribosomal protein L38 / / eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein 60S ribosomal protein L40 / / eL40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: 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

+
Signal recognition particle ... , 5 types, 5 molecules ABACAIADAE

#86: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 47844.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P61010
#88: Protein Signal recognition particle subunit SRP19 /


Mass: 12159.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: J9PAS6
#89: Protein Signal recognition particle subunit SRP68 / / SRP68 / Signal recognition particle 68 kDa protein


Mass: 23220.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q00004
#90: Protein Signal recognition particle 9 kDa protein / SRP9


Mass: 8705.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: F1Q0Z5
#91: Protein Signal recognition particle 14 kDa protein / SRP14


Mass: 10651.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P16255

+
Non-polymers , 2 types, 304 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Structure of XBP1u-paused ribosome nascent chain complex with SRP.RIBOSOME#1-#920MULTIPLE SOURCES
2Structure of XBP1u-paused nascent chain complex with SRP.COMPLEX#1-#921NATURALribosome
3P- and E- site tRNACOMPLEX#3-#41NATURAL
4X-box-binding protein 1COMPLEX#21RECOMBINANTPausing sequence of XBP1u
5mRNA encoding XBP1uCOMPLEX#51RECOMBINANT
6SRPCOMPLEX#86-#911NATURAL
7Signal sequence (HR2)COMPLEX#921NATURAL
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
56Canis lupus familiaris (dog)9615
67Homo 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

-
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24875 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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