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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
  • eL32
  • eL33
  • eL34
  • eL39
  • eL42
  • eL8
  • eS10
  • eS17
  • eS19
  • eS31
  • mRNA
  • 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


SRP-dependent cotranslational protein targeting to membrane / positive regulation of vascular wound healing / positive regulation of protein acetylation / ATF6-mediated unfolded protein response / endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / sterol homeostasis / IRE1alpha activates chaperones ...SRP-dependent cotranslational protein targeting to membrane / positive regulation of vascular wound healing / positive regulation of protein acetylation / ATF6-mediated unfolded protein response / endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / sterol homeostasis / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of plasma cell differentiation / positive regulation of phospholipid biosynthetic process / negative regulation of myotube differentiation / positive regulation of ERAD pathway / intracellular triglyceride homeostasis / signal recognition particle binding / signal-recognition-particle GTPase / negative regulation of translational elongation / positive regulation of hepatocyte proliferation / cellular response to fructose stimulus / positive regulation of lactation / exocrine pancreas development / cellular response to fluid shear stress / protein targeting to ER / cellular response to laminar fluid shear stress / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / XBP1(S) activates chaperone genes / endothelial cell proliferation / cellular response to nutrient / positive regulation of MHC class II biosynthetic process / SRP-dependent cotranslational protein targeting to membrane / positive regulation of vascular associated smooth muscle cell migration / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of cytokine production involved in inflammatory response / cellular response to peptide hormone stimulus / positive regulation of B cell differentiation / muscle organ development / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / IRE1-mediated unfolded protein response / adipose tissue development / cellular response to interleukin-4 / negative regulation of SMAD protein signal transduction / cellular response to vascular endothelial growth factor stimulus / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ubiquitin-like protein ligase binding / neuron development / positive regulation of endothelial cell apoptotic process / fatty acid homeostasis / positive regulation of fat cell differentiation / vascular endothelial growth factor receptor signaling pathway / positive regulation of TOR signaling / ribonucleoprotein complex binding / response to insulin-like growth factor stimulus / ubiquitin ligase inhibitor activity / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / 90S preribosome / positive regulation of signal transduction by p53 class mediator / cellular response to glucose starvation / positive regulation of vascular associated smooth muscle cell proliferation / cis-regulatory region sequence-specific DNA binding / neutrophil chemotaxis / phagocytic cup / gastrulation / endoplasmic reticulum unfolded protein response / ERAD pathway / cholesterol homeostasis / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / MDM2/MDM4 family protein binding / liver development / positive regulation of autophagy / response to endoplasmic reticulum stress / positive regulation of apoptotic signaling pathway / nuclear estrogen receptor binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid stimulus / regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / regulation of cell growth / small-subunit processome / negative regulation of ERK1 and ERK2 cascade / protein destabilization / chromatin DNA binding / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / positive regulation of protein phosphorylation
Similarity search - Function
: / Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain ...: / Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Signal recognition particle, SRP54 subunit / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / : / Ribosomal protein L6e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L36e signature. / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L35Ae signature. / : / Ribosomal protein L44e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Signal recognition particle 9 kDa protein / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Signal recognition particle 9 kDa protein / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Uncharacterized protein / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL34 / Signal recognition particle 19 kDa protein / Signal recognition particle 14 kDa protein / X-box-binding protein 1 / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (brewer'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.
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
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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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
Water00
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


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 (brewer'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 (brewer's yeast)
#5: RNA chain mRNA


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)


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)


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


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

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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

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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

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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

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Non-polymers , 2 types, 304 molecules

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


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


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

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Details

Has protein modificationY

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Experimental details

-
Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
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 (brewer'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

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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 FIELD
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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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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