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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


positive regulation of plasma cell differentiation / epithelial cell maturation involved in salivary gland development / positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter / positive regulation of histone methylation / sterol homeostasis / positive regulation of vascular wound healing / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / organelle organization / negative regulation of pathway-restricted SMAD protein phosphorylation / endoplasmic reticulum signal peptide binding ...positive regulation of plasma cell differentiation / epithelial cell maturation involved in salivary gland development / positive regulation of phospholipid biosynthetic process by positive regulation of transcription from RNA polymerase II promoter / positive regulation of histone methylation / sterol homeostasis / positive regulation of vascular wound healing / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / organelle organization / negative regulation of pathway-restricted SMAD protein phosphorylation / endoplasmic reticulum signal peptide binding / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / positive regulation of protein acetylation / response to insulin-like growth factor stimulus / positive regulation of immunoglobulin production / ATF6-mediated unfolded protein response / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / signal recognition particle, endoplasmic reticulum targeting / negative regulation of translational elongation / positive regulation of lactation / signal recognition particle binding / protein targeting to ER / go:0001158: / negative regulation of myotube differentiation / cellular response to fructose stimulus / SRP-dependent cotranslational protein targeting to membrane, translocation / cellular triglyceride homeostasis / positive regulation of hepatocyte proliferation / negative regulation of endoplasmic reticulum unfolded protein response / response to TNF agonist / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / regulation of translation involved in cellular response to UV / negative regulation of DNA repair / 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 / oxidized pyrimidine DNA binding / positive regulation of immunoglobulin secretion / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to nutrient / NF-kappaB complex / mammalian oogenesis stage / endothelial cell proliferation / 7S RNA binding / positive regulation of T cell differentiation / cytosolic ribosome / positive regulation of endothelial cell apoptotic process / positive regulation of endodeoxyribonuclease activity / positive regulation of TOR signaling / cellular response to laminar fluid shear stress / protein kinase A binding / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of MHC class II biosynthetic process / activation-induced cell death of T cells / supercoiled DNA binding / positive regulation of B cell differentiation / exocrine pancreas development / ubiquitin-like protein conjugating enzyme binding / positive regulation of vascular associated smooth muscle cell migration / positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress / positive regulation of T cell receptor signaling pathway / muscle organ development / positive regulation of activated T cell proliferation / erythrocyte development / integral component of endoplasmic reticulum membrane / adipose tissue development / oxidized purine DNA binding / positive regulation of interleukin-6 secretion / neuron development / TOR signaling / T cell proliferation involved in immune response / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / spindle assembly / cellular response to peptide hormone stimulus / positive regulation of interleukin-2 production / ribosomal small subunit biogenesis / ribosomal large subunit biogenesis / SRP-dependent cotranslational protein targeting to membrane / positive regulation of JUN kinase activity / gastrulation / IRE1-mediated unfolded protein response / cellular response to glucose starvation / positive regulation of microtubule polymerization / cellular response to interleukin-4 / phosphatidylinositol 3-kinase signaling / positive regulation of fat cell differentiation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of autophagy / polysome / endoplasmic reticulum unfolded protein response / fatty acid homeostasis / polysomal ribosome / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / mitotic cell cycle checkpoint / Hsp70 protein binding / response to endoplasmic reticulum stress / positive regulation of vascular smooth muscle cell proliferation / cellular response to leukemia inhibitory factor / endodeoxyribonuclease activity / regulation of autophagy
Ribosomal protein S6e / Ribosomal protein S3, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site ...Ribosomal protein S6e / Ribosomal protein S3, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, 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 S19e, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, 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 L13e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S9, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L30e, conserved site / 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 L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Signal recognition particle, SRP54 subunit / Ribosomal protein S7, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / 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 L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S4, conserved site / Ribosomal protein L30, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S25 / 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 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 / Basic-leucine zipper domain / Ribosomal protein S12/S23 / Signal recognition particle, SRP54 subunit, M-domain / K Homology domain, type 2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / AAA+ ATPase domain / Signal recognition particle, SRP14 subunit / RNA-binding S4 domain / Ribosomal protein S27a / Ribosomal protein L14e domain / Signal recognition particle, SRP19 subunit / Ribosomal protein L29e / Ribosomal protein L28e / Ribosomal protein L6, conserved site-2 / Ribosomal protein S19/S15 / Ribosomal protein L7, eukaryotic / Signal recognition particle, SRP54 subunit, eukaryotic / WD40-repeat-containing domain / Ribosomal protein L30, N-terminal / Ribosomal protein L10e/L16
Signal recognition particle subunit SRP68 / Ribosomal protein L37 / 40S ribosomal protein S7 / Ribosomal_L18e/L15P domain-containing protein / Ribosomal_S13_N domain-containing protein / KOW domain-containing protein / 40S ribosomal protein S3a / Ribosomal_L7Ae domain-containing protein / Uncharacterized protein / Ribos_L4_asso_C domain-containing protein ...Signal recognition particle subunit SRP68 / Ribosomal protein L37 / 40S ribosomal protein S7 / Ribosomal_L18e/L15P domain-containing protein / Ribosomal_S13_N domain-containing protein / KOW domain-containing protein / 40S ribosomal protein S3a / Ribosomal_L7Ae domain-containing protein / Uncharacterized protein / Ribos_L4_asso_C domain-containing protein / 60S ribosomal protein L6 / VP5 / 60S ribosomal protein L5 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L15 / Uncharacterized protein / Ubiquitin-like domain-containing protein / 40S ribosomal protein S30 / Ribosomal_L23eN domain-containing protein / 60s ribosomal protein l41 / Ribosomal protein L10 (Predicted) / Ribosomal protein S9 (Predicted) / Signal recognition particle 9 kDa protein / Uncharacterized protein / TRASH domain-containing protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S12 / Uncharacterized protein / Uncharacterized protein / Outer capsid protein VP2 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S25 / Ribosomal_L14e domain-containing protein / 60S acidic ribosomal protein P0 / Uncharacterized protein / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein / 60S ribosomal protein L27 / 40S ribosomal protein S27 / Uncharacterized protein / Ribosomal_L28e domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Signal recognition particle 19 / Signal recognition particle 14 kDa protein / X-box-binding protein 1 / Signal recognition particle 54 kDa protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_L7Ae domain-containing protein / Uncharacterized protein / Ribosomal_S7 domain-containing protein / Uncharacterized protein / Ribosomal protein S28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / 40S ribosomal protein S6 / KH type-2 domain-containing protein / 60S ribosomal protein L36 / Uncharacterized protein / 60S ribosomal protein L13 / S10_plectin domain-containing protein / Ribosomal_S17_N domain-containing protein / Ribosomal_L2_C domain-containing protein / 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 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/peptide , 36 types, 36 molecules 019ABCFGHIIKKPPPQSSSTVWWXabcdefghlo...

#1: Protein/peptide eS31


Mass: 7986.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#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
#10: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide uL6


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33
#28: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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/peptide uL29


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#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
#74: Protein/peptide 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/peptide uS2


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


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


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


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

-
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.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, 85, 86, 87, 88, 89, 90, 91, 920MULTIPLE SOURCES
2Structure of XBP1u-paused nascent chain complex with SRP.COMPLEX1, 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, 85, 86, 87, 88, 89, 90, 91, 921NATURALribosome
3P- and E- site tRNACOMPLEX3, 41NATURAL
4X-box-binding protein 1COMPLEX21RECOMBINANTPausing sequence of XBP1u
5mRNA encoding XBP1uCOMPLEX51RECOMBINANT
6SRPCOMPLEX86, 87, 88, 89, 90, 911NATURAL
7Signal sequence (HR2)COMPLEX921NATURAL
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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