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- PDB-6r7q: Structure of XBP1u-paused ribosome nascent chain complex with Sec61. -

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Entry
Database: PDB / ID: 6r7q
TitleStructure of XBP1u-paused ribosome nascent chain complex with Sec61.
Components
  • (40S ribosomal protein ...) x 8
  • (60S ribosomal protein ...) x 6
  • (Protein transport protein Sec61 subunit ...Protein targeting) x 3
  • (Ribosomal protein ...) x 19
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • E-tRNA
  • P-tRNA
  • X-box-binding protein 1
  • eL14
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL42
  • eL8
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS26
  • eS31
  • messenger RNA
  • uL11
  • uL13
  • uL15
  • uL2
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS13
  • uS14
  • uS19
  • uS2
  • uS5
KeywordsRIBOSOME / translational pausing / XBP1 / UPR
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / XBP1(S) activates chaperone genes / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / 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 protein acetylation ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / XBP1(S) activates chaperone genes / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / 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 protein acetylation / organelle organization / positive regulation of vascular wound healing / negative regulation of pathway-restricted SMAD protein phosphorylation / positive regulation of ER-associated ubiquitin-dependent protein catabolic process / pronephric nephron development / membrane docking / endoplasmic reticulum Sec complex / Sec61 translocon complex / response to insulin-like growth factor stimulus / positive regulation of immunoglobulin production / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / ATF6-mediated unfolded protein response / positive regulation of lactation / exocrine pancreas development / protein targeting to ER / enhancer sequence-specific DNA binding / positive regulation of MHC class II biosynthetic process / negative regulation of myotube differentiation / posttranslational protein targeting to membrane, translocation / cellular response to fructose stimulus / posttranslational protein targeting to endoplasmic reticulum membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / ARF guanyl-nucleotide exchange factor activity / cellular triglyceride homeostasis / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / negative regulation of protein neddylation / positive regulation of hepatocyte proliferation / signal sequence binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / oxidized pyrimidine DNA binding / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of base-excision repair / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of immunoglobulin secretion / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mammalian oogenesis stage / NF-kappaB complex / retrograde protein transport, ER to cytosol / cellular response to nutrient / ubiquitin ligase inhibitor activity / negative regulation of RNA splicing / endothelial cell proliferation / positive regulation of TOR signaling / positive regulation of T cell differentiation / positive regulation of endothelial cell apoptotic process / positive regulation of endodeoxyribonuclease activity / activation-induced cell death of T cells / positive regulation of endoplasmic reticulum unfolded protein response / protein kinase A binding / cellular response to laminar fluid shear stress / supercoiled DNA binding / cytosolic ribosome / positive regulation of B cell differentiation / ubiquitin-like protein conjugating enzyme binding / positive regulation of vascular associated smooth muscle cell migration / epidermal growth factor binding / integral component of endoplasmic reticulum membrane / oxidized purine DNA binding / 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 / erythrocyte development / positive regulation of activated T cell proliferation / positive regulation of interleukin-6 secretion / adipose tissue development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein transmembrane transporter activity / T cell proliferation involved in immune response / cellular response to interleukin-4 / spindle assembly / ribosomal small subunit biogenesis / positive regulation of interleukin-2 production / neuron development / cellular response to peptide hormone stimulus / ribosomal large subunit biogenesis / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of JUN kinase activity / gastrulation / protein targeting / IRE1-mediated unfolded protein response / cellular response to glucose starvation / positive regulation of microtubule polymerization / phosphatidylinositol 3-kinase signaling
Ribosomal protein L13e, conserved site / Translocon Sec61/SecY, plug domain / 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 L13e, conserved site / Translocon Sec61/SecY, plug domain / 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 / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L11, C-terminal / 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 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 S7, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L29, conserved site / Protein translocase SecE domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L24e, conserved site / SecY domain superfamily / Ribosomal protein L11, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, 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 L10e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / 50S ribosomal protein L30e-like / Plectin/S10, N-terminal / Ribosomal protein L7, eukaryotic / Ribosomal protein L24/L26, conserved site / KOW / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein 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 / Ribosomal protein S25 / Ribosomal protein S30 / Basic-leucine zipper domain / K Homology domain, type 2 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / RNA-binding S4 domain / Ribosomal protein S27a / Ribosomal protein L14e domain / Ribosomal protein L37ae / Ribosomal protein L29e / Ribosomal protein L28e / Ribosomal protein L6, conserved site-2 / Ribosomal protein S19/S15 / SecY/SEC61-alpha family / Ribosomal protein L2 / Ribosomal protein L4/L1e / Ribosomal protein S12/S23 / Ribosomal protein L41
60S ribosomal protein L13 / 60S ribosomal protein L36 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S8 / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S6 ...60S ribosomal protein L13 / 60S ribosomal protein L36 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S8 / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S6 / Uncharacterized protein / 40S ribosomal protein S4 / Uncharacterized protein / Ribosomal protein S28 / Uncharacterized protein / 40S ribosomal protein S27 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Protein transport protein Sec61 subunit beta / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit alpha isoform 1 / X-box-binding protein 1 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 60S acidic ribosomal protein P0 / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L27 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 60S ribosomal protein L6 / 60s ribosomal protein l41 / Ribosomal protein L10 (Predicted) / Ribosomal protein S9 (Predicted) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S12 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S30 / Uncharacterized protein / Ribosomal protein L15 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S7 / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S3a / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L37
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Saccharomyces cerevisiae (baker's yeast)
Canis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsShanmuganathan, V. / Cheng, J. / Braunger, K. / Berninghausen, O. / Beatrix, B. / Beckmann, R.
Funding supportGermany , 1件
OrganizationGrant numberCountry
German Research FoundationGermany
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
DateDeposition: Mar 29, 2019 / Release: Jul 10, 2019
RevisionDateData content typeProviderType
1.0Jul 10, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
AA: 40S ribosomal protein S30
BB: 40S ribosomal protein S7
CC: 40S ribosomal protein S8
DD: Ribosomal protein S9 (Predicted)
EE: Ribosomal protein S11
FF: Ribosomal protein S28
GG: uS10
HH: eS21
II: uS13
JJ: 40S ribosomal protein S27
KK: eS17
LL: eS26
MM: uS11
0: eS31
1: X-box-binding protein 1
2: P-tRNA
3: E-tRNA
4: messenger RNA
5: 28S ribosomal RNA
6: ribosomal protein RACK1
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
9: uS14
NN: eS24
OO: ribosomal protein eS25
PP: eS19
QQ: ribosomal protein uS15
RR: 40S ribosomal protein S12
A: uL2
B: uL3
C: uL4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: uL30
G: eL8
H: uL6
I: Ribosomal protein L10 (Predicted)
J: Ribosomal protein L11
K: 18S ribosomal RNA
L: 60S ribosomal protein L13
M: Ribosomal protein L14
N: Ribosomal protein L15
O: uL13
P: uL22
Q: eL18
R: eL19
S: eL20
T: eL21
U: eL22
V: eL14
W: Ribosomal protein L24
X: uL23
Y: Ribosomal protein L26
Z: 60S ribosomal protein L27
SS: eS10
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: eL38
l: eL39
m: eL40
n: 60s ribosomal protein l41
o: eL42
p: ribosomal protein eL43
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
TT: Ribosomal protein S15a
UU: Ribosomal protein S16
VV: Ribosomal protein S23
WW: uS19
XX: Protein transport protein Sec61 subunit alpha isoform 1
YY: Protein transport protein Sec61 subunit gamma
ZZ: Protein transport protein Sec61 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,256,771393
Polymers3,249,11188
Non-polymers7,660305
Water0
1


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

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Components

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40S ribosomal protein ... , 8 types, 8 molecules AABBCCJJRRuxz

#1: 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
#2: 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
#3: 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
#10: 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
#28: 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
#76: 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
#79: 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
#81: 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

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Ribosomal protein ... , 19 types, 19 molecules DDEEFF6OOQQIJMNWYjpwyTTUUVV

#4: 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
#5: 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
#6: 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
#20: 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
#25: 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
#27: 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
#37: 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
#38: 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
#41: 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
#42: 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
#51: 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
#53: 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
#65: 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
#71: 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
#78: 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
#80: 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
#82: 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
#83: 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
#84: 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

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Protein/peptide , 45 types, 45 molecules GGHHIIKKLLMM019NNPPABCFGHOPQRSTUVXSSabc...

#7: Protein/peptide uS10


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


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: 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
#11: 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
#12: Protein/peptide eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#13: Protein/peptide uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: 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
#15: 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
#23: 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
#24: Protein/peptide eS24


Mass: 14432.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: 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
#29: 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
#30: 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
#31: 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
#34: 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
#35: 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
#36: 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
#43: Protein/peptide uL13


Mass: 23144.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: 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
#45: 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
#46: Protein/peptide eL19


Mass: 21613.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#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 eL21 /


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


Mass: 11495.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: 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
#52: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: 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
#66: Protein/peptide eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#67: 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
#68: Protein/peptide eL40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#70: 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
#72: Protein/peptide uS2


Mass: 24361.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#73: 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
#74: 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
#75: 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
#77: Protein/peptide uS5


Mass: 24441.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#85: 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

+
RNA chain , 7 types, 7 molecules 234578K

#16: 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)
#17: 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)
#18: RNA chain messenger RNA /


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


Mass: 1148460.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#21: 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)
#22: 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)
#39: 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)

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

#32: 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
#33: 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
#40: 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
#54: 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
#64: 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
#69: 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

+
Protein transport protein Sec61 subunit ... , 3 types, 3 molecules XXYYZZ

#86: Protein/peptide Protein transport protein Sec61 subunit alpha isoform 1 / Protein targeting / Sec61 alpha-1


Mass: 50728.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P38377
#87: Protein/peptide Protein transport protein Sec61 subunit gamma / Protein targeting


Mass: 7019.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P60058
#88: Protein/peptide Protein transport protein Sec61 subunit beta / Protein targeting


Mass: 3265.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P60467

+
Non-polymers , 2 types, 305 molecules

#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Zinc
#90: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 299 / Source method: obtained synthetically / Formula: Mg / Magnesium

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of XBP1u-paused ribosome nascent chain complex with Sec61.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, 880MULTIPLE SOURCES
2RibosomeCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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, 851NATURAL
3X-box-binding protein 1ORGANELLE OR CELLULAR COMPONENT151RECOMBINANT
4tRNATransfer RNAORGANELLE OR CELLULAR COMPONENT16, 171NATURAL
5Sec61ORGANELLE OR CELLULAR COMPONENT86, 87, 881NATURAL
6mRNAMessenger RNAORGANELLE OR CELLULAR COMPONENT181RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Homo sapiens (human)9606
34Saccharomyces cerevisiae (baker's yeast)4932
45Canis lupus familiaris (dog)9615
56Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Oryctolagus cuniculus (rabbit)9986
26synthetic 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

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12749 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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