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- PDB-3jah: Structure of a mammalian ribosomal termination complex with ABCE1... -

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Entry
Database: PDB / ID: 3jah
TitleStructure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon
Components
  • (uL14) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • ABCE1
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL6
  • eL8
  • eRF1Eukaryotic translation termination factor 1
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • mRNAMessenger RNA
  • peptide
  • tRNA(Lys)
  • tRNA(Val)
  • uL10
  • uL11
  • uL13
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / termination / eRF1 / ABCE1
Function / homology
Function and homology information


translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / ribosomal subunit / aminoacyl-tRNA hydrolase activity ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / protein methylation / translation release factor activity, codon specific / sequence-specific mRNA binding / ribosomal subunit / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / negative regulation of DNA repair / oxidized purine DNA binding / G1 to G0 transition / supercoiled DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / NF-kappaB complex / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / Protein hydroxylation / protein kinase A binding / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / cellular response to actinomycin D / translational termination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / rough endoplasmic reticulum / gastrulation / spindle assembly / signaling adaptor activity / MDM2/MDM4 family protein binding / : / rescue of stalled ribosome / negative regulation of smoothened signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of peptidyl-serine phosphorylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / positive regulation of intrinsic apoptotic signaling pathway / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of microtubule polymerization / ribosomal large subunit biogenesis / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / cellular response to leukemia inhibitory factor / small-subunit processome / SH2 domain binding / cyclin binding / DNA endonuclease activity / positive regulation of translation / protein kinase C binding / : / cellular response to glucose stimulus / positive regulation of protein-containing complex assembly / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / base-excision repair / cellular response to gamma radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / transcription coactivator binding / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / mitotic spindle / small ribosomal subunit rRNA binding / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / cellular response to growth factor stimulus / ruffle membrane / rRNA processing / positive regulation of canonical Wnt signaling pathway / cytosolic small ribosomal subunit
Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / 4Fe-4S binding domain / 60S acidic ribosomal protein P0 / Ubiquitin-like protein FUBI / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / TRASH domain / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal L29e protein family / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L44e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein S7e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Eukaryotic Ribosomal Protein L27, KOW domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L41 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL23 N-terminal domain-containing protein ...ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L41 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL23 N-terminal domain-containing protein / Large ribosomal subunit protein eL33 / 40S ribosomal protein S12 / ATP binding cassette subfamily E member 1 / 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 uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / 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 / 60S ribosomal protein L7a / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L37a / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL42 / Ribosomal protein L15 / Ribosomal protein S14 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like domain-containing protein / 40S ribosomal protein S25 / Ribosomal protein S5 / 60S ribosomal protein L6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / Large ribosomal subunit protein uL3 / TRASH domain-containing protein / 40S ribosomal protein S6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS3 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / 60S ribosomal protein L36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Ribosomal protein L32 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L27 / 40S ribosomal protein S27 / 40S ribosomal protein S15 / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Uncharacterized protein / Eukaryotic peptide chain release factor subunit 1 / Large ribosomal subunit protein eL14 / Ribosomal protein L37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsBrown, A. / Shao, S. / Murray, J. / Hegde, R.S. / Ramakrishnan, V.
CitationJournal: Nature / Year: 2015
Title: Structural basis for stop codon recognition in eukaryotes.
Authors: Alan Brown / Sichen Shao / Jason Murray / Ramanujan S Hegde / V Ramakrishnan /
Abstract: Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal ...Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: uL2
B: uL3
C: uL4
D: uL18
E: eL6
F: uL30
G: eL8
H: uL6
I: uL16
J: uL5
L: eL13
M: eL14
N: eL15
O: uL13
P: uL22
Q: uL14
R: eL19
S: eL20
T: eL21
U: eL22
V: uL14
W: eL24
X: uL23
Y: uL24
Z: eL27
a: uL15
b: eL29
c: eL30
d: eL31
e: eL32
f: eL33
g: eL34
h: uL29
i: eL36
j: eL37
k: eL38
l: eL39
m: eL40
n: eL41
o: eL42
p: eL43
r: eL28
s: uL10
t: uL11
1: peptide
2: tRNA(Val)
3: tRNA(Lys)
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
9: 18S ribosomal RNA
AA: uS2
BB: eS1
CC: uS5
DD: uS3
EE: eS4
FF: uS7
GG: eS6
HH: eS7
II: eS8
JJ: uS4
KK: eS10
LL: uS17
MM: eS12
NN: uS15
OO: uS11
PP: uS19
QQ: uS9
RR: eS17
SS: uS13
TT: eS19
UU: uS10
VV: eS21
WW: uS8
XX: uS12
YY: eS24
ZZ: eS25
aa: eS26
bb: eS27
cc: eS28
dd: uS14
ee: eS30
ff: eS31
gg: RACK1
hh: mRNA
ii: eRF1
jj: ABCE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,344,057294
Polymers3,337,23787
Non-polymers6,820207
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 77 types, 77 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#1: Protein uL2


Mass: 26570.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TT27
#2: Protein uL3


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


Mass: 41115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SVW5
#4: Protein uL18


Mass: 34006.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SYJ6
#5: Protein eL6


Mass: 28529.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TG04
#6: Protein uL30


Mass: 26662.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#7: Protein eL8


Mass: 27480.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1STW0
#8: Protein uL6


Mass: 21627.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#9: Protein uL16


Mass: 24511.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: B7NZQ2
#10: Protein uL5


Mass: 19270.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TUB8
#11: Protein eL13


Mass: 24216.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#12: Protein eL14


Mass: 16217.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: U3KNW6
#13: Protein eL15 / List of Subaru engines


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T0C1
#14: Protein uL13


Mass: 23248.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#15: Protein uL22


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#16: Protein uL14


Mass: 21457.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#17: Protein eL19


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


Mass: 20696.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#19: Protein eL21 /


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


Mass: 11481.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#21: Protein uL14


Mass: 13972.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T6D1
#22: Protein eL24


Mass: 7512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TLD5
#23: Protein uL23


Mass: 13856.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SE76
#24: Protein uL24


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SQH0
#25: Protein eL27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TXF6
#26: Protein uL15


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


Mass: 8706.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SGR6, UniProt: G1TN82*PLUS
#28: Protein eL30


Mass: 10496.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#29: Protein eL31


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


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


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


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


Mass: 14435.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SIT5
#34: Protein eL36


Mass: 11888.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TTQ5
#35: Protein eL37


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: U3KPD5
#36: Protein eL38


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


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


Mass: 12198.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T040
#41: Protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SY53
#42: Protein eL28


Mass: 14319.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1U7L1
#43: Protein uL10


Mass: 21747.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1U6N2
#44: Protein uL11


Mass: 17689.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SMR7
#52: Protein uS2


Mass: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#53: Protein eS1


Mass: 24759.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SS70
#54: Protein uS5


Mass: 24050.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TUT9
#55: Protein uS3


Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TNM3
#56: Protein eS4


Mass: 29497.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TK17
#57: Protein uS7


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TFM5
#58: Protein eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TM55
#59: Protein eS7


Mass: 21603.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SVB0
#60: Protein eS8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TJW1
#61: Protein uS4


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: B7NZS8
#62: Protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TPV3
#63: Protein uS17


Mass: 17657.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TRM4
#64: Protein eS12


Mass: 13766.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SFR8
#65: Protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SP51
#66: Protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T1F0
#67: Protein uS19


Mass: 15151.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1U0Q2
#68: Protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SGX4
#69: Protein eS17


Mass: 14969.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TU13
#70: Protein uS13


Mass: 16170.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SZI5
#71: Protein eS19


Mass: 15683.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TN62
#72: Protein uS10


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SIZ2
#73: Protein eS21


Mass: 9115.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TM82
#74: Protein uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TG89
#75: Protein uS12


Mass: 15626.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SZ47
#76: Protein eS24


Mass: 14604.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T3D8
#77: Protein eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TDB3
#78: Protein eS26


Mass: 11184.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#79: Protein eS27


Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TZ76
#80: Protein eS28


Mass: 6819.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1TIB4
#81: Protein uS14


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1U7M4
#82: Protein eS30


Mass: 6512.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1T8A2
#83: Protein eS31


Mass: 8001.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SK22
#84: Protein RACK1 / Receptor for activated C kinase 1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SJB4
#86: Protein eRF1 / Eukaryotic translation termination factor 1


Mass: 46650.305 Da / Num. of mol.: 1 / Mutation: G183A, G184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: eRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62495
#87: Protein ABCE1 /


Mass: 66857.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SG72

-
Protein/peptide , 3 types, 3 molecules ln1

#37: Protein/peptide eL39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: G1SYU7
#39: Protein/peptide eL41


Mass: 3213.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate / References: UniProt: A0A087WNH4
#45: Protein/peptide peptide /


Mass: 1788.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate

-
RNA chain , 7 types, 7 molecules 235789hh

#46: RNA chain tRNA(Val)


Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#47: RNA chain tRNA(Lys)


Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#48: RNA chain 28S ribosomal RNA /


Mass: 1186579.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#49: 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) / Cell: reticulocyte lysate
#50: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#51: RNA chain 18S ribosomal RNA /


Mass: 554751.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate
#85: RNA chain mRNA / Messenger RNA


Mass: 3837.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: reticulocyte lysate

-
Non-polymers , 4 types, 207 molecules

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


Mass: 24.305 Da / Num. of mol.: 195 / Source method: obtained synthetically / Formula: Mg
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#90: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#91: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-IDSynonym
180S ribosome-nascent chain complex containing the UAG stop codon bound to eRF1(AAQ) and ABCE1RIBOSOME0
280S ribosomeEukaryotic ribosomeRIBOSOME1
3eukaryotic release factor 1, G183A, G184A mutant1eRF1(AAQ)
4ATP binding cassette E11ABCE1, Rli1
5messenger RNA1
6in vitro translated substrate1
7tRNATransfer RNA1
Buffer solutionName: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT
pH: 7.4
Details: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh Cu grid with thin continuous carbon support, glow discharged
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %
Details: After 30 second wait time, blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Method: After 30 second wait time, blot for 3 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 25, 2015 / Details: Automated data acquisition using EPU (FEI)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1601
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Cootmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20515 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITRECIPROCALREFINEMENT PROTOCOL--flexible
2FLEXIBLE FITRECIPROCALREFINEMENT PROTOCOL--flexible DETAILS--Sequence was modified in Coot to agree with rabbit sequence.
3FLEXIBLE FITRECIPROCALREFINEMENT PROTOCOL--flexible DETAILS--Sequence was modified in Coot to agree with the most prevalent tRNA sequence for each particular codon.
Atomic model building
IDPDB-ID 3D fitting-ID
13J921
23J7P1
31DT91
43BK72
54V513
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms101677 124504 273 0 226454

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