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- PDB-6w2t: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I... -

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Basic information

Entry
Database: PDB / ID: 6w2t
TitleStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
Components
  • (Eukaryotic translation initiation factor 3 subunit ...) x 9
  • 18S rRNA
  • CrPV 5'-UTR IRES
  • RACK1
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS29
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / CrPV 5'-UTR IRES / Internal ribosome entry site
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / ribosomal subunit / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / PML body / fibrillar center / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / metallopeptidase activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / cysteine-type deubiquitinase activity / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain ...Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / : / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e 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 S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Eukaryotic translation initiation factor 3 subunit L / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Eukaryotic translation initiation factor 3 subunit L / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S24 / Eukaryotic translation initiation factor 3 subunit K / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit D
Similarity search - Component
Biological speciesCricket paralysis virus
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsNeupane, R. / Pisareva, V. / Rodriguez, C.F. / Pisarev, A. / Fernandez, I.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097014 United States
CitationJournal: Elife / Year: 2020
Title: A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.
Authors: Ritam Neupane / Vera P Pisareva / Carlos F Rodriguez / Andrey V Pisarev / Israel S Fernández /
Abstract: Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have ...Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called nternal ibosomal ntry ites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs.
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • EMDB-21530
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Structure viewerMolecule:
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Assembly

Deposited unit
a: 18S rRNA
B: uS2
C: eS1
D: uS5
F: eS4
H: eS6
I: eS7
J: eS8
K: uS4
M: uS17
O: uS15
P: uS11
W: eS21
X: uS8
Y: uS12
Z: eS24
b: eS26
c: eS27
f: eS30
E: uS3
G: uS7
L: eS10
N: eS12
Q: uS19
R: uS9
S: eS17
T: uS13
U: eS19
V: uS10
i: eS25
d: eS28
e: eS29
g: eS31
h: RACK1
3: Eukaryotic translation initiation factor 3 subunit E
4: Eukaryotic translation initiation factor 3 subunit F
6: Eukaryotic translation initiation factor 3 subunit K
7: Eukaryotic translation initiation factor 3 subunit L
8: Eukaryotic translation initiation factor 3 subunit M
1: Eukaryotic translation initiation factor 3 subunit A
2: Eukaryotic translation initiation factor 3 subunit C
9: Eukaryotic translation initiation factor 3 subunit D
5: Eukaryotic translation initiation factor 3 subunit H
A: CrPV 5'-UTR IRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,904,56646
Polymers1,904,47644
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Sucrose density gradient analysis, microscopy, Low resolution cryo-EM at 200 kV
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules aA

#1: RNA chain 18S rRNA


Mass: 547733.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: RNA chain CrPV 5'-UTR IRES


Mass: 121094.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Positions 211 to 220 are only modeled as a polyuridine stretch.
Source: (gene. exp.) Cricket paralysis virus / Production host: Escherichia coli (E. coli) / References: GenBank: 8895506

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Protein , 33 types, 33 molecules BCDFHIJKMOPWXYZbcfEGLNQRSTUVid...

#2: Protein uS2 / 40S ribosomal protein SA


Mass: 33022.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TWL4
#3: Protein eS1 / 40S ribosomal protein S3a


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#4: Protein uS5 / S5 DRBM domain-containing protein


Mass: 27529.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWM1
#5: Protein eS4 / 40S ribosomal protein S4


Mass: 29596.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#6: Protein eS6 / 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#7: Protein eS7 / 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#8: Protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#9: Protein uS4 / Ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#10: Protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#11: Protein uS15 / Ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#12: Protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#13: Protein eS21


Mass: 9098.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#14: Protein uS8 / Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#15: Protein uS12 / Ribosomal protein S23


Mass: 15784.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#16: Protein eS24 / 40S ribosomal protein S24


Mass: 15548.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#17: Protein eS26 / 40S ribosomal protein S26


Mass: 13015.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#18: Protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#19: Protein eS30 / 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#20: Protein uS3 / Ribosomal protein S3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#21: Protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#22: Protein eS10


Mass: 17156.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#23: Protein eS12 / 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#24: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#25: Protein uS9 / Ribosomal protein S16


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#26: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#27: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#28: Protein eS19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#29: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#30: Protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#31: Protein eS28 / Ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#32: Protein eS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#33: Protein eS31 / Ribosomal protein S27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#34: Protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4

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Eukaryotic translation initiation factor 3 subunit ... , 9 types, 9 molecules 346781295

#35: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / eIF-3 p48


Mass: 54199.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SUC8
#36: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37846.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLC2
#37: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / eIF-3 p25


Mass: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3L2
#38: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 71001.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SED9
#39: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLW8
#40: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta


Mass: 164902.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMZ5
#41: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105706.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U971
#42: Protein Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7


Mass: 64517.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: K7IM66
#43: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3 gamma / eIF3 p40 subunit


Mass: 41083.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1ST95

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Non-polymers , 2 types, 2 molecules

#45: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#46: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)
Type: RIBOSOME / Entity ID: #1-#44 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Grids were blotted for 2.5s and flash cooled in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 8 sec. / Electron dose: 56.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: REFMAC / Version: 5.8.0253 / Classification: refinement
EM software
IDNameCategoryDetails
1Gautomatchparticle selectionno templates, diameter value 260 pixels
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10REFMACmodel refinement
11PHENIXmodel refinement
12RELIONinitial Euler assignment
13RELIONfinal Euler assignment
14RELIONclassification
15RELION3D reconstruction
Image processingDetails: The microscope was equipped with an energy filter with slits aperture of 20eV, installed before the detector.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 915647
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23444 / Num. of class averages: 1 / Symmetry type: POINT
RefinementResolution: 3.36→286.34 Å / Cor.coef. Fo:Fc: 0.839 / SU B: 20.006 / SU ML: 0.318 / ESU R: 0.389
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39389 --
obs0.39389 1450503 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.31 Å20.12 Å2
2---0.16 Å2-0.18 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Total: 109684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.012115993
ELECTRON MICROSCOPYr_bond_other_d0.0020.01884872
ELECTRON MICROSCOPYr_angle_refined_deg1.1561.482166455
ELECTRON MICROSCOPYr_angle_other_deg1.1771.929198852
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.38758207
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.21821.133717
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.9541512828
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.21815613
ELECTRON MICROSCOPYr_chiral_restr0.0590.216849
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0298466
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0225146
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.90913.49532969
ELECTRON MICROSCOPYr_mcbond_other0.90913.49532968
ELECTRON MICROSCOPYr_mcangle_it1.6720.2441129
ELECTRON MICROSCOPYr_mcangle_other1.6720.2441130
ELECTRON MICROSCOPYr_scbond_it0.7212.30783024
ELECTRON MICROSCOPYr_scbond_other0.7212.30783023
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.31118.403125326
ELECTRON MICROSCOPYr_long_range_B_refined3.223134324
ELECTRON MICROSCOPYr_long_range_B_other3.223134325
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.36→3.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.213 107621 -
obs--100 %

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