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- PDB-4d61: Cryo-EM structures of ribosomal 80S complexes with termination fa... -

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Basic information

Entry
Database: PDB / ID: 4d61
TitleCryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state
Components
  • (40S RIBOSOMAL PROTEIN ...) x 31
  • (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR ...) x 2
  • 18S RRNA18S ribosomal RNA
  • CRICKET PARALYSIS VIRUS IRES RNA
  • GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
  • UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
KeywordsRIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS
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 / ribosomal subunit / sequence-specific mRNA binding / 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 / ribosomal subunit / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / translational termination / laminin binding / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / : / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / cytoplasmic translation / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / : / Ribosomal protein S26e signature. / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / S25 ribosomal protein / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S12e signature. / Ribosomal protein S27a / Ribosomal protein S19e, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S5, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27 / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal_S19e / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e / Ribosomal protein S28e signature. / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ubiquitin family / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S19 signature.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / 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 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Plectin/eS10 N-terminal domain-containing protein / Ribosomal protein S14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / 40S ribosomal protein S8 / 40S ribosomal protein S4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
CRICKET PARALYSIS VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsMuhs, M. / Hilal, T. / Mielke, T. / Skabkin, M.A. / Sanbonmatsu, K.Y. / Pestova, T.V. / Spahn, C.M.T.
CitationJournal: Mol Cell / Year: 2015
Title: Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES.
Authors: Margarita Muhs / Tarek Hilal / Thorsten Mielke / Maxim A Skabkin / Karissa Y Sanbonmatsu / Tatyana V Pestova / Christian M T Spahn /
Abstract: The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the ...The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling.
History
DepositionNov 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / em_software ...atom_site / em_software / entity / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -7-STRANDED BARREL THIS IS REPRESENTED BY A -6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Assembly

Deposited unit
1: 18S RRNA
A: 40S RIBOSOMAL PROTEIN SA
B: 40S RIBOSOMAL PROTEIN S3A
C: 40S RIBOSOMAL PROTEIN S2
D: 40S RIBOSOMAL PROTEIN S3
E: 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1
F: 40S RIBOSOMAL PROTEIN S5
G: 40S RIBOSOMAL PROTEIN S6
H: 40S RIBOSOMAL PROTEIN S7
I: 40S RIBOSOMAL PROTEIN S8
J: 40S RIBOSOMAL PROTEIN S9
K: 40S RIBOSOMAL PROTEIN S10
L: 40S RIBOSOMAL PROTEIN S11
M: 40S RIBOSOMAL PROTEIN S12
N: 40S RIBOSOMAL PROTEIN S13
O: 40S RIBOSOMAL PROTEIN S14
P: 40S RIBOSOMAL PROTEIN S15
Q: 40S RIBOSOMAL PROTEIN S16
R: 40S RIBOSOMAL PROTEIN S17
S: 40S RIBOSOMAL PROTEIN S18
T: 40S RIBOSOMAL PROTEIN S19
U: 40S RIBOSOMAL PROTEIN S20
V: 40S RIBOSOMAL PROTEIN S21
W: 40S RIBOSOMAL PROTEIN S15A
X: 40S RIBOSOMAL PROTEIN S23
Y: 40S RIBOSOMAL PROTEIN S24
Z: 40S RIBOSOMAL PROTEIN S25
a: 40S RIBOSOMAL PROTEIN S26
b: 40S RIBOSOMAL PROTEIN S27
c: 40S RIBOSOMAL PROTEIN S28
d: 40S RIBOSOMAL PROTEIN S29
e: 40S RIBOSOMAL PROTEIN S30
f: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
g: GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
h: EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1
i: EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A
j: CRICKET PARALYSIS VIRUS IRES RNA


Theoretical massNumber of molelcules
Total (without water)1,383,13637
Polymers1,383,13637
Non-polymers00
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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RNA chain , 2 types, 2 molecules 1j

#1: RNA chain 18S RRNA / 18S ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#37: RNA chain CRICKET PARALYSIS VIRUS IRES RNA


Mass: 64363.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) CRICKET PARALYSIS VIRUS / References: GenBank: AF218039

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40S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcde

#2: Protein 40S RIBOSOMAL PROTEIN SA / / 40S RIBOSOMAL PROTEIN US2 / 37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR ...40S RIBOSOMAL PROTEIN US2 / 37 KDA LAMININ RECEPTOR PRECURSOR / 37LRP / 37/67 KDA LAMININ RECEPTOR / LRP/LR / 67 KDA LAMININ RECEPTOR / 67LR / COLON CARCINOMA LAMININ-BINDING PROTEIN / LAMININ RECEPTOR 1 / LAMR / LAMININ-BINDING PROTEIN PRECURSOR P40 / LBP/P40 / MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN MGR1-AG / NEM/1CHD4


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TWL4*PLUS
#3: Protein 40S RIBOSOMAL PROTEIN S3A / / 40S RIBOSOMAL PROTEIN ES1 / V-FOS TRANSFORMATION EFFECTOR PROTEIN / FTE-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SS70*PLUS
#4: Protein 40S RIBOSOMAL PROTEIN S2 / / 40S RIBOSOMAL PROTEIN US5 / PROTEIN LLREP3


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SWM1*PLUS
#5: Protein 40S RIBOSOMAL PROTEIN S3 / / 40S RIBOSOMAL PROTEIN US3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TNM3*PLUS
#6: Protein 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 / Ribosome / 40S RIBOSOMAL PROTEIN ES4


Mass: 29512.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TK17*PLUS
#7: Protein 40S RIBOSOMAL PROTEIN S5 / / 40S RIBOSOMAL PROTEIN US7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TFM5*PLUS
#8: Protein 40S RIBOSOMAL PROTEIN S6 / / 40S RIBOSOMAL PROTEIN ES6 / PHOSPHOPROTEIN NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TM55*PLUS
#9: Protein 40S RIBOSOMAL PROTEIN S7 / / 40S RIBOSOMAL PROTEIN ES7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SVB0*PLUS
#10: Protein 40S RIBOSOMAL PROTEIN S8 / / 40S RIBOSOMAL PROTEIN ES8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TJW1*PLUS
#11: Protein 40S RIBOSOMAL PROTEIN S9 / / 40S RIBOSOMAL PROTEIN US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: B7NZS8*PLUS
#12: Protein 40S RIBOSOMAL PROTEIN S10 / / 40S RIBOSOMAL PROTEIN ES10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1T168*PLUS
#13: Protein 40S RIBOSOMAL PROTEIN S11 / / 40S RIBOSOMAL PROTEIN US17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TRM4*PLUS
#14: Protein 40S RIBOSOMAL PROTEIN S12 / / 40S RIBOSOMAL PROTEIN ES12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SFR8*PLUS
#15: Protein 40S RIBOSOMAL PROTEIN S13 / / 40S RIBOSOMAL PROTEIN US15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SP51*PLUS
#16: Protein 40S RIBOSOMAL PROTEIN S14 / / 40S RIBOSOMAL PROTEIN US11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1T1F0*PLUS
#17: Protein 40S RIBOSOMAL PROTEIN S15 / / 40S RIBOSOMAL PROTEIN US19 / RIG PROTEIN


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1U0Q2*PLUS
#18: Protein 40S RIBOSOMAL PROTEIN S16 / / 40S RIBOSOMAL PROTEIN US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SGX4*PLUS
#19: Protein 40S RIBOSOMAL PROTEIN S17 / / 40S RIBOSOMAL PROTEIN ES17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TU13*PLUS
#20: Protein 40S RIBOSOMAL PROTEIN S18 / / 40S RIBOSOMAL PROTEIN US13 / KE-3 / KE3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TPG3*PLUS
#21: Protein 40S RIBOSOMAL PROTEIN S19 / / 40S RIBOSOMAL PROTEIN ES19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TN62*PLUS
#22: Protein 40S RIBOSOMAL PROTEIN S20 / / 40S RIBOSOMAL 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*PLUS
#23: Protein 40S RIBOSOMAL PROTEIN S21 / / 40S RIBOSOMAL PROTEIN ES21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TM82*PLUS
#24: Protein 40S RIBOSOMAL PROTEIN S15A / / 40S RIBOSOMAL PROTEIN US8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TG89*PLUS
#25: Protein 40S RIBOSOMAL PROTEIN S23 / / 40S RIBOSOMAL PROTEIN US12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SZ47*PLUS
#26: Protein 40S RIBOSOMAL PROTEIN S24 / / 40S RIBOSOMAL PROTEIN ES24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TS40*PLUS
#27: Protein 40S RIBOSOMAL PROTEIN S25 / / 40S RIBOSOMAL 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*PLUS
#28: Protein 40S RIBOSOMAL PROTEIN S26 / / 40S RIBOSOMAL PROTEIN ES26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TFE8*PLUS
#29: Protein 40S RIBOSOMAL PROTEIN S27 / / 40S RIBOSOMAL PROTEIN ES27 / METALLOPAN-STIMULIN 1 / MPS-1


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TZ76*PLUS
#30: Protein 40S RIBOSOMAL PROTEIN S28 / / 40S RIBOSOMAL PROTEIN ES28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TIB4*PLUS
#31: Protein 40S RIBOSOMAL PROTEIN S29 / / 40S RIBOSOMAL PROTEIN US14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1U7M4*PLUS
#32: Protein 40S RIBOSOMAL PROTEIN S30 / / 40S RIBOSOMAL PROTEIN ES30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1T8A2*PLUS

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Protein , 2 types, 2 molecules fg

#33: Protein UBIQUITIN-40S RIBOSOMAL PROTEIN S27A / 40S RIBOSOMAL PROTEIN ES31 / UBIQUITIN CARBOXYL EXTENSION PROTEIN 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SK22*PLUS
#34: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 / CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEO TIDE-BINDING PROTEIN SUBUNIT BETA-LIKE ...CELL PROLIFERATION-INDUCING GENE 21 PROTEIN / GUANINE NUCLEO TIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN 12.3 / HUMAN LUNG CA NCER ONCOGENE 7 PROTEIN / HLC-7 / RECEPTOR FOR ACTIVATED C KINASE / R ECEPTOR OF ACTIVATED PROTEIN KINASE C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SJB4*PLUS

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EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR ... , 2 types, 2 molecules hi

#35: Protein EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 / EUKARYOTIC RELEASE FACTOR 1 / ERF1 / PROTEIN CL1 / TB3-1 /


Mass: 49040.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62495
#36: Protein EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A / EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 3A / ERF3A / G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG


Mass: 47888.246 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, UNP RESIDUES 210-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15170

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Details

Sequence detailsAUTHORS HAVE USED HUMAN SEQUENCE FOR MODEL BUILDING, WITH FOLLOWING PDB-GENBANK OR UNIPROT RESIDUE ...AUTHORS HAVE USED HUMAN SEQUENCE FOR MODEL BUILDING, WITH FOLLOWING PDB-GENBANK OR UNIPROT RESIDUE MAPPING: CHAIN: 1 1-1742 GB X03205.1 1 1742 CHAIN: A 1-295 UNP P08865 1 295 CHAIN: B 1- 264 UNP P61247 1 264 CHAIN: C 1-293 UNP P15880 1 293 CHAIN: D 1-243 UNP P23396 1 243 CHAIN: E 1-263 UNP P22090 1 263 CHAIN: F 1-204 UNP P46782 1 204 CHAIN: G 1-249 UNP P62753 1 249 CHAIN: H 1-194 UNP P62081 1 194 CHAIN: I 1-208 UNP P62241 1 208 CHAIN: J 1-194 UNP P46781 1 194 CHAIN: K 1-165 UNP P46783 1 165 CHAIN: L 1-158 UNP P62280 1 158 CHAIN: M 1-132 UNP P25398 1 132 CHAIN: N 1-151 UNP P62277 1 151 CHAIN: O 1-151 UNP P62263 1 151 CHAIN: P 1-145 UNP P62841 1 145 CHAIN: Q 1-146 UNP P62249 1 146 CHAIN: R 1-135 UNP P08708 1 135 CHAIN: S 1-152 UNP P62269 1 152 CHAIN: T 1-145 UNP P39019 1 145 CHAIN: U 1-119 UNP P60866 1 119 CHAIN: V 1- 83 UNP P63220 1 83 CHAIN: W 1-130 UNP P62244 1 130 CHAIN: X 1-143 UNP P62266 1 143 CHAIN: Y 1-133 UNP P62847 1 133 CHAIN: Z 1-125 UNP P62851 1 125 CHAIN: a 1-115 UNP P62854 1 115 CHAIN: b 1-84 UNP P42677 1 84 CHAIN: c 1-69 UNP P62857 1 69 CHAIN: d 1-56 UNP P62273 1 56 CHAIN: e 1-59 UNP P62861 1 59 CHAIN: f 1-156 UNP P62979 1 156 CHAIN: g 1-317 UNP P63244 1 317

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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: CRICKET PARALYSIS VIRUS IRES RNA BOUND TO MAMMALIAN 80S RIBOSOME, ERF1 AND ERF3
Type: RIBOSOME
Details: MICROGRAPHS WERE SELECTED FOR DRIFT AND ASTIGMATISM
Buffer solutionName: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 8.5 MM MGCL2, 0.133 MM GTP, 2.33 MM GMPPNP
pH: 7.5
Details: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 8.5 MM MGCL2, 0.133 MM GTP, 2.33 MM GMPPNP
SpecimenConc.: 1.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 5, 2012
Details: MICROGRAPHS WERE SELECTED FOR DRIFT AND ASTIGMATISM
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 115000 X / Calibrated magnification: 194805 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNum. digital images: 1
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPARX3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUPS
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 9 Å / Num. of particles: 64902 / Nominal pixel size: 1.56 Å / Actual pixel size: 1.56 Å
Magnification calibration: CROSS- -CORRELATION DENSITIES WITH REFERENCE STRUCTURE
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--RIGID BODY, FLEXIBLE FIT
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44968 41416 0 0 86384

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