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- PDB-4d5l: Cryo-EM structures of ribosomal 80S complexes with termination fa... -

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Basic information

Entry
Database: PDB / ID: 4d5l
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 33
  • 18S RRNA 2
KeywordsRIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS
Function / homology
Function and homology information


ribosomal subunit / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / translation regulator activity ...ribosomal subunit / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spindle / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / dendrite / synapse / centrosome / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 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 S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein L7, eukaryotic / Ribosomal protein S7e / Ribosomal protein L30, N-terminal / Ribosomal protein S7e / Ribosomal L30 N-terminal domain / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain
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 / Ubiquitin-ribosomal protein eS31 fusion protein ...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 uS12 / Small ribosomal subunit protein eS10 / 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 eS21 / 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 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / 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
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
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 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software / 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
Revision 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
1: 18S RRNA 2
A: 40S RIBOSOMAL PROTEIN ES26
B: 40S RIBOSOMAL PROTEIN ES27
C: 40S RIBOSOMAL PROTEIN ES28
D: 40S RIBOSOMAL PROTEIN US14
E: 40S RIBOSOMAL PROTEIN ES30
F: 40S RIBOSOMAL PROTEIN ES31
G: 40S RIBOSOMAL PROTEIN RACK1
H: 40S RIBOSOMAL PROTEIN ES7
I: 40S RIBOSOMAL PROTEIN ES8
J: 40S RIBOSOMAL PROTEIN US4
K: 40S RIBOSOMAL PROTEIN ES10
L: 40S RIBOSOMAL PROTEIN US17
M: 40S RIBOSOMAL PROTEIN ES12
N: 40S RIBOSOMAL PROTEIN US15
O: 40S RIBOSOMAL PROTEIN US11
P: 40S RIBOSOMAL PROTEIN US19
Q: 40S RIBOSOMAL PROTEIN US9
R: 40S RIBOSOMAL PROTEIN ES17
S: 40S RIBOSOMAL PROTEIN US13
T: 40S RIBOSOMAL PROTEIN ES19
U: 40S RIBOSOMAL PROTEIN US10
V: 40S RIBOSOMAL PROTEIN ES21
W: 40S RIBOSOMAL PROTEIN US8
X: 40S RIBOSOMAL PROTEIN US12
Y: 40S RIBOSOMAL PROTEIN ES24
Z: 40S RIBOSOMAL PROTEIN ES25
a: 40S RIBOSOMAL PROTEIN US2
b: 40S RIBOSOMAL PROTEIN ES1
c: 40S RIBOSOMAL PROTEIN US5
d: 40S RIBOSOMAL PROTEIN US3
e: 40S RIBOSOMAL PROTEIN ES4
f: 40S RIBOSOMAL PROTEIN US7
g: 40S RIBOSOMAL PROTEIN ES6


Theoretical massNumber of molelcules
Total (without water)1,221,71234
Polymers1,221,71234
Non-polymers00
Water00
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 , 1 types, 1 molecules 1

#1: RNA chain 18S RRNA 2


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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40S RIBOSOMAL PROTEIN ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#2: Protein 40S RIBOSOMAL PROTEIN ES26


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 ES27


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 40S RIBOSOMAL PROTEIN ES28


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TUT9*PLUS
#5: Protein 40S RIBOSOMAL PROTEIN US14


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 ES30


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 ES31


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TFM5
#8: Protein 40S RIBOSOMAL PROTEIN RACK1


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TM55
#9: Protein 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
#10: Protein 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 US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: B7NZS8
#12: Protein 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: G1TPV3, UniProt: G1T168*PLUS
#13: Protein 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
#14: Protein 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
#15: Protein 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
#16: Protein 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: G1U472*PLUS
#17: Protein 40S RIBOSOMAL PROTEIN US19


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 US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SGX4
#19: Protein 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 US13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TPG3
#21: Protein 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 US10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SIZ2
#23: Protein 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 US8


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


Mass: 15713.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1SZ47
#26: Protein 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 ES25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TDB3
#28: Protein 40S RIBOSOMAL PROTEIN US2


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 ES1


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TZ76
#30: Protein 40S RIBOSOMAL PROTEIN US5


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TIB4
#31: Protein 40S RIBOSOMAL PROTEIN US3


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1U7M4
#32: Protein 40S RIBOSOMAL PROTEIN ES4


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1T8A2*PLUS
#33: Protein 40S RIBOSOMAL PROTEIN US7


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 40S RIBOSOMAL PROTEIN ES6


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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Details

Has protein modificationY
Sequence detailsFOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 ...FOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 293 UNP P15880 RS2_HUMAN 1 293 CHAIN D 1 243 UNP P23396 RS3_HUMAN 1 243 CHAIN E 1 263 UNP P22090 RS4Y1_HUMAN 1 263 CHAIN I 1 208 UNP P62241 RS8_HUMAN 1 208 CHAIN O 1 151 UNP P62263 RS14_HUMAN 1 151 CHAIN P 1 145 UNP P62841 RS15_HUMAN 1 145 CHAIN R 1 135 UNP P08708 RS17_HUMAN 1 135 CHAIN T 1 145 UNP P39019 RS19_HUMAN 1 145 CHAIN V 1 83 UNP P63220 RS21_HUMAN 1 83 CHAIN Y 1 133 UNP P62847 RS24_HUMAN 1 133 CHAIN a 1 115 UNP P62854 RS26_HUMAN 1 115 CHAIN e 1 59 UNP P62861 RS30_HUMAN 1 59

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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: RIBOSOMAL 80S TERMINATION COMPLEX WITH CRPV IRES-RNA AND ERF1
Type: RIBOSOME / Details: MICROGRAPH SELECTED FOR ASTIGMATISM AND DRIFT
Buffer solutionName: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 2.5 MM MGCL2, 0.5 MM GTP
pH: 7.5
Details: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 2.5 MM MGCL2, 0.5 MM GTP
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: Apr 17, 2012 / Details: MINIMAL DOSE SYSTEM
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 366

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPARX3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 9 Å / Num. of particles: 109596 / Nominal pixel size: 1.56 Å / Actual pixel size: 1.56 Å
Magnification calibration: CROSS- -CORRELATION DENSITIES WITH REFERENCE STRUCTURE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2810. (DEPOSITION ID: 12907).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 4CXC

4cxc
PDB Unreleased entry


Accession code: 4CXC / Source name: PDB / Type: experimental model
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38161 37159 0 0 75320

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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