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- PDB-4d67: Cryo-EM structures of ribosomal 80S complexes with termination fa... -

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Basic information

Entry
Database: PDB / ID: 4d67
TitleCryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state
Components
  • (60S RIBOSOMAL PROTEIN ...) x 42
  • 28S RRNA
  • 5.8S RRNA
  • 5S RRNA
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
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 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
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 2.1Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.2Oct 16, 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 "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VB" 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. THE SHEETS PRESENTED AS "fA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: 60S RIBOSOMAL PROTEIN L8
B: 60S RIBOSOMAL PROTEIN L3
C: 60S RIBOSOMAL PROTEIN L4
D: 60S RIBOSOMAL PROTEIN L5
E: 60S RIBOSOMAL PROTEIN L6
F: 60S RIBOSOMAL PROTEIN L7
G: 60S RIBOSOMAL PROTEIN L7A
H: 60S RIBOSOMAL PROTEIN L9
I: 60S RIBOSOMAL PROTEIN L10
J: 60S RIBOSOMAL PROTEIN L11
L: 60S RIBOSOMAL PROTEIN L13
M: 60S RIBOSOMAL PROTEIN L14
N: 60S RIBOSOMAL PROTEIN L15
O: 60S RIBOSOMAL PROTEIN L13A
P: 60S RIBOSOMAL PROTEIN L17
Q: 60S RIBOSOMAL PROTEIN L18
R: 60S RIBOSOMAL PROTEIN L19
S: 60S RIBOSOMAL PROTEIN L18A
T: 60S RIBOSOMAL PROTEIN L21
U: 60S RIBOSOMAL PROTEIN L22
V: 60S RIBOSOMAL PROTEIN L23
W: 60S RIBOSOMAL PROTEIN L24
X: 60S RIBOSOMAL PROTEIN L23A
Y: 60S RIBOSOMAL PROTEIN L26
Z: 60S RIBOSOMAL PROTEIN L27
a: 60S RIBOSOMAL PROTEIN L27A
b: 60S RIBOSOMAL PROTEIN L29
c: 60S RIBOSOMAL PROTEIN L30
d: 60S RIBOSOMAL PROTEIN L31
e: 60S RIBOSOMAL PROTEIN L32
f: 60S RIBOSOMAL PROTEIN L35A
g: 60S RIBOSOMAL PROTEIN L34
h: 60S RIBOSOMAL PROTEIN L35
i: 60S RIBOSOMAL PROTEIN L36
j: 60S RIBOSOMAL PROTEIN L37
k: 60S RIBOSOMAL PROTEIN L38
l: 60S RIBOSOMAL PROTEIN L39
m: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
n: 60S RIBOSOMAL PROTEIN L41
o: 60S RIBOSOMAL PROTEIN L36A
p: 60S RIBOSOMAL PROTEIN L37A
t: 60S RIBOSOMAL PROTEIN L28
u: 60S RIBOSOMAL PROTEIN L10A
2: 28S RRNA
3: 5.8S RRNA
4: 5S RRNA


Theoretical massNumber of molelcules
Total (without water)2,579,34146
Polymers2,579,34146
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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60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#1: Protein 60S RIBOSOMAL PROTEIN L8 / 60S RIBOSOMAL PROTEIN UL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#2: Protein 60S RIBOSOMAL PROTEIN L3 / 60S RIBOSOMAL PROTEIN UL3 / HIV-1 TAR RNA-BINDING PROTEIN B / TARBP-B


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#3: Protein 60S RIBOSOMAL PROTEIN L4 / 60S RIBOSOMAL PROTEIN UL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#4: Protein 60S RIBOSOMAL PROTEIN L5 / 60S RIBOSOMAL PROTEIN UL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#5: Protein 60S RIBOSOMAL PROTEIN L6 / 60S RIBOSOMAL PROTEIN EL6 / NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEM ENT- ...60S RIBOSOMAL PROTEIN EL6 / NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEM ENT-BINDING PROTEIN 107 / TAXREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#6: Protein 60S RIBOSOMAL PROTEIN L7 / 60S RIBOSOMAL PROTEIN UL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#7: Protein 60S RIBOSOMAL PROTEIN L7A / 60S RIBOSOMAL PROTEIN EL8 / PLA-X POLYPEPTIDE / SURFEIT LOCUS PROTEIN 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#8: Protein 60S RIBOSOMAL PROTEIN L9 / 60S RIBOSOMAL PROTEIN UL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#9: Protein 60S RIBOSOMAL PROTEIN L10 / 60S RIBOSOMAL PROTEIN UL16 / LAMININ RECEPTOR HOMOLOG / PROTEIN QM / TUMOR SUPPRESSOR QM


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#10: Protein 60S RIBOSOMAL PROTEIN L11 / 60S RIBOSOMAL PROTEIN UL5 / CLL-ASSOCIATED ANTIGEN KW-12


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#11: Protein 60S RIBOSOMAL PROTEIN L13 / 60S RIBOSOMAL PROTEIN EL13 / BREAST BASIC CONSERVED PROTEIN 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#12: Protein 60S RIBOSOMAL PROTEIN L14 / 60S RIBOSOMAL PROTEIN EL14 / CAG-ISL 7


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#13: Protein 60S RIBOSOMAL PROTEIN L15 / 60S RIBOSOMAL PROTEIN EL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#14: Protein 60S RIBOSOMAL PROTEIN L13A / 60S RIBOSOMAL PROTEIN UL13 / 23 KDA HIGHLY BASIC PROTEIN


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#15: Protein 60S RIBOSOMAL PROTEIN L17 / 60S RIBOSOMAL PROTEIN UL22 / 60S RIBOSOMAL PROTEIN L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#16: Protein 60S RIBOSOMAL PROTEIN L18 / 60S RIBOSOMAL PROTEIN EL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#17: Protein 60S RIBOSOMAL PROTEIN L19 / 60S RIBOSOMAL PROTEIN EL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#18: Protein 60S RIBOSOMAL PROTEIN L18A / 60S RIBOSOMAL PROTEIN EL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#19: Protein 60S RIBOSOMAL PROTEIN L21 / 60S RIBOSOMAL PROTEIN EL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#20: Protein 60S RIBOSOMAL PROTEIN L22 / 60S RIBOSOMAL PROTEIN EL22 / EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA- ...60S RIBOSOMAL PROTEIN EL22 / EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA- ASSOCIATED PROTEIN / HEPARIN-BINDING PROTEIN HBP15


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#21: Protein 60S RIBOSOMAL PROTEIN L23 / 60S RIBOSOMAL PROTEIN UL14 / 60S RIBOSOMAL PROTEIN L17


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#22: Protein 60S RIBOSOMAL PROTEIN L24 / 60S RIBOSOMAL PROTEIN EL24 / 60S RIBOSOMAL PROTEIN L30


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#23: Protein 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN UL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#24: Protein 60S RIBOSOMAL PROTEIN L26 / 60S RIBOSOMAL PROTEIN UL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#25: Protein 60S RIBOSOMAL PROTEIN L27 / 60S RIBOSOMAL PROTEIN EL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#26: Protein 60S RIBOSOMAL PROTEIN L27A / 60S RIBOSOMAL PROTEIN UL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#27: Protein 60S RIBOSOMAL PROTEIN L29 / 60S RIBOSOMAL PROTEIN EL29 / CELL SURFACE HEPARIN-BINDING PROTEIN HIP


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#28: Protein 60S RIBOSOMAL PROTEIN L30 / 60S RIBOSOMAL PROTEIN EL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#29: Protein 60S RIBOSOMAL PROTEIN L31 / 60S RIBOSOMAL PROTEIN EL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#30: Protein 60S RIBOSOMAL PROTEIN L32 / 60S RIBOSOMAL PROTEIN EL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#31: Protein 60S RIBOSOMAL PROTEIN L35A / 60S RIBOSOMAL PROTEIN EL33 / CELL GROWTH-INHIBITING GENE 33 PROTEIN


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#32: Protein 60S RIBOSOMAL PROTEIN L34 / 60S RIBOSOMAL PROTEIN EL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#33: Protein 60S RIBOSOMAL PROTEIN L35 / 60S RIBOSOMAL PROTEIN UL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#34: Protein 60S RIBOSOMAL PROTEIN L36 / 60S RIBOSOMAL PROTEIN EL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#35: Protein 60S RIBOSOMAL PROTEIN L37 / 60S RIBOSOMAL PROTEIN EL37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#36: Protein 60S RIBOSOMAL PROTEIN L38 / 60S RIBOSOMAL PROTEIN EL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#37: Protein 60S RIBOSOMAL PROTEIN L39 / 60S RIBOSOMAL PROTEIN EL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#39: Protein/peptide 60S RIBOSOMAL PROTEIN L41 / 60S RIBOSOMAL PROTEIN EL41 / HG12


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#40: Protein 60S RIBOSOMAL PROTEIN L36A / 60S RIBOSOMAL PROTEIN EL44 / 60S RIBOSOMAL PROTEIN L44 / CELL GROWTH-INHIBITING GENE 15 PROTEIN / ...60S RIBOSOMAL PROTEIN EL44 / 60S RIBOSOMAL PROTEIN L44 / CELL GROWTH-INHIBITING GENE 15 PROTEIN / CELL MIGRATION-INDUCING GENE 6 PROTEIN


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#41: Protein 60S RIBOSOMAL PROTEIN L37A / 60S RIBOSOMAL PROTEIN EL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#42: Protein 60S RIBOSOMAL PROTEIN L28 / 60S RIBOSOMAL PROTEIN EL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#43: Protein 60S RIBOSOMAL PROTEIN L10A / 60S RIBOSOMAL PROTEIN UL1 / CSA-19 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED ...60S RIBOSOMAL PROTEIN UL1 / CSA-19 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 6 / NEDD-6


Mass: 23174.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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Protein , 1 types, 1 molecules m

#38: Protein UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / 60S RIBOSOMAL PROTEIN EL40 / EP52 / UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION PRODUCT 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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RNA chain , 3 types, 3 molecules 234

#44: RNA chain 28S RRNA


Mass: 1625917.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#45: RNA chain 5.8S RRNA


Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#46: RNA chain 5S RRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

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Details

Has protein modificationY
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: A 1-257 UNP P62917 1- 257 CHAIN: B 1-403 UNP P39023 1- 403 CHAIN: C 1-427 UNP P36578 1- 427 CHAIN: D 1-297 UNP P46777 1- 297 CHAIN: E 1-288 UNP Q02878 1- 288 CHAIN: F 1-248 UNP P18124 1- 248 CHAIN: G 1-266 UNP P62424 1- 266 CHAIN: H 1-192 UNP P32969 1- 192 CHAIN: I 1-214 UNP P27635 1- 214 CHAIN: J 1-178 UNP P62913 1- 178 CHAIN: L 1-211 UNP P26373 1- 211 CHAIN: M 1-215 UNP P50914 1- 215 CHAIN: N 1-204 UNP P61313 1- 204 CHAIN: O 1-203 UNP P40429 1- 203 CHAIN: P 1-184 UNP P18621 1- 184 CHAIN: Q 1-188 UNP Q07020 1- 188 CHAIN: R 1-196 UNP P84098 1- 196 CHAIN: S 1-176 UNP Q02543 1- 176 CHAIN: T 1-160 UNP P46778 1- 160 CHAIN: U 1-128 UNP P35268 1- 128 CHAIN: V 1-140 UNP P62829 1- 140 CHAIN: W 1-157 UNP P83731 1- 157 CHAIN: X 1-156 UNP P62750 1- 156 CHAIN: Y 1-145 UNP P61254 1- 145 CHAIN: Z 1-136 UNP P61353 1- 136 CHAIN: a 1-148 UNP P46776 1- 148 CHAIN: b 1-159 UNP P47914 1- 159 CHAIN: c 1-115 UNP P62888 1- 115 CHAIN: d 1-125 UNP P62899 1- 125 CHAIN: e 1-135 UNP P62910 1- 135 CHAIN: f 1-110 UNP P18077 1- 110 CHAIN: g 1-117 UNP P49207 1- 117 CHAIN: h 1-123 UNP P42766 1- 123 CHAIN: i 1-105 UNP Q9Y3U8 1- 105 CHAIN: j 1- 97 UNP P61927 1- 97 CHAIN: k 1- 70 UNP P63173 1- 70 CHAIN: l 1- 51 UNP P62891 1- 51 CHAIN: m 1-128 UNP P62987 1- 128 CHAIN: n 1- 25 UNP P62945 1- 25 CHAIN: o 1-106 UNP P83881 1- 106 CHAIN: p 1- 92 UNP P61513 1- 92 CHAIN: t 1-137 UNP P46779 1- 137 CHAIN: u 1-210 UNP P62906 1- 210

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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, ERF1 AND ERF3
Type: RIBOSOME / Details: MICROGRAPH SELECTED FOR ASTIGMATISM AND DRIFT
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: MINIMAL DOSE SYSTEM
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 115000 X / Calibrated magnification: 194805 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNum. digital images: 2000
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: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 4CXD

4cxd
PDB Unreleased entry


Accession code: 4CXD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53135 0 0 0 53135

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