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- PDB-4d5y: Cryo-EM structures of ribosomal 80S complexes with termination fa... -

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Basic information

Entry
Database: PDB / ID: 4d5y
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 43
  • 28S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
KeywordsRIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS
Function / homology
Function and homology information


cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome
Similarity search - Function
Ribosomal protein L2, archaeal-type / Ribosomal protein L2, conserved site / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 ...Ribosomal protein L2, archaeal-type / Ribosomal protein L2, conserved site / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL2
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 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Source and taxonomy
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 30, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 2.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 2.3Oct 9, 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 700SHEET 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.

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Structure visualization

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Assembly

Deposited unit
A: 60S RIBOSOMAL PROTEIN UL2
B: 60S RIBOSOMAL PROTEIN UL3
C: 60S RIBOSOMAL PROTEIN UL4
D: 60S RIBOSOMAL PROTEIN UL18
E: 60S RIBOSOMAL PROTEIN EL6
F: 60S RIBOSOMAL PROTEIN UL30
G: 60S RIBOSOMAL PROTEIN EL8
H: 60S RIBOSOMAL PROTEIN UL6
I: 60S RIBOSOMAL PROTEIN UL16
J: 60S RIBOSOMAL PROTEIN UL5
L: 60S RIBOSOMAL PROTEIN EL13
M: 60S RIBOSOMAL PROTEIN EL14
N: 60S RIBOSOMAL PROTEIN EL15
O: 60S RIBOSOMAL PROTEIN UL13
P: 60S RIBOSOMAL PROTEIN UL22
Q: 60S RIBOSOMAL PROTEIN EL18
R: 60S RIBOSOMAL PROTEIN UL19
S: 60S RIBOSOMAL PROTEIN EL20
T: 60S RIBOSOMAL PROTEIN EL21
U: 60S RIBOSOMAL PROTEIN EL22
V: 60S RIBOSOMAL PROTEIN UL14
W: 60S RIBOSOMAL PROTEIN EL24
X: 60S RIBOSOMAL PROTEIN UL23
Y: 60S RIBOSOMAL PROTEIN UL24
Z: 60S RIBOSOMAL PROTEIN EL27
a: 60S RIBOSOMAL PROTEIN UL15
b: 60S RIBOSOMAL PROTEIN EL29
c: 60S RIBOSOMAL PROTEIN EL30
d: 60S RIBOSOMAL PROTEIN EL31
e: 60S RIBOSOMAL PROTEIN EL32
f: 60S RIBOSOMAL PROTEIN EL33
g: 60S RIBOSOMAL PROTEIN EL34
h: 60S RIBOSOMAL PROTEIN UL29
i: 60S RIBOSOMAL PROTEIN EL36
j: 60S RIBOSOMAL PROTEIN EL37
k: 60S RIBOSOMAL PROTEIN EL38
l: 60S RIBOSOMAL PROTEIN EL39
m: 60S RIBOSOMAL PROTEIN EL40
n: 60S RIBOSOMAL PROTEIN EL41
o: 60S RIBOSOMAL PROTEIN EL44
p: 60S RIBOSOMAL PROTEIN EL43
t: 60S RIBOSOMAL PROTEIN EL28
u: 60S RIBOSOMAL PROTEIN UL1
2: 28S Ribosomal RNA
3: 5.8S Ribosomal RNA
4: 5S Ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)2,578,72846
Polymers2,578,72846
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 ... , 43 types, 43 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...

#1: Protein 60S RIBOSOMAL PROTEIN UL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TT27
#2: Protein 60S RIBOSOMAL PROTEIN UL3


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 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 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 EL6


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 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 EL8


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 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 UL16


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 UL5


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 EL13


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 EL14


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 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 UL13


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 UL22


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 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 UL19


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 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 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 EL22


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 UL14


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 EL24


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 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 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 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 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 EL29


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 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 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 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 EL33


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 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 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 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 EL37


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 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 EL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#38: Protein 60S RIBOSOMAL PROTEIN EL40


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#39: Protein/peptide 60S RIBOSOMAL PROTEIN EL41


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 EL44


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 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 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 UL1


Mass: 23174.504 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 Ribosomal RNA


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 Ribosomal RNA


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


Mass: 38385.750 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 details4D5Y B 1 403 UNP P39023 RL3_HUMAN 1 403 4D5Y C 1 427 UNP P36578 RL4_HUMAN 1 427 4D5Y D 1 297 UNP ...4D5Y B 1 403 UNP P39023 RL3_HUMAN 1 403 4D5Y C 1 427 UNP P36578 RL4_HUMAN 1 427 4D5Y D 1 297 UNP P46777 RL5_HUMAN 1 297 4D5Y E 1 288 UNP Q02878 RL6_HUMAN 1 288 4D5Y F 1 248 UNP P18124 RL7_HUMAN 1 248 4D5Y G 1 266 UNP P62424 RL7A_HUMAN 1 266 4D5Y H 1 192 UNP P32969 RL9_HUMAN 1 192 4D5Y I 1 214 UNP P27635 RL10_HUMAN 1 214 4D5Y J 1 178 UNP P62913 RL11_HUMAN 1 178 4D5Y L 1 211 UNP P26373 RL13_HUMAN 1 211 4D5Y M 1 215 UNP P50914 RL14_HUMAN 1 215 4D5Y N 1 204 UNP P61313 RL15_HUMAN 1 204 4D5Y O 1 203 UNP P40429 RL13A_HUMAN 1 203 4D5Y P 1 184 UNP P18621 RL17_HUMAN 1 184 4D5Y Q 1 188 UNP Q07020 RL18_HUMAN 1 188 4D5Y R 1 196 UNP P84098 RL19_HUMAN 1 196 4D5Y S 1 176 UNP Q02543 RL18A_HUMAN 1 176 4D5Y T 1 160 UNP P46778 RL21_HUMAN 1 160 4D5Y U 1 128 UNP P35268 RL22_HUMAN 1 128 4D5Y V 1 140 UNP P62829 RL23_HUMAN 1 140 4D5Y W 1 157 UNP P83731 RL24_HUMAN 1 157 4D5Y X 1 156 UNP P62750 RL23A_HUMAN 1 156 4D5Y Y 1 145 UNP P61254 RL26_HUMAN 1 145 4D5Y Z 1 136 UNP P61353 RL27_HUMAN 1 136 4D5Y a 1 159 UNP P46776 RL27A_HUMAN 1 159 4D5Y b 1 159 UNP P47914 RL29_HUMAN 1 159 4D5Y c 1 115 UNP P62888 RL30_HUMAN 1 115 4D5Y d 1 125 UNP P62899 RL31_HUMAN 1 125 4D5Y e 1 135 UNP P62910 RL32_HUMAN 1 135 4D5Y f 1 110 UNP P18077 RL35A_HUMAN 1 110 4D5Y g 1 117 UNP P49207 RL34_HUMAN 1 117 4D5Y h 1 123 UNP P42766 RL35_HUMAN 1 123 4D5Y i 1 105 UNP Q9Y3U8 RL36_HUMAN 1 105 4D5Y j 1 97 UNP P61927 RL37_HUMAN 1 97 4D5Y k 1 70 UNP P63173 RL38_HUMAN 1 70 4D5Y l 1 51 UNP P62891 RL39_HUMAN 1 51 4D5Y m 1 128 UNP P62987 RL40_HUMAN 1 128 4D5Y o 1 106 UNP P83881 RL36A_HUMAN 1 106 4D5Y p 1 92 UNP P61513 RL37A_HUMAN 1 92 4D5Y t 1 137 UNP P46779 RL28_HUMAN 1 137 DBREF1 4D5Y u 1 210 UNP A0A087WNH5 DBREF2 4D5Y u A0A087WNH5_RABIT 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: CRICKET PARALYSIS VIRUS IRES RNA BOUND TO MAMMALIAN 80S RIBOSOME AND ERF1
Type: RIBOSOME / Details: MICROGRAPHS 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: IMAGES SELECTED FOR ASTIGMATISM AND DRIFT
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
Specimen holderTemperature: 77 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 366
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: 109596 / 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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