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- PDB-3jam: CryoEM structure of 40S-eIF1A-eIF1 complex from yeast -

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Basic information

Entry
Database: PDB / ID: 3jam
TitleCryoEM structure of 40S-eIF1A-eIF1 complex from yeast
Components
  • 18S rRNA18S ribosomal RNA
  • RACK1Receptor for activated C kinase 1
  • eIF1
  • eIF1AEIF1AX
  • eL41
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsTRANSLATION / Eukaryotic translation initiation / 48S / small ribosome subunit / 40S / 43S
Function / homology
Function and homology information


formation of translation initiation ternary complex / translation reinitiation / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...formation of translation initiation ternary complex / translation reinitiation / multi-eIF complex / eukaryotic 43S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / ribosomal small subunit binding / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / regulation of translational fidelity / translation initiation factor binding / translational initiation / translation initiation factor activity / cytosolic ribosome / maintenance of translational fidelity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / ribosome binding / double-stranded RNA binding / small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / protein kinase binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / SUI1-like domain / Ribosomal protein S17 / Translation Initiation Factor Eif1 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 ...N-terminal domain of TfIIb - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2650 / SUI1-like domain / Ribosomal protein S17 / Translation Initiation Factor Eif1 / Ribosomal protein S26 / Ribosomal protein S8e, subdomain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Phosducin; domain 2 / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / Diphtheria Toxin Repressor; domain 2 / N-terminal domain of TfIIb / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / K homology (KH) domain / Ribosomal protein L30/S12 / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Other non-globular / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S19e, conserved site / : / S27a-like superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Double Stranded RNA Binding Domain / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 / Eukaryotic translation initiation factor 1A / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLlacer, J.L. / Hussain, T. / Ramakrishnan, V.
CitationJournal: Mol Cell / Year: 2015
Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan /
Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
2: 18S rRNA
A: uS2
B: eS1
C: uS5
D: uS3
E: eS4
F: uS7
G: eS6
H: eS7
I: eS8
J: uS4
K: eS10
L: uS17
M: eS12
N: uS15
O: uS11
P: uS19
Q: uS9
R: eS17
S: uS13
T: eS19
U: uS10
V: eS21
W: uS8
X: uS12
Y: eS24
Z: eS25
a: eS26
b: eS27
c: eS28
d: uS14
e: eS30
f: eS31
g: RACK1
h: eL41
i: eIF1A
j: eIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,208,666120
Polymers1,206,52637
Non-polymers2,14183
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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Protein , 35 types, 35 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#2: Protein uS2


Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#3: Protein eS1


Mass: 28971.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#4: Protein uS5


Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#5: Protein uS3


Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#6: Protein eS4


Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#7: Protein uS7


Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#8: Protein eS6


Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#9: Protein eS7


Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#10: Protein eS8


Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#11: Protein uS4


Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#12: Protein eS10


Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#13: Protein uS17


Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#14: Protein eS12


Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#15: Protein uS15


Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#16: Protein uS11


Mass: 14530.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#17: Protein uS19


Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#18: Protein uS9


Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#19: Protein eS17


Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#20: Protein uS13


Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#21: Protein eS19


Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#22: Protein uS10


Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#23: Protein eS21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#24: Protein uS8


Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#25: Protein uS12


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: F2Z602
#26: Protein eS24


Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#27: Protein eS25


Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#28: Protein eS26


Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#29: Protein eS27


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#30: Protein eS28


Mass: 7549.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#31: Protein uS14


Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#32: Protein eS30


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#33: Protein eS31


Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#36: Protein eIF1A / EIF1AX


Mass: 17462.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P38912
#37: Protein eIF1 /


Mass: 12330.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P32911

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RNA chain / Protein/peptide , 2 types, 2 molecules 2h

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


Mass: 579545.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: NC_006040.1
#35: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P0CX86

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Non-polymers , 2 types, 83 molecules

#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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

Component
IDNameTypeParent-ID
1Initiation factors eIF1A and eIF1 bound to the 40S ribosomeRIBOSOME0
2Ribosome small subunit 40SRIBOSOME1
3Eukaryotic initiation factor eIF1A1
4Eukaryotic initiation factor eIF11
Buffer solutionName: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
pH: 6.5
Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %
Details: Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Method: Blot for 2.5 to 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 28, 2014
Details: Complete dataset was collected over two non-consecutive days.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 X / Calibrated magnification: 104478 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 2056
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 2015/06/03 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86055 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Details: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingB value: 89 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor, FSC / Details: METHOD--Local refinement
Atomic model buildingPDB-ID: 3J80

3j80


Accession code: 3J80 / Source name: PDB / Type: experimental model
RefinementDetails: Hydrogens have been added in their riding positions
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms39970 37797 83 0 77850

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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