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- PDB-6gsm: Structure of a partial yeast 48S preinitiation complex in open co... -

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Entry
Database: PDB / ID: 6gsm
TitleStructure of a partial yeast 48S preinitiation complex in open conformation.
Components
  • (40S ribosomal protein ...) x 17
  • (Eukaryotic translation initiation factor ...) x 10
  • 18S ribosomal RNA
  • 60S ribosomal protein L41-A
  • KLLA0A07194p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B06182p
  • KLLA0B08173p
  • KLLA0B11231p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E12277p
  • KLLA0E23673p
  • KLLA0F07843p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • Met-tRNAi
  • Ubiquitin-40S ribosomal protein S27a
  • mRNA (5'-R(P*AP*AP*U)-3')
KeywordsRIBOSOME / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / tRNAi / 48S PIC / small ribosome subunit
Function / homology
Function and homology information


formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex ...formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor binding / translation initiation factor activity / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / double-stranded RNA binding / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A ...Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site
Similarity search - Domain/homology
Chem-7NO / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta ...Chem-7NO / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta / Small ribosomal subunit protein eS32A / Eukaryotic translation initiation factor 2 subunit alpha / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit gamma / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 1A / Eukaryotic translation initiation factor 3 subunit I / Ubiquitin-ribosomal protein eS31 fusion protein / Eukaryotic translation initiation factor 3 subunit G / 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 / RPS23 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Kluyveromyces lactis NRRL Y-1140 (yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.15 Å
AuthorsLlacer, J.L. / Hussain, T. / Gordiyenko, Y. / Ramakrishnan, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT096570 United Kingdom
Citation
Journal: Nucleic Acids Res / Year: 2021
Title: Large-scale movement of eIF3 domains during translation initiation modulate start codon selection.
Authors: Jose L Llácer / Tanweer Hussain / Jinsheng Dong / Laura Villamayor / Yuliya Gordiyenko / Alan G Hinnebusch /
Abstract: The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single ...The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.
#1: Journal: 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 14, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionJul 31, 2019ID: 3JAQ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Provider: author / Type: Coordinate replacement
Revision 1.2Oct 27, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / em_sample_support / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_sample_support.grid_type / _em_software.category / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_nat.common_name / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_asym_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_asym_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Polymer geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 22, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / refine
Item: _em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low
Revision 2.3Sep 25, 2024Group: Data collection / Source and taxonomy / Category: em_admin / em_entity_assembly_recombinant
Item: _em_admin.last_update / _em_entity_assembly_recombinant.id

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Assembly

Deposited unit
1: Met-tRNAi
2: 18S ribosomal RNA
A: 40S ribosomal protein S0
3: mRNA (5'-R(P*AP*AP*U)-3')
B: 40S ribosomal protein S1
C: KLLA0F09812p
D: KLLA0D08305p
E: 40S ribosomal protein S4
F: KLLA0D10659p
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: KLLA0E23673p
K: KLLA0B08173p
L: KLLA0A10483p
M: 40S ribosomal protein S12
N: KLLA0F18040p
O: 40S ribosomal protein S14
P: KLLA0F07843p
Q: 40S ribosomal protein S16
R: KLLA0B01474p
S: KLLA0B01562p
T: KLLA0A07194p
U: KLLA0F25542p
V: 40S ribosomal protein S21
W: 40S ribosomal protein S22
X: KLLA0B11231p
Y: 40S ribosomal protein S24
Z: KLLA0B06182p
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: KLLA0E12277p
h: 60S ribosomal protein L41-A
i: Eukaryotic translation initiation factor 1A
j: Eukaryotic translation initiation factor 2 subunit alpha
k: Eukaryotic translation initiation factor 2 subunit gamma
l: Eukaryotic translation initiation factor 2 subunit beta
m: Eukaryotic translation initiation factor eIF-1
o: Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3a
p: Eukaryotic translation initiation factor 3 subunit B
q: Eukaryotic translation initiation factor 3 subunit C
s: Eukaryotic translation initiation factor 3 subunit I
r: Eukaryotic translation initiation factor 3 subunit G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,532,959135
Polymers1,529,70547
Non-polymers3,25488
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain Met-tRNAi


Mass: 24799.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#2: RNA chain 18S ribosomal RNA


Mass: 579239.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
#4: RNA chain mRNA (5'-R(P*AP*AP*U)-3')


Mass: 919.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast)

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40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVWYabcde

#3: Protein 40S ribosomal protein S0


Mass: 23140.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CN12
#5: Protein 40S ribosomal protein S1


Mass: 26404.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CWD0
#8: Protein 40S ribosomal protein S4


Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CWJ2
#10: Protein 40S ribosomal protein S6


Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CM04
#11: Protein 40S ribosomal protein S7


Mass: 21033.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CTD6
#12: Protein 40S ribosomal protein S8


Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CMG3
#16: Protein 40S ribosomal protein S12


Mass: 12710.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CLU4
#18: Protein 40S ribosomal protein S14 / RP59


Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: P27069
#20: Protein 40S ribosomal protein S16


Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q875N2
#25: Protein 40S ribosomal protein S21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CXT6
#26: Protein 40S ribosomal protein S22


Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CW21
#28: Protein 40S ribosomal protein S24


Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CU44
#30: Protein 40S ribosomal protein S26


Mass: 11166.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CS01
#31: Protein 40S ribosomal protein S27


Mass: 8753.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CNL2
#32: Protein 40S ribosomal protein S28 / S33


Mass: 6972.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: P33285
#33: Protein 40S ribosomal protein S29


Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CPG3
#34: Protein 40S ribosomal protein S30


Mass: 6608.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CUH5

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Protein , 16 types, 16 molecules CDFJKLNPRSTUXZfg

#6: Protein KLLA0F09812p


Mass: 23162.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CKL3
#7: Protein KLLA0D08305p


Mass: 24830.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CRK7
#9: Protein KLLA0D10659p


Mass: 22912.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CRA3
#13: Protein KLLA0E23673p


Mass: 20882.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CM18
#14: Protein KLLA0B08173p


Mass: 11423.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CVZ5
#15: Protein KLLA0A10483p


Mass: 17712.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CX80
#17: Protein KLLA0F18040p


Mass: 16858.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CJK0
#19: Protein KLLA0F07843p


Mass: 13448.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CKV4
#21: Protein KLLA0B01474p


Mass: 14200.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CWU3
#22: Protein KLLA0B01562p


Mass: 16953.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CWT9
#23: Protein KLLA0A07194p


Mass: 15747.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CXM0
#24: Protein KLLA0F25542p


Mass: 12032.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CIM1
#27: Protein KLLA0B11231p


Mass: 15916.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: F2Z602, UniProt: Q875M3*PLUS
#29: Protein KLLA0B06182p


Mass: 7939.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CW78
#35: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 7958.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: P69061
#36: Protein KLLA0E12277p


Mass: 35612.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
References: UniProt: Q6CNI7

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Protein/peptide , 1 types, 1 molecules h

#37: Protein/peptide 60S ribosomal protein L41-A / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX86

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Eukaryotic translation initiation factor ... , 10 types, 10 molecules ijklmopqsr

#38: Protein Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 10953.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38912
#39: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 30221.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20459
#40: Protein Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 47230.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32481
#41: Protein Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 16458.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09064
#42: Protein Eukaryotic translation initiation factor eIF-1 / Protein translation factor SUI1


Mass: 10919.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SUI1, RFR1, YNL244C, N0905 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32911
#43: Protein Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3a / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / ...eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / Translation initiation factor eIF3 / p110 subunit homolog


Mass: 62822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38249
#44: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation ...eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation initiation factor eIF3 p90 subunit


Mass: 75014.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: PRT1, CDC63, YOR361C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06103
#45: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport ...eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 76963.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32497
#46: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit / eIF3 p39


Mass: 38229.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: TIF34, YMR146C, YM9375.16C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40217
#47: Protein/peptide Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Translation initiation factor eIF3 p33 subunit / eIF3 p33


Mass: 5576.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: TIF35, YDR429C, D9461.16 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04067, UniProt: A6ZZ25*PLUS

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Non-polymers , 4 types, 88 molecules

#48: Chemical ChemComp-7NO / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate


Mass: 478.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N6O8PS
#49: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 82 / Source method: obtained synthetically / Formula: Mg
#50: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#51: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN

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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
IDNameTypeEntity IDParent-IDSource
1Structure of a partial yeast 48S preinitiation complex in open conformationRIBOSOME#1-#470MULTIPLE SOURCES
2RibosomeCOMPLEX#2-#3, #5-#371NATURAL
3tRNACOMPLEX#11NATURAL
5Initiation factors eIF1 and eIF1ACOMPLEX#39-#41, #43-#471RECOMBINANT
4Initiation factors eIF2 and eIF3COMPLEX#38, #421RECOMBINANT
6mRNACOMPLEX#41RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)284590
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
45Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
56Kluyveromyces lactis (yeast)28985
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
15Saccharomyces cerevisiae (brewer's yeast)4932
24Escherichia coli BL21(DE3) (bacteria)469008
36synthetic construct (others)32630
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 mMMES1
25 mMMagnessium acetate1
380 mMPotassium acetate1
410 mMAmmonium acetate1
52 mMDithiothreitol (DTT)1
60.001 mMZinc acetate1
70.6 mMATP1
80.25 mMGDPCP1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2610
Details: Images were collected in movie-mode at 40 frames per second

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameVersionCategory
2EMANparticle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15REFMAC5.8model refinement
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 360729
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5750 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: FSC
RefinementResolution: 5.15→5.15 Å / Cor.coef. Fo:Fc: 0.535 / SU B: 368.377 / SU ML: 3.484 / ESU R: 1.194
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.54744 --
obs0.54744 967595 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 264.057 Å2
Baniso -1Baniso -2Baniso -3
1--12.79 Å20.96 Å211.64 Å2
2--13.78 Å2-0.27 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Total: 99882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.016106336
ELECTRON MICROSCOPYr_bond_other_d0.0040.0277172
ELECTRON MICROSCOPYr_angle_refined_deg1.1111.658151655
ELECTRON MICROSCOPYr_angle_other_deg1.3193180667
ELECTRON MICROSCOPYr_dihedral_angle_1_deg19.4468.63118478
ELECTRON MICROSCOPYr_dihedral_angle_2_deg42.51723.0752517
ELECTRON MICROSCOPYr_dihedral_angle_3_deg21.03515.01110635
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.34215517
ELECTRON MICROSCOPYr_chiral_restr0.1070.20717196
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0288798
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0222088
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.39931.57130497
ELECTRON MICROSCOPYr_mcbond_other5.39931.5730496
ELECTRON MICROSCOPYr_mcangle_it10.17947.33138007
ELECTRON MICROSCOPYr_mcangle_other10.17847.33238008
ELECTRON MICROSCOPYr_scbond_it3.71726.23475839
ELECTRON MICROSCOPYr_scbond_other3.71726.23575840
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.90839.31113649
ELECTRON MICROSCOPYr_long_range_B_refined30.24470950
ELECTRON MICROSCOPYr_long_range_B_other30.24470951
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 5.2→5.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.592 71392 -
Rfree-0 -
obs--100 %

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