[English] 日本語
Yorodumi
- PDB-5jbh: Cryo-EM structure of a full archaeal ribosomal translation initia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jbh
TitleCryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN conformation
Components
  • (30S ribosomal protein ...) x 27
  • 16S ribosomal RNA
  • 50S ribosomal protein uL30
  • aIF1
  • aIF1A
  • aIF2-alpha
  • aIF2-beta
  • aIF2-gamma
  • initiator Met-tRNA fMet from E. coli (A1U72 variant)
  • mRNA
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


translation reinitiation / protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor activity / translational initiation / ribosome biogenesis / ribosome binding ...translation reinitiation / protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor activity / translational initiation / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation factor SUI1 homolog, archaea / Archaeal/bacterial translation initiation factor SUI1 / : / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Ribosomal protein S27ae / Translation initiation factor 2, gamma subunit / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal ...Translation factor SUI1 homolog, archaea / Archaeal/bacterial translation initiation factor SUI1 / : / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Ribosomal protein S27ae / Translation initiation factor 2, gamma subunit / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 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. / Ribosomal protein L7Ae, archaea / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / 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. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Elongation factor Tu domain 2 / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Protein translation factor SUI1 homolog / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS27 / Translation initiation factor 2 subunit beta / Translation initiation factor 2 subunit alpha / Translation initiation factor 2 subunit gamma / Small ribosomal subunit protein eS19 / Translation initiation factor 1A
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
Escherichia coli (E. coli)
Pyrococcus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.34 Å
AuthorsCoureux, P.-D. / Schmitt, E. / Mechulam, Y.
CitationJournal: Nat Commun / Year: 2016
Title: Cryo-EM study of start codon selection during archaeal translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Auriane Monestier / Eric Larquet / Lionel Cladière / Bruno P Klaholz / Emmanuelle Schmitt / Yves Mechulam /
Abstract: Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal ...Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Data collection
Revision 1.2Feb 8, 2017Group: Database references / Source and taxonomy
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / pdbx_validate_close_contact / struct_conn
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _audit_author.name / _em_admin.last_update ..._audit_author.name / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.6Jun 12, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8149
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
2: 16S ribosomal RNA
Z: 30S ribosomal protein uS3
3: 50S ribosomal protein uL30
L: 30S ribosomal protein uS10
O: 30S ribosomal protein uS13
P: 30S ribosomal protein uS14
S: 30S ribosomal protein eS17
T: 30S ribosomal protein uS19
U: 30S ribosomal protein eS19
X: 30S ribosomal protein eS28
Y: 30S ribosomal protein eS27
H: 30S ribosomal protein uS7
K: 30S ribosomal protein uS9
M: 30S ribosomal protein uS11
N: 30S ribosomal protein uS12
Q: 30S ribosomal protein uS15
R: 30S ribosomal protein uS17
A: 30S ribosomal protein uS3
B: 30S ribosomal protein uS2
V: 30S ribosomal protein eS24
W: 30S ribosomal protein eS27
D: 30S ribosomal protein uS4
E: 30S ribosomal protein eS4
F: 30S ribosomal protein uS5
G: 30S ribosomal protein eS6
I: 30S ribosomal protein uS8
J: 30S ribosomal protein eS8
C: 30S ribosomal protein SX
0: 30S ribosomal protein eL41
5: mRNA
1: aIF1
4: initiator Met-tRNA fMet from E. coli (A1U72 variant)
6: aIF1A
7: aIF2-gamma
8: aIF2-beta
9: aIF2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,065,14840
Polymers1,064,38736
Non-polymers7614
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area156180 Å2
ΔGint-1222 kcal/mol
Surface area368780 Å2
MethodPISA

-
Components

-
RNA chain , 3 types, 3 molecules 254

#1: RNA chain 16S ribosomal RNA


Mass: 492800.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 16S model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea)
#30: RNA chain mRNA


Mass: 8394.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus (archaea)
#32: RNA chain initiator Met-tRNA fMet from E. coli (A1U72 variant)


Mass: 24488.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNA model from Sulfolobus solfataricus (PDB code 3V11) used for fitting
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

+
30S ribosomal protein ... , 27 types, 27 molecules ZLOPSTUXYHKMNQRABVWDEFGIJC0

#2: Protein 30S ribosomal protein uS3


Mass: 23464.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS3 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U004*PLUS
#4: Protein 30S ribosomal protein uS10


Mass: 11769.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS10 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61885*PLUS
#5: Protein 30S ribosomal protein uS13


Mass: 16948.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS13 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0E2*PLUS
#6: Protein 30S ribosomal protein uS14


Mass: 6634.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS14 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U013*PLUS
#7: Protein 30S ribosomal protein eS17


Mass: 7942.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS17 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0U1*PLUS
#8: Protein 30S ribosomal protein uS19


Mass: 15357.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS19 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U002*PLUS
#9: Protein 30S ribosomal protein eS19


Mass: 17394.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS19 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0G8*PLUS
#10: Protein 30S ribosomal protein eS28


Mass: 8116.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS28 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U159*PLUS
#11: Protein/peptide 30S ribosomal protein eS27


Mass: 5864.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS27 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U443*PLUS
#12: Protein 30S ribosomal protein uS7


Mass: 24701.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS5 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0M8*PLUS
#13: Protein 30S ribosomal protein uS9


Mass: 15317.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS9 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0E7*PLUS
#14: Protein 30S ribosomal protein uS11


Mass: 14756.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS11 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0E3*PLUS
#15: Protein 30S ribosomal protein uS12


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS12 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61994*PLUS
#16: Protein 30S ribosomal protein uS15


Mass: 18640.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS15 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8TZD9*PLUS
#17: Protein 30S ribosomal protein uS17


Mass: 13296.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS17 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U008*PLUS
#18: Protein 30S ribosomal protein uS3


Mass: 22984.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS3 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8TZE1*PLUS
#19: Protein 30S ribosomal protein uS2


Mass: 23039.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS2 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U0F0*PLUS
#20: Protein 30S ribosomal protein eS24


Mass: 11698.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS24 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U442*PLUS
#21: Protein 30S ribosomal protein eS27


Mass: 6888.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS27 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U474*PLUS
#22: Protein 30S ribosomal protein uS4


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS4 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61992*PLUS
#23: Protein 30S ribosomal protein eS4


Mass: 28197.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS4 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U011*PLUS
#24: Protein 30S ribosomal protein uS5


Mass: 26590.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS5 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U017*PLUS
#25: Protein 30S ribosomal protein eS6


Mass: 14002.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS6 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U3H8*PLUS
#26: Protein 30S ribosomal protein uS8


Mass: 14684.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein uS8 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U014*PLUS
#27: Protein 30S ribosomal protein eS8


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eS8 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U1Y5*PLUS
#28: Protein 30S ribosomal protein SX


Mass: 4868.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein SX model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea)
#29: Protein/peptide 30S ribosomal protein eL41


Mass: 3050.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 30S ribosomal protein eL41 model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U232*PLUS

-
Protein , 6 types, 6 molecules 316789

#3: Protein 50S ribosomal protein uL30


Mass: 13414.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 50S ribosomal protein L7AE model from Pyrococcus furiosus (PDB code 4V6U) used for fitting
Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62008*PLUS
#31: Protein aIF1


Mass: 11621.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57902*PLUS
#33: Protein aIF1A


Mass: 13078.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138*PLUS
#34: Protein aIF2-gamma


Mass: 45849.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: aIF2-gamma model from Sulfolobus solfataricus (PDB code 3V11) used for fitting
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5*PLUS
#35: Protein aIF2-beta


Mass: 15942.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: aIF2-beta model from Sulfolobus solfataricus (PDB code 3V11) used for fitting
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W59*PLUS
#36: Protein aIF2-alpha


Mass: 30432.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: aIF2-alpha model from Sulfolobus solfataricus (PDB code 3V11) used for fitting
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z79*PLUS

-
Non-polymers , 4 types, 4 molecules

#37: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#38: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Nonpolymer detailsPSU was indeed built as U for technical reasons and the resolution of the map is far from being ...PSU was indeed built as U for technical reasons and the resolution of the map is far from being sufficient to distinguish between U and PSU.
Sequence detailsthe pyrococcus furiosus model of the 30S subunit was fitted in the electron density map of the 30S ...the pyrococcus furiosus model of the 30S subunit was fitted in the electron density map of the 30S subunit from pyrococcus abyssi. This explain the alignment mismatches

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
130S archaeal translation initiation complexCOMPLEX#1-#360MULTIPLE SOURCES
230S archaeal translation initiation complexCOMPLEX#1-#291NATURAL
330S archaeal translation initiation complexCOMPLEX#31, #33-#361RECOMBINANT
430S archaeal translation initiation complexCOMPLEX#321RECOMBINANT
530S archaeal translation initiation complexCOMPLEX#301RECOMBINANT
Molecular weightValue: 0.982 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pyrococcus abyssi GE5 (archaea)272844
23Pyrococcus abyssi GE5 (archaea)272844
34Escherichia coli (E. coli)562
45Pyrococcus (archaea)2260
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24synthetic construct (others)32630
35Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 44 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12600 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more