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- PDB-6swc: IC2B model of cryo-EM structure of a full archaeal ribosomal tran... -

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Entry
Database: PDB / ID: 6swc
TitleIC2B model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Components
  • (30S ribosomal protein ...) x 26
  • (Translation initiation factor 2 subunit ...Initiation factor) x 3
  • 16S ribosomal rRNA
  • 50S ribosomal protein L7AeRibosome
  • Translation initiation factor 1A
  • Zn-ribbon RNA-binding protein involved in translation
  • initiator Met-tRNA fMet from E. coli (A1U72 variant)
  • mRNAMessenger RNA
KeywordsRIBOSOME / Translation initiation / cryo-EM / tRNA / evolution / archaea / rRNA modifications
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome / ribosome binding ...protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome / ribosome binding / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S17 / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / Ribosomal protein S27ae / Translation initiation factor 2, gamma subunit / : ...Ribosomal protein S17 / Translation initiation factor 2, alpha subunit, archaeal / Translation initiation factor 2, beta subunit / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / 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 / Diphtheria Toxin Repressor; domain 2 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / 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) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / 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 / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Ribosomal protein L7Ae, archaea / S15/NS1, RNA-binding / Ribosomal protein L30/S12 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein S19e, conserved site / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / S1 domain profile. / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / 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 / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Translation initiation factor 2 subunit beta / Translation initiation factor 2 subunit alpha / Translation initiation factor 2 subunit gamma / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Translation initiation factor 1A / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
Saccharolobus solfataricus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCoureux, P.-D. / Mechulam, Y. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0037 France
CitationJournal: Commun Biol / Year: 2020
Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
2: 16S ribosomal rRNA
A: 30S ribosomal protein S3Ae
B: 30S ribosomal protein S2
C: Zn-ribbon RNA-binding protein involved in translation
D: 30S ribosomal protein S4
E: 30S ribosomal protein S4e
F: 30S ribosomal protein S5
G: 30S ribosomal protein S6e
H: 30S ribosomal protein S7
I: 30S ribosomal protein S8
J: 30S ribosomal protein S8e
K: 30S ribosomal protein S9
L: 30S ribosomal protein S10
M: 30S ribosomal protein S11
N: 30S ribosomal protein S12
O: 30S ribosomal protein S13
P: 30S ribosomal protein S14 type Z
Q: 30S ribosomal protein S15
R: 30S ribosomal protein S17
S: 30S ribosomal protein S17e
T: 30S ribosomal protein S19
U: 30S ribosomal protein S19e
V: 30S ribosomal protein S24e
W: 30S ribosomal protein S27e
X: 30S ribosomal protein S28e
Y: 30S ribosomal protein S27ae
Z: 30S ribosomal protein S3
0: 30S ribosomal protein aL41
3: 50S ribosomal protein L7Ae
5: mRNA
4: initiator Met-tRNA fMet from E. coli (A1U72 variant)
6: Translation initiation factor 1A
7: Translation initiation factor 2 subunit gamma
8: Translation initiation factor 2 subunit beta
9: Translation initiation factor 2 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,052,56877
Polymers1,050,67835
Non-polymers1,89042
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area177310 Å2
ΔGint-1330 kcal/mol
Surface area393310 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 254

#1: RNA chain 16S ribosomal rRNA


Mass: 487700.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#30: RNA chain mRNA / Messenger RNA


Mass: 6448.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea)
#31: RNA chain initiator Met-tRNA fMet from E. coli (A1U72 variant)


Mass: 24504.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Variant: A1U72 / Production host: Escherichia coli (E. coli)

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30S ribosomal protein ... , 26 types, 26 molecules ABDEFGHIJKLMNOPQRSTUVWXYZ0

#2: Protein 30S ribosomal protein S3Ae / Ribosome / Ribosomal protein S1e


Mass: 22888.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V2K7
#3: Protein 30S ribosomal protein S2 /


Mass: 23026.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V191
#5: Protein 30S ribosomal protein S4 /


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61992
#6: Protein 30S ribosomal protein S4e / Ribosome


Mass: 28246.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1U8
#7: Protein 30S ribosomal protein S5 /


Mass: 26523.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1V5
#8: Protein 30S ribosomal protein S6e / Ribosome


Mass: 14029.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9UYS3
#9: Protein 30S ribosomal protein S7 /


Mass: 24662.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V109
#10: Protein 30S ribosomal protein S8 /


Mass: 14772.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1V0
#11: Protein 30S ribosomal protein S8e / Ribosome


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9UZL4
#12: Protein 30S ribosomal protein S9 /


Mass: 15293.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V195
#13: Protein 30S ribosomal protein S10 /


Mass: 11795.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0V6
#14: Protein 30S ribosomal protein S11 /


Mass: 14772.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P62010
#15: Protein 30S ribosomal protein S12 /


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61994
#16: Protein 30S ribosomal protein S13 /


Mass: 16992.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1A0
#17: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6644.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P62012
#18: Protein 30S ribosomal protein S15 /


Mass: 18697.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V2K9
#19: Protein 30S ribosomal protein S17 /


Mass: 13364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1U5
#20: Protein 30S ribosomal protein S17e / Ribosome


Mass: 8059.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0G0
#21: Protein 30S ribosomal protein S19 /


Mass: 15307.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1T9
#22: Protein 30S ribosomal protein S19e / Ribosome


Mass: 17422.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0G8
#23: Protein 30S ribosomal protein S24e / Ribosome


Mass: 11798.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9UY20
#24: Protein 30S ribosomal protein S27e / Ribosome


Mass: 7186.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9UXZ3
#25: Protein 30S ribosomal protein S28e / Ribosome


Mass: 8102.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61029
#26: Protein 30S ribosomal protein S27ae / Ribosome


Mass: 5992.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61238
#27: Protein 30S ribosomal protein S3 /


Mass: 23472.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1U1
#28: Protein/peptide 30S ribosomal protein aL41 /


Mass: 4910.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U232*PLUS

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Protein , 3 types, 3 molecules C36

#4: Protein Zn-ribbon RNA-binding protein involved in translation


Mass: 7163.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: G8ZFK7
#29: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P62008
#32: Protein Translation initiation factor 1A / aIF-1A


Mass: 13078.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: eIF1A, aif1A, PYRAB05910, PAB2441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138

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Translation initiation factor 2 subunit ... , 3 types, 3 molecules 789

#33: Protein Translation initiation factor 2 subunit gamma / Initiation factor


Mass: 45849.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Model from high resolution structures of aIF2 gamma of Saccharolobus solfataricus
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5*PLUS
#34: Protein Translation initiation factor 2 subunit beta / Initiation factor


Mass: 15942.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Model from high resolution structures of aIF2 beta of Saccharolobus solfataricus
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W59*PLUS
#35: Protein Translation initiation factor 2 subunit alpha / Initiation factor / aIF2-alpha / eIF-2-alpha


Mass: 30432.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Model from high resolution structures of aIF2 alpha of Saccharolobus solfataricus
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2a, aif2a, SSO1050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z79

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Non-polymers , 5 types, 84 molecules

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


Mass: 24.305 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: Mg
#37: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#38: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#39: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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
1Archaeal translation initiation complex devoid of aIF1 - IC2B stateRIBOSOME#1-#350MULTIPLE SOURCES
2Ribosomal proteins + RNARibosomeCOMPLEX#1-#291NATURAL
3mRNAMessenger RNACOMPLEX#301RECOMBINANT
4tRNAiCOMPLEX#311RECOMBINANT
5Translation initiation factor 1ACOMPLEX#321RECOMBINANT
6Translation initiation factor 2 subunit gammaInitiation factorCOMPLEX#351RECOMBINANT
7Translation initiation factor 2 subunit alpha, betaInitiation factorCOMPLEX#33-#341RECOMBINANT
Molecular weightValue: 1.05 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pyrococcus abyssi GE5 (archaea)272844
23Pyrococcus abyssi GE5 (archaea)272844
34Escherichia coli (E. coli)562
45Pyrococcus abyssi GE5 (archaea)272844
56Saccharolobus solfataricus P2 (archaea)273057
67Pyrococcus abyssi GE5 (archaea)272844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
24Escherichia coli (E. coli)562
35Escherichia coli (E. coli)562
46Escherichia coli (E. coli)562
57Escherichia coli (E. coli)562
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0175377
ELECTRON MICROSCOPYf_angle_d0.883109616
ELECTRON MICROSCOPYf_dihedral_angle_d11.78541983
ELECTRON MICROSCOPYf_chiral_restr0.05113386
ELECTRON MICROSCOPYf_plane_restr0.0067937

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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

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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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