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- PDB-7zah: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiat... -

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Basic information

Entry
Database: PDB / ID: 7zah
TitleCryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA, aIF1A and aIF5B
Components
  • (30S ribosomal protein ...) x 25
  • (50S ribosomal protein ...) x 2
  • (Translation initiation factor ...) x 2
  • 16S rRNA
  • Zn-ribbon RNA-binding protein involved in translation
  • mRNA
  • tRNA-MET
KeywordsTRANSLATION / Initiation complex / translation initiation / small ribosomal subunit / aIF5b
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...intron homing / intein-mediated protein splicing / ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor aIF-2, archaea / Ribosomal protein S17 / 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 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal ...Translation initiation factor aIF-2, archaea / Ribosomal protein S17 / 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 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Ribosomal protein S27ae / 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 / Diphtheria Toxin Repressor; domain 2 / Ribosomal protein S8e, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Intein splicing domain / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding domain, S1, IF1 type / Intein C-terminal splicing region / Translation initiation factor 1A / IF-1 / Intein C-terminal splicing motif profile. / S1 domain IF1 type profile. / Ribosomal protein L7Ae, archaea / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Helicase, Ruva Protein; domain 3 - #50 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Elongation factor Tu domain 2 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / 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 S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic
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 ...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 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Probable translation initiation factor IF-2 / 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 speciesPyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsCoureux, P.D. / Bourgeois, G. / Mechulam, Y. / Schmitt, E. / Kazan, R.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Role of aIF5B in archaeal translation initiation.
Authors: Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt /
Abstract: In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
History
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: 16S 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: 50S ribosomal protein L41e
3: 50S ribosomal protein L7Ae
5: mRNA
4: tRNA-MET
6: Translation initiation factor 1A
7: Translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,032,978104
Polymers1,030,38333
Non-polymers2,59571
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 254

#1: RNA chain 16S rRNA


Mass: 487993.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: GenBank: 5457433
#30: RNA chain mRNA


Mass: 7107.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea)
#31: RNA chain tRNA-MET


Mass: 24833.904 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: GenBank: 1334604293

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30S ribosomal protein ... , 25 types, 25 molecules ABDEFGHIJKLMNOPQRSTUVWXYZ

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


Mass: 22888.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61992
#6: Protein 30S ribosomal protein S4e


Mass: 28246.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1V5
#8: Protein 30S ribosomal protein S6e


Mass: 14029.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1V0
#11: Protein 30S ribosomal protein S8e


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (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 GE5 (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 GE5 (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 GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1A0
#17: Protein 30S ribosomal protein S14 type Z


Mass: 6644.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1U5
#20: Protein 30S ribosomal protein S17e


Mass: 8059.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1T9
#22: Protein 30S ribosomal protein S19e


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


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


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


Mass: 7369.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P61029
#26: Protein 30S ribosomal protein S27ae


Mass: 5992.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: Q9V1U1

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Protein , 1 types, 1 molecules C

#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 GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: G8ZFK7

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50S ribosomal protein ... , 2 types, 2 molecules 03

#28: Protein/peptide 50S ribosomal protein L41e / Large ribosomal subunit protein eL41


Mass: 4910.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U232
#29: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P62008

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Translation initiation factor ... , 2 types, 2 molecules 67

#32: Protein Translation initiation factor 1A / aIF-1A


Mass: 15336.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: eIF1A, aif1A, PYRAB05910, PAB2441 / Strain: GE5 / Orsay / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138
#33: Protein Translation initiation factor 5B


Mass: 69122.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: infB, PYRAB11390, PAB0755 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZK7

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Non-polymers , 5 types, 450 molecules

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


Mass: 24.305 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: Mg
#35: Chemical
ChemComp-ZN / ZINC ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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
1Initiation complex with 30S ribosomal subunit,tRNA, mRNA and initiation factors 1A and 5BCOMPLEX#1-#330MULTIPLE SOURCES
230S and 50S ribosomal proteinsRIBOSOME#1-#291NATURAL
3mRNACOMPLEX#301RECOMBINANT
4tRNA-MET, Translation initiation factor 1A and Translation initiation factor 5BCOMPLEX#31-#331RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Pyrococcus abyssi GE5 (archaea)272844
33Pyrococcus abyssi GE5 (archaea)272844
44Pyrococcus abyssi GE5 (archaea)272844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Synthetic construct (others)32630
24Escherichia coli (E. coli)562
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2000000
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37410 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00873624
ELECTRON MICROSCOPYf_angle_d0.707107265
ELECTRON MICROSCOPYf_dihedral_angle_d13.73232968
ELECTRON MICROSCOPYf_chiral_restr0.04713084
ELECTRON MICROSCOPYf_plane_restr0.0067657

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