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- PDB-6i84: Structure of transcribing RNA polymerase II-nucleosome complex -

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Entry
Database: PDB / ID: 6i84
TitleStructure of transcribing RNA polymerase II-nucleosome complex
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • DNA (158-MER)
  • DNA (170-MER)
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • RNA
KeywordsTRANSCRIPTION / Nucleosome / elongation / chromatin / RNA polymerase II
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase III transcription / positive regulation of translational initiation / RNA polymerase I activity ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase III transcription / positive regulation of translational initiation / RNA polymerase I activity / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / mRNA cleavage / RNA polymerase II, core complex / transcription by RNA polymerase I / transcription by RNA polymerase III / transcription, RNA-templated / termination of RNA polymerase II transcription / translation initiation factor binding / ribonucleoside binding / single-stranded RNA binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription, initiation / P-body / nucleosome / ribosome biogenesis / transcription-coupled nucleotide-excision repair / cytoplasmic stress granule / single-stranded DNA binding / translesion synthesis / transcription by RNA polymerase II / transcription initiation from RNA polymerase II promoter / nucleic acid binding / protein dimerization activity / mRNA binding / cellular response to DNA damage stimulus / nucleolus / nucleotide binding / protein heterodimerization activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
C-terminus of histone H2A / Histone H2A conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Histone H2A, C-terminal domain / Pol II subunit B9, C-terminal zinc ribbon / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit ...C-terminus of histone H2A / Histone H2A conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Histone H2A, C-terminal domain / Pol II subunit B9, C-terminal zinc ribbon / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / CENP-T/Histone H4, histone fold / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, insert domain / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / HRDC-like superfamily / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Histone H4, conserved site / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase RBP11 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb4 / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb6 / S1 RNA binding domain / RNA polymerase Rpb8 / RNA polymerase Rpb2, domain 4 / Transcription factor S-II (TFIIS) / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA directed RNA polymerase, 7 kDa subunit / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 6 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / Histone-fold / Histone H2A/H2B/H3 / RNA polymerase, Rpb5, N-terminal / RNA polymerase, beta subunit, conserved site / Histone H3/CENP-A / DNA-directed RNA polymerase, subunit N/Rpb10 / Histone H2B / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase, subunit H/Rpb5 C-terminal / Zinc finger, TFIIS-type / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase, M/15kDa subunit / Histone H4 / Histone H2A / S1 domain / TATA box binding protein associated factor (TAF) / RNA polymerase, Rpb8 / RNA polymerase, alpha subunit / RNA polymerase subunit RPB4/RPC9 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / Histone H3.2 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Histone H2A type 1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / Histone H3.2 / Histone H4 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / Histone H2B 1.1
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (baker's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsFarnung, L. / Vos, S.M. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
European Research CouncilTransregulon (693023) Germany
European Molecular Biology OrganizationALTF-725-2014 Germany
German Research FoundationSFB1064 Germany
German Research FoundationSFB860 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structure of transcribing RNA polymerase II-nucleosome complex.
Authors: Lucas Farnung / Seychelle M Vos / Patrick Cramer /
Abstract: Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of ...Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
M: Histone H3.2
Q: Histone H2A type 1
V: Histone H2A type 1
T: DNA (170-MER)
N: DNA (158-MER)
O: Histone H4
R: Histone H2B 1.1
S: Histone H3.2
U: Histone H4
W: Histone H2B 1.1
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
P: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,09132
Polymers731,54323
Non-polymers5489
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein , 4 types, 8 molecules MSQVOURW

#1: Protein Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#6: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules TN

#3: DNA chain DNA (170-MER)


Mass: 52041.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (158-MER)


Mass: 49537.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#7: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04050, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P08518, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 38809.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P16370
#10: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20433
#13: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P34087
#15: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P27999
#17: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20434
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20435
#14: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20436
#16: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22139
#18: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40422

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RNA chain , 1 types, 1 molecules P

#19: RNA chain RNA /


Mass: 3137.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#20: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#21: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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
1Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX1,2,3,4,5,6,7, 9,10,11,12,13,14,16,17,18,19,8,150MULTIPLE SOURCES
2Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX1,2,5,61RECOMBINANT
3Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX7,8,9,10,11,12,13,14,16,17,18,151NATURAL
4Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX3,4,191NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Xenopus laevis (African clawed frog)8355
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
34synthetic construct (others)32630
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil, UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / 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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Warp1.0.5CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49703 / Symmetry type: POINT

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