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Entry
Database: PDB / ID: 8p4e
TitleStructural insights into human co-transcriptional capping - structure 5
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (RNA polymerase II subunit ...) x 2
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
  • DNA (26-MER)
  • DNA (35-MER)
  • DNA-directed RNA polymerase subunit beta
  • RNA (5'-D(*(MGT))-R(P*GP*AP*CP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')
  • Transcription elongation factor SPT5
  • mRNA-capping enzyme
KeywordsTRANSCRIPTION / rna polymerase II / capping
Function / homology
Function and homology information


RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / mRNA 5'-triphosphate monophosphatase activity / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events ...RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / mRNA 5'-triphosphate monophosphatase activity / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / phosphoprotein phosphatase activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 7-methylguanosine mRNA capping / Tat-mediated elongation of the HIV-1 transcript / transcription by RNA polymerase III / transcription by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA processing / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / positive regulation of RNA splicing / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / fibrillar center / mRNA processing / mRNA guanylyltransferase activity / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / mRNA guanylyltransferase / methyltransferase cap1 / methylation / methyltransferase cap1 activity / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / hydrolase activity / protein dimerization activity / nuclear speck / protein heterodimerization activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / nucleotide binding / intracellular membrane-bounded organelle / DNA-templated transcription
Similarity search - Function
RrmJ-type ribose 2-O-methyltransferase domain / : / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / Spt5, KOW domain repeat 6 ...RrmJ-type ribose 2-O-methyltransferase domain / : / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Dual specificity phosphatase, catalytic domain / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Gyrase A; domain 2 - #140 / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / NusG, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / WW/rsp5/WWP domain signature. / DNA-directed RNA polymerase II subunit Rpb4-like / Domain with 2 conserved Trp (W) residues / WW domain / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / mRNA-capping enzyme / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGarg, G. / Dienemann, C. / Farnung, L. / Schwarz, J. / Linden, A. / Urlaub, H. / Cramer, P.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)693023European Union
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Mol Cell / Year: 2023
Title: Structural insights into human co-transcriptional capping.
Authors: Gaurika Garg / Christian Dienemann / Lucas Farnung / Juliane Schwarz / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights ...Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
History
DepositionMay 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _em_admin.last_update / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: Transcription elongation factor SPT5
M: mRNA-capping enzyme
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerase II subunit F
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-a
L: RNA polymerase II subunit K
D: RNA polymerase II subunit D
G: DNA-directed RNA polymerase II subunit RPB7
O: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
P: RNA (5'-D(*(MGT))-R(P*GP*AP*CP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')
N: DNA (26-MER)
T: DNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)828,91827
Polymers828,37118
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules ZMBO

#1: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121145.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / References: UniProt: O00267
#2: Protein mRNA-capping enzyme / HCAP1 / HCE


Mass: 68655.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNGTT, CAP1A / Production host: Escherichia coli (E. coli)
References: UniProt: O60942, mRNA 5'-phosphatase, mRNA guanylyltransferase
#4: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase
#15: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 / Cap methyltransferase 1 / Cap1 2'O-ribose methyltransferase 1 / MTr1 / hMTr1 / FtsJ ...Cap methyltransferase 1 / Cap1 2'O-ribose methyltransferase 1 / MTr1 / hMTr1 / FtsJ methyltransferase domain-containing protein 2 / Interferon-stimulated gene 95 kDa protein / ISG95


Mass: 95454.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMTR1, FTSJD2, KIAA0082, MTR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1G2, methyltransferase cap1

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

#3: Protein DNA-directed RNA polymerase II subunit RPB1


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P11414
#5: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#6: Protein DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7
#7: Protein DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / II / and III subunit RPABC2 / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899
#11: Protein DNA-directed RNA polymerase II subunit RPB11-a


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4
#14: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ

#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0

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RNA polymerase II subunit ... , 2 types, 2 molecules LD

#12: Protein RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51
#13: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4

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RNA chain , 1 types, 1 molecules P

#16: RNA chain RNA (5'-D(*(MGT))-R(P*GP*AP*CP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')


Mass: 6958.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules NT

#17: DNA chain DNA (26-MER)


Mass: 8050.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain DNA (35-MER)


Mass: 10721.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#19: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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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

ComponentName: Pol II - TPase complex / Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48148 / Symmetry type: POINT

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