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- PDB-7oqy: Cryo-EM structure of the cellular negative regulator TFS4 bound t... -

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Basic information

Entry
Database: PDB / ID: 7oqy
TitleCryo-EM structure of the cellular negative regulator TFS4 bound to the archaeal RNA polymerase
Components
  • (DNA-directed RNA polymerase subunit ...) x 10
  • (DNA-directed RNA polymerase, subunit ...) x 3
  • Conserved protein
KeywordsTRANSCRIPTION / negative regulator / inhibitor / Archaea / Sso TFS4 / trancript cleavage factor
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / defense response to virus / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo4 / Transcription factor S4
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
Saccharolobus solfataricus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsPilotto, S. / Fouqueau, T. / Lukoyanova, N. / Sheppard, C. / Lucas-Staat, S. / Diaz-Santin, L.M. / Matelska, D. / Prangishvili, D. / Cheung, A.C.M. / Werner, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of RNA polymerase inhibition by viral and host factors.
Authors: Simona Pilotto / Thomas Fouqueau / Natalya Lukoyanova / Carol Sheppard / Soizick Lucas-Staat / Luis Miguel Díaz-Santín / Dorota Matelska / David Prangishvili / Alan C M Cheung / Finn Werner /
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution ...RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Nov 3, 2021Group: Data collection
Category: em_admin / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _em_admin.last_update / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.3Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A'
B: DNA-directed RNA polymerase subunit B
C: DNA-directed RNA polymerase subunit A''
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase, subunit F
G: DNA-directed RNA polymerase, subunit G
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Q: Conserved protein
Y: DNA-directed RNA polymerase, subunit M (RpoM-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,52724
Polymers415,68414
Non-polymers84310
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, BS3 was used to cross-link the complex
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area69760 Å2
ΔGint-462 kcal/mol
Surface area136430 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase subunit ... , 10 types, 10 molecules ABCDEHKLNP

#1: Protein DNA-directed RNA polymerase subunit A' / DNA-dependent RNA polymerase subunit RPOA' (RPO1N)


Mass: 99929.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOA' (RPO1N)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P11512, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit B / DNA-dependent RNA polymerase subunit RPOB (RPO2)


Mass: 126647.102 Da / Num. of mol.: 1 / Mutation: V772I natural variant / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOB (RPO2)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P11513, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit A'' / DNA-dependent RNA polymerase subunit RPOA'' (RPO1C)


Mass: 44507.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-dependent RNA polymerase subunit RPOA'' (RPO1C)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P11514, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D / DNA-dependent RNA polymerase subunit RPOD (RPO3)


Mass: 29858.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOD (RPO3)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P39471, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit E / DNA-dependent RNA polymerase subunit RPOE (RPO7)


Mass: 20496.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOE (RPO7)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P39466, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit H / DNA-dependent RNA polymerase subunit RPOH (RPO5)


Mass: 9477.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOH (RPO5)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P11521, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit K / DNA-dependent RNA polymerase subunit RPOK (RPO6)


Mass: 10251.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOK (RPO6)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P39463, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit L / DNA-dependent RNA polymerase subunit RPOL (RPO11)


Mass: 10061.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOL (RPO11)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P46217, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase subunit N / DNA-dependent RNA polymerase subunit RPON (RPO10)


Mass: 7673.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPON (RPO10)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: P39472, DNA-directed RNA polymerase
#12: Protein/peptide DNA-directed RNA polymerase subunit P / DNA-dependent RNA polymerase subunit RPOP (RPO12)


Mass: 5662.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOP (RPO12)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: Q4JAE8, DNA-directed RNA polymerase

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DNA-directed RNA polymerase, subunit ... , 3 types, 3 molecules FGY

#6: Protein DNA-directed RNA polymerase, subunit F / DNA-dependent RNA polymerase subunit RPOF (RPO4)


Mass: 13070.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPOF (RPO4)
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: Q4JB12, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase, subunit G / DNA-dependent RNA polymerase subunit RPOG (RPO8)


Mass: 15292.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-dependent RNA polymerase subunit RPOG (RPO8)
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: rpoG, Saci_0661
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
Production host: Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAY4, DNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerase, subunit M (RpoM-2) / DNA-directed RNA polymerase subunit RpoM-2 (TFS4)


Mass: 10422.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-directed RNA polymerase subunit RpoM-2 (TFS4)
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: rpoM-2, SSO9221 / Plasmid: pET21a+
Details (production host): Cloned within NdeI and XhoI restriction sites with a stop codon at the end of the protein sequence
Production host: Escherichia coli (E. coli) / Strain (production host): DE3 Rosetta2 / References: UniProt: Q97X43, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules Q

#13: Protein Conserved protein / DNA-dependent RNA polymerase subunit RPO13


Mass: 12331.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-dependent RNA polymerase subunit RPO13
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Plasmid details: genetically manipulated to insert an additional copy of Rpo8 with a hexa-his tag at the C-terminus
References: UniProt: Q4JAJ6

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Non-polymers , 3 types, 10 molecules

#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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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

ComponentName: TFS4 bound to the RNA polymerase / Type: COMPLEX / Entity ID: #1-#14 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.414 MDa / Experimental value: YES
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesC8H18N2O4S1
2200 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
4100 microMzinc sulfateZnSO41
55 mMDTTC4H10O2S21
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the sample was applied twice on the grid before vetrification
Specimen supportDetails: the grid was coated with graphene oxide after to be glow discharged and before applying the sample
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 45.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1760
Details: images were collected as movie-stacks of 40 frames in super resolution mode
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3particle selectionLaplacian method
2SerialEMimage acquisition
4GctfCTF correctionwithin Relion
7PHENIX1.15.2model fittingfit to map
9RELION3initial Euler assignment2D classification
10RELION3final Euler assignment3D classification
11RELION3classification3D classification
12RELION33D reconstruction3D refinement
13PHENIX1.19.2model refinementreal space refinement
14Coot0.8.9.1model refinementmanual editing when needed
Image processingDetails: All images were binned 2x, aligned and summed by using MotionCor2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1161535
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350682 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: CC
Atomic model buildingPDB-ID: 7OK0

7ok0


Accession code: 7OK0 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328492
ELECTRON MICROSCOPYf_angle_d0.48938454
ELECTRON MICROSCOPYf_dihedral_angle_d4.5293889
ELECTRON MICROSCOPYf_chiral_restr0.0454382
ELECTRON MICROSCOPYf_plane_restr0.0044926

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