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- PDB-7okx: Structure of active transcription elongation complex Pol II-DSIF ... -

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Entry
Database: PDB / ID: 7okx
TitleStructure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5)-ELL2-EAF1 (composite structure)
Components
  • (DNA-directed RNA polymerase II subunit ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (RNA polymerase II subunit ...) x 2
  • DNA-directed RNA polymerase subunit beta
  • ELL-associated factor 1
  • Non-template DNA
  • RNA
  • RNA polymerase II elongation factor ELL2
  • RNA_pol_L_2 domain-containing protein
  • Template DNA
  • Transcription elongation factor SPT5
KeywordsTRANSCRIPTION / Pol II / Super elongation complex / ELL2 / EAF1
Function / homology
Function and homology information


super elongation complex / negative regulation of DNA-templated transcription, elongation / : / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events ...super elongation complex / negative regulation of DNA-templated transcription, elongation / : / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / 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 / transcription elongation factor 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / organelle membrane / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / positive regulation of translational initiation / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III complex / Cajal body / transcription-coupled nucleotide-excision repair / intercellular bridge / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / cis-regulatory region sequence-specific DNA binding / : / 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 / positive regulation of RNA splicing / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / P-body / ribonucleoside binding / : / : / : / : / : / : / fibrillar center / DNA-directed RNA polymerase / single-stranded DNA binding / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / hydrolase activity / protein dimerization activity / nuclear speck / nuclear body / protein heterodimerization activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / nucleotide binding / intracellular membrane-bounded organelle / DNA-templated transcription
Similarity search - Function
Transcription elongation factor Eaf, N-terminal / EAF family / RNA polymerase II transcription elongation factor / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / E3 ubiquitin-protein ligase ELL-like ...Transcription elongation factor Eaf, N-terminal / EAF family / RNA polymerase II transcription elongation factor / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / E3 ubiquitin-protein ligase ELL-like / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 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 / RNA-binding domain, S1 / 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 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / RNA polymerase Rpb1, domain 3 / NusG, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / 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 / Gyrase A; domain 2 / RNA polymerase RBP11 / 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 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS)
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 ...DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / RNA polymerase II elongation factor ELL2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / ELL-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV whole-genome vector AA1305#18 (others)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, Y. / Vos, S.M. / Dienemann, C. / Ninov, M. / Urlaub, H. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)Advanced Grant CHROMATRANS 693023 Germany
German Research Foundation (DFG)SFB1286 Germany
CitationJournal: Mol Cell / Year: 2021
Title: Allosteric transcription stimulation by RNA polymerase II super elongation complex.
Authors: Ying Chen / Seychelle M Vos / Christian Dienemann / Momchil Ninov / Henning Urlaub / Patrick Cramer /
Abstract: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we ...The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 1, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RNA polymerase II subunit D
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerase II subunit F
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: RNA_pol_L_2 domain-containing protein
L: RNA polymerase II subunit K
M: RNA polymerase II elongation factor ELL2
N: Non-template DNA
O: ELL-associated factor 1
P: RNA
T: Template DNA
Z: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)798,28827
Polymers797,74018
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area83900 Å2
ΔGint-424 kcal/mol
Surface area163880 Å2

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Components

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DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACEFGI

#1: 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
#3: 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
#5: 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
#6: 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
#7: 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: I3LJZ9
#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

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Protein , 5 types, 5 molecules BKMOZ

#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 142426.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase
#11: Protein RNA_pol_L_2 domain-containing protein


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25
#13: Protein RNA polymerase II elongation factor ELL2


Mass: 72435.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00472
#15: Protein ELL-associated factor 1


Mass: 29075.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EAF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96JC9
#18: 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 BL21(DE3) (bacteria) / References: UniProt: O00267

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

#4: Protein RNA polymerase II subunit D


Mass: 20962.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4
#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

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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: A0A4X1ULF2
#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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DNA chain , 2 types, 2 molecules NT

#14: DNA chain Non-template DNA


Mass: 14672.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: synthetic construct
#17: DNA chain Template DNA


Mass: 14934.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: synthetic construct

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RNA chain , 1 types, 1 molecules P

#16: RNA chain RNA


Mass: 15076.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last nucleotide (A47) was extended at the 3' of the original RNA scaffold (46-mer) during complex assembly in the presence of ATP.
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: synthetic construct

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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: isolated from a genetically manipulated source
Formula: Mg
#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn

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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
IDNameTypeDetailsEntity IDParent-IDSource
1Transcription elongation complex of RNA polymerase II with elongation factors DSIF(SPT5-KOW5)and ELL2-EAF1COMPLEXHuman SPT4 protein is also part of the complex assembly, however, the density of SPT4 was not visible in this map.#1-#180MULTIPLE SOURCES
2RNA polymeraseCOMPLEX#1-#121NATURAL
3elongation and association factorsCOMPLEX#13, #151RECOMBINANT
4DNA and RNACOMPLEX#14, #16-#171RECOMBINANT
5Transcription elongation factor SPT5COMPLEX#181RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34HIV whole-genome vector AA1305#18 (others)672471
45Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Trichoplusia ni (cabbage looper)7111
24synthetic construct (others)32630
35Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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
Image recordingElectron dose: 43.21 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364641
Details: This is a composite map of three focused maps: map 5, 6, and 7.
Symmetry type: POINT
Atomic model buildingSpace: REAL

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