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- EMDB-14697: M. tuberculosis RNA polymerase in complex with sigma-b initiation... -

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Entry
Database: EMDB / ID: EMD-14697
TitleM. tuberculosis RNA polymerase in complex with sigma-b initiation factor: octameric assembly of (alpha)2-beta-beta'-omega-sigB protomers.
Map data
Sample
  • Complex: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor: octameric assembly of (alpha)2-beta-beta'-omega-sigB protomers.
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma factor SigB
KeywordsRNA polymerase / self-assembly / octamer / tuberculosis / stress response / hibernation / TRANSCRIPTION
Function / homology
Function and homology information


Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic ...Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 ...Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor SigB / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsBron P / Trapani S / Lai Kee Him J / Brodolin K / Morichaud Z / Vishwakarma R
Funding support France, 3 items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0025 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
Strasbourg INSTRUCT-ERIC CentrePID: 1309
Citation
Journal: Nat Commun / Year: 2023
Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization.
Authors: Zakia Morichaud / Stefano Trapani / Rishi K Vishwakarma / Laurent Chaloin / Corinne Lionne / Joséphine Lai-Kee-Him / Patrick Bron / Konstantin Brodolin /
Abstract: Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression ...Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σ factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σ is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization
Authors: Morichaud Z / Trapani S / Vishwakarma R / Chaloin L / Lionne C / Lai-Kee-Him J / Bron P / Brodolin K
History
DepositionMar 31, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14697.png

Downloads & links

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Map

FileDownload / File: emd_14697.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0043945448 - 0.01990391
Average (Standard dev.)0.00006783778 (±0.0013558471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_14697_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_14697_half_map_2.map
Projections & Slices
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Sample components

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Entire : M. tuberculosis RNA polymerase in complex with sigma-b initiation...

EntireName: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor: octameric assembly of (alpha)2-beta-beta'-omega-sigB protomers.
Components
  • Complex: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor: octameric assembly of (alpha)2-beta-beta'-omega-sigB protomers.
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma factor SigB

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Supramolecule #1: M. tuberculosis RNA polymerase in complex with sigma-b initiation...

SupramoleculeName: M. tuberculosis RNA polymerase in complex with sigma-b initiation factor: octameric assembly of (alpha)2-beta-beta'-omega-sigB protomers.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 402 KDa

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEED EPVTMYLRKQ GPGEVTAGDI VPPAGVTVHN PGMHIATLND KGKLEVELVV ERGRGYVPAV QNRASGAEIG RIPVDSIYSP ...String:
MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEED EPVTMYLRKQ GPGEVTAGDI VPPAGVTVHN PGMHIATLND KGKLEVELVV ERGRGYVPAV QNRASGAEIG RIPVDSIYSP VLKVTYKVDA TRVEQRTDFD KLILDVETKN SISPRDALAS AGKTLVELFG LARELNVEAE GIEIGPSPAE ADHIASFALP IDDLDLTVRS YNCLKREGVH TVGELVARTE SDLLDIRNFG QKSIDEVKIK LHQLGLSLKD SPPSFDPSEV AGYDVATGTW STEGAYDEQD YAETEQL

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVLADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYELS PIEDFSGSMS LSFSDPRFDD VKAPVDECKD KDMTYAAPLF VTAEFINNNT GEIKSQTVFM GDFPMMTEKG TFIINGTERV ...String:
MVLADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYELS PIEDFSGSMS LSFSDPRFDD VKAPVDECKD KDMTYAAPLF VTAEFINNNT GEIKSQTVFM GDFPMMTEKG TFIINGTERV VVSQLVRSPG VYFDETIDKS TDKTLHSVKV IPSRGAWLEF DVDKRDTVGV RIDRKRRQPV TVLLKALGWT SEQIVERFGF SEIMRSTLEK DNTVGTDEAL LDIYRKLRPG EPPTKESAQT LLENLFFKEK RYDLARVGRY KVNKKLGLHV GEPITSSTLT EEDVVATIEY LVRLHEGQTT MTVPGGVEVP VETDDIDHFG NRRLRTVGEL IQNQIRVGMS RMERVVRERM TTQDVEAITP QTLINIRPVV AAIKEFFGTS QLSQFMDQNN PLSGLTHKRR LSALGPGGLS RERAGLEVRD VHPSHYGRMC PIETPEGPNI GLIGSLSVYA RVNPFGFIET PYRKVVDGVV SDEIVYLTAD EEDRHVVAQA NSPIDADGRF VEPRVLVRRK AGEVEYVPSS EVDYMDVSPR QMVSVATAMI PFLEHDDANR ALMGANMQRQ AVPLVRSEAP LVGTGMELRA AIDAGDVVVA EESGVIEEVS ADYITVMHDN GTRRTYRMRK FARSNHGTCA NQCPIVDAGD RVEAGQVIAD GPCTDDGEMA LGKNLLVAIM PWEGHNYEDA IILSNRLVEE DVLTSIHIEE HEIDARDTKL GAEEITRDIP NISDEVLADL DERGIVRIGA EVRDGDILVG KVTPKGETEL TPEERLLRAI FGEKAREVRD TSLKVPHGES GKVIGIRVFS REDEDELPAG VNELVRVYVA QKRKISDGDK LAGRHGNKGV IGKILPVEDM PFLADGTPVD IILNTHGVPR RMNIGQILET HLGWCAHSGW KVDAAKGVPD WAARLPDELL EAQPNAIVST PVFDGAQEAE LQGLLSCTLP NRDGDVLVDA DGKAMLFDGR SGEPFPYPVT VGYMYIMKLH HLVDDKIHAR STGPYSMITQ QPLGGKAQFG GQRFGEMECW AMQAYGAAYT LQELLTIKSD DTVGRVKVYE AIVKGENIPE PGIPESFKVL LKELQSLCLN VEVLSSDGAA IELREGEDED LERAAANLGI NLSRNESASV EDLA

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VNFFDELRIG LATAEDIRQW SYGEVKKPET INYRTLKPEK DGLFCEKIFG PTRDWECYCG KYKRVRFKGI ICERCGVEVT RAKVRRERMG HIELAAPVTH IWYFKGVPSR LGYLLDLAPK DLEKIIYFAA YVITSVDEEM RHNELSTLEA EMAVERKAVE DQRDGELEAR ...String:
VNFFDELRIG LATAEDIRQW SYGEVKKPET INYRTLKPEK DGLFCEKIFG PTRDWECYCG KYKRVRFKGI ICERCGVEVT RAKVRRERMG HIELAAPVTH IWYFKGVPSR LGYLLDLAPK DLEKIIYFAA YVITSVDEEM RHNELSTLEA EMAVERKAVE DQRDGELEAR AQKLEADLAE LEAEGAKADA RRKVRDGGER EMRQIRDRAQ RELDRLEDIW STFTKLAPKQ LIVDENLYRE LVDRYGEYFT GAMGAESIQK LIENFDIDAE AESLRDVIRN GKGQKKLRAL KRLKVVAAFQ QSGNSPMGMV LDAVPVIPPE LRPMVQLDGG RFATSDLNDL YRRVINRNNR LKRLIDLGAP EIIVNNEKRM LQESVDALFD NGRRGRPVTG PGNRPLKSLS DLLKGKQGRF RQNLLGKRVD YSGRSVIVVG PQLKLHQCGL PKLMALELFK PFVMKRLVDL NHAQNIKSAK RMVERQRPQV WDVLEEVIAE HPVLLNRAPT LHRLGIQAFE PMLVEGKAIQ LHPLVCEAFN ADFDGDQMAV HLPLSAEAQA EARILMLSSN NILSPASGRP LAMPRLDMVT GLYYLTTEVP GDTGEYQPAS GDHPETGVYS SPAEAIMAAD RGVLSVRAKI KVRLTQLRPP VEIEAELFGH SGWQPGDAWM AETTLGRVMF NELLPLGYPF VNKQMHKKVQ AAIINDLAER YPMIVVAQTV DKLKDAGFYW ATRSGVTVSM ADVLVPPRKK EILDHYEERA DKVEKQFQRG ALNHDERNEA LVEIWKEATD EVGQALREHY PDDNPIITIV DSGATGNFTQ TRTLAGMKGL VTNPKGEFIP RPVKSSFREG LTVLEYFINT HGARKGLADT ALRTADSGYL TRRLVDVSQD VIVREHDCQT ERGIVVELAE RAPDGTLIRD PYIETSAYAR TLGTDAVDEA GNVIVERGQD LGDPEIDALL AAGITQVKVR SVLTCATSTG VCATCYGRSM ATGKLVDIGE AVGIVAAQSI GEPGTQLTMR TFHQGGVGED ITGGLPRVQE LFEARVPRGK APIADVTGRV RLEDGERFYK ITIVPDDGGE EVVYDKISKR QRLRVFKHED GSERVLSDGD HVEVGQQLME GSADPHEVLR VQGPREVQIH LVREVQEVYR AQGVSIHDKH IEVIVRQMLR RVTIIDSGST EFLPGSLIDR AEFEAENRRV VAEGGEPAAG RPVLMGITKA SLATDSWLSA ASFQETTRVL TDAAINCRSD KLNGLKENVI IGKLIPAGTG INRYRNIAVQ PTEEARAAAY TIPSYEDQYY SPDFGAATGA AVPLDDYGYS DYRHHHHHH

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQEK PLSIALREIH ADLLEHTEGE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma factor SigB

MacromoleculeName: RNA polymerase sigma factor SigB / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MADAPTRATT SRVDSDLDAQ SPAADLVRVY LNGIGKTALL NAAGEVELAK RIEAGLYAEH LLETRKRLGE NRKRDLAAVV RDGEAARRHL LEANLRLVVS LAKRYTGRGM PLLDLIQEGN LGLIRAMEKF DYTKGFKFST YATWWIRQAI ...String:
MGSSHHHHHH SSGLVPRGSH MADAPTRATT SRVDSDLDAQ SPAADLVRVY LNGIGKTALL NAAGEVELAK RIEAGLYAEH LLETRKRLGE NRKRDLAAVV RDGEAARRHL LEANLRLVVS LAKRYTGRGM PLLDLIQEGN LGLIRAMEKF DYTKGFKFST YATWWIRQAI TRGMADQSRT IRLPVHLVEQ VNKLARIKRE MHQHLGREAT DEELAAESGI PIDKINDLLE HSRDPVSLDM PVGSEEEAPL GDFIEDAEAM SAENAVIAEL LHTDIRSVLA TLDEREHQVI RLRFGLDDGQ PRTLDQIGKL FGLSRERVRQ IERDVMSKLR HGERADRLRS YAS

UniProtKB: RNA polymerase sigma factor SigB

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.21 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mmol/LHEPES
150.0 mmol/Lsodium chlorideNaClSodium chloride
5.0 mmol/Lmagnesium sulfateMgSO4
GridModel: Quantifoil R2/2 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3064 / Average exposure time: 8.0 sec. / Average electron dose: 49.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 94141
DetailsMovie frames were aligned, dose-weighted, binned by two and averaged using Motioncor2 (Zheng S.Q Nat. Methods. 2017; 14: 331-332). Movie sums were used for contrast transfer function (CTF) estimation with Gctf (Zhang K. J. Struct. Biol. 2016; 193: 1-12)
FSC plot (resolution estimation)

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