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- EMDB-14974: Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase ho... -

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Basic information

Entry
Database: EMDB / ID: EMD-14974
TitleCryo-EM structure of Mycobacterium tuberculosis RNA polymerase holoenzyme dimer comprising sigma factor SigB, conformation 2
Map dataRNA polymerase dimer conformation 2
Sample
  • Complex: RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • 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
KeywordsDNA-dependent RNA polymerase / alternative sigma / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase core enzyme binding / 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 / response to heat ...RNA polymerase core enzyme binding / 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 / response to heat / response to hypoxia / protein dimerization activity / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / positive regulation of 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 H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.75 Å
AuthorsBrodolin K
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0025 France
Citation
Journal: Nucleic Acids Res / Year: 2014
Title: Mycobacterium RbpA cooperates with the stress-response σB subunit of RNA polymerase in promoter DNA unwinding.
Authors: Yangbo Hu / Zakia Morichaud / Ayyappasamy Sudalaiyadum Perumal / Françoise Roquet-Baneres / Konstantin Brodolin /
Abstract: RbpA, a transcriptional activator that is essential for Mycobacterium tuberculosis replication and survival during antibiotic treatment, binds to RNA polymerase (RNAP) in the absence of promoter DNA. ...RbpA, a transcriptional activator that is essential for Mycobacterium tuberculosis replication and survival during antibiotic treatment, binds to RNA polymerase (RNAP) in the absence of promoter DNA. It has been hypothesized that RbpA stimulates housekeeping gene expression by promoting assembly of the σ(A) subunit with core RNAP. Here, using a purified in vitro transcription system of M. tuberculosis, we show that RbpA functions in a promoter-dependent manner as a companion of RNAP essential for promoter DNA unwinding and formation of the catalytically active open promoter complex (RPo). Screening for RbpA activity using a full panel of the M. tuberculosis σ subunits demonstrated that RbpA targets σ(A) and stress-response σ(B), but not the alternative σ subunits from the groups 3 and 4. In contrast to σ(A), the σ(B) subunit activity displayed stringent dependency upon RbpA. These results suggest that RbpA-dependent control of RPo formation provides a mechanism for tuning gene expression during the switch between different physiological states, and in the stress response.
#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
DepositionMay 12, 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_14974.png

Downloads & links

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Map

FileDownload / File: emd_14974.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA polymerase dimer conformation 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.5290195 - 1.3410263
Average (Standard dev.)-0.0020605747 (±0.041922376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_14974_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_14974_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2

EntireName: RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2
Components
  • Complex: RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • 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: RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2

SupramoleculeName: RNA polymerase holoenzyme dimer with sigma factor sigB, conformation 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: RNA polymerase holoenzyme assembled from individually expressed RNA polymerase core and sigma factor sigB
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 800 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 H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 #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 H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 beta

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Macromolecule #4: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 4 / Details: contains C-terminal 6xHis-tag / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 #5: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQEK PLSIALREIH ADLLEHTEGE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #6: RNA polymerase sigma factor SigB

MacromoleculeName: RNA polymerase sigma factor SigB / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

Concentration1.4 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3064 / Average electron dose: 49.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 254380
Startup modelType of model: NONE / Details: ab-into reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.1) / Number images used: 48593
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7pp4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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