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Yorodumi- EMDB-36453: Structural basis of transcriptional activation by the OmpR/PhoB-f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36453 | ||||||||||||
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Title | Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | PmrA / RNA polymerase / cryo-EM / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / phosphorelay signal transduction system / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / phosphorelay signal transduction system / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli BL21(DE3) (bacteria) / synthetic construct (others) / Klebsiella pneumoniae JM45 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||||||||
Authors | Lou Y-C / Huang H-Y / Chen C / Wu K-P | ||||||||||||
Funding support | Taiwan, 3 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA. Authors: Yuan-Chao Lou / Hsuan-Yu Huang / Hsin-Hong Yeh / Wei-Hung Chiang / Chinpan Chen / Kuen-Phon Wu / Abstract: PmrA, an OmpR/PhoB-family response regulator, triggers gene transcription responsible for polymyxin resistance in bacteria by recognizing promoters where the canonical-35 element is replaced by the ...PmrA, an OmpR/PhoB-family response regulator, triggers gene transcription responsible for polymyxin resistance in bacteria by recognizing promoters where the canonical-35 element is replaced by the pmra-box, representing the PmrA recognition sequence. Here, we report a cryo-electron microscopy (cryo-EM) structure of a bacterial PmrA-dependent transcription activation complex (TAC) containing a PmrA dimer, an RNA polymerase σ70 holoenzyme (RNAPH) and the pbgP promoter DNA. Our structure reveals that the RNAPH mainly contacts the PmrA C-terminal DNA-binding domain (DBD) via electrostatic interactions and reorients the DBD three base pairs upstream of the pmra-box, resulting in a dynamic TAC conformation. In vivo assays show that the substitution of the DNA-recognition residue eliminated its transcriptional activity, while variants with altered RNAPH-interacting residues resulted in enhanced transcriptional activity. Our findings suggest that both PmrA recognition-induced DNA distortion and PmrA promoter escape play crucial roles in its transcriptional activation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36453.map.gz | 398.7 MB | EMDB map data format | |
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Header (meta data) | emd-36453-v30.xml emd-36453.xml | 27.4 KB 27.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36453_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_36453.png | 91.4 KB | ||
Filedesc metadata | emd-36453.cif.gz | 8.6 KB | ||
Others | emd_36453_additional_1.map.gz emd_36453_half_map_1.map.gz emd_36453_half_map_2.map.gz | 398.2 MB 392 MB 392 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36453 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36453 | HTTPS FTP |
-Related structure data
Related structure data | 8jo2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36453.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: local focus map of PmrA-DNA complex
File | emd_36453_additional_1.map | ||||||||||||
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Annotation | local focus map of PmrA-DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36453_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36453_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structural basis of transcriptional activation by the OmpR/PhoB-f...
Entire | Name: Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA |
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Components |
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-Supramolecule #1: Structural basis of transcriptional activation by the OmpR/PhoB-f...
Supramolecule | Name: Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: DNA (65-MER)
Macromolecule | Name: DNA (65-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 20.107924 KDa |
Sequence | String: (DA)(DG)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DA) (DA)(DT)(DT)(DT)(DC)(DT)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DA)(DT)(DC)(DC)(DT)(DA) (DA)(DG)(DC)(DA)(DA)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DT)(DA)(DA)(DT)(DG) ...String: (DA)(DG)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DA) (DA)(DT)(DT)(DT)(DC)(DT)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DA)(DT)(DC)(DC)(DT)(DA) (DA)(DG)(DC)(DA)(DA)(DG)(DG)(DT)(DC)(DG) (DT) (DA)(DT)(DA)(DA)(DT)(DG)(DT)(DG) (DT)(DG)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DA) (DC)(DG) (DC)(DG)(DG)(DC)(DG) |
-Macromolecule #2: DNA (65-MER)
Macromolecule | Name: DNA (65-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 20.027875 KDa |
Sequence | String: (DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DA) (DG)(DA)(DC)(DT)(DC)(DG)(DT)(DA)(DG)(DG) (DA)(DT)(DT)(DA)(DT)(DA)(DC)(DG)(DA) (DC)(DC)(DT)(DT)(DG)(DC)(DT)(DT)(DA)(DG) (DG) (DA)(DT)(DA)(DA)(DT)(DA) ...String: (DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DA) (DG)(DA)(DC)(DT)(DC)(DG)(DT)(DA)(DG)(DG) (DA)(DT)(DT)(DA)(DT)(DA)(DC)(DG)(DA) (DC)(DC)(DT)(DT)(DG)(DC)(DT)(DT)(DA)(DG) (DG) (DA)(DT)(DA)(DA)(DT)(DA)(DT)(DT) (DA)(DA)(DG)(DA)(DA)(DA)(DT)(DT)(DA)(DA) (DT)(DA) (DT)(DT)(DT)(DC)(DT) |
-Macromolecule #3: DNA-directed RNA polymerase subunit alpha
Macromolecule | Name: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 36.55868 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI ...String: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI GRLLVDACYS PVERIAYNVE AARVEQRTDL DKLVIEMETN GTIDPEEAIR RAATILAEQL EAFVDLRDVR QP EVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK KSLTEIKDVL ASRGLSLGMR LEN WPPASI ADE UniProtKB: DNA-directed RNA polymerase subunit alpha |
-Macromolecule #4: DNA-directed RNA polymerase subunit beta
Macromolecule | Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 150.820875 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG ...String: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG KVLYNARIIP YRGSWLDFEF DPKDNLFVRI DRRRKLPATI ILRALNYTTE QILDLFFEKV IFEIRDNKLQ ME LVPERLR GETASFDIEA NGKVYVEKGR RITARHIRQL EKDDVKLIEV PVEYIAGKVV AKDYIDESTG ELICAANMEL SLD LLAKLS QSGHKRIETL FTNDLDHGPY ISETLRVDPT NDRLSALVEI YRMMRPGEPP TREAAESLFE NLFFSEDRYD LSAV GRMKF NRSLLREEIE GSGILSKDDI IDVMKKLIDI RNGKGEVDDI DHLGNRRIRS VGEMAENQFR VGLVRVERAV KERLS LGDL DTLMPQDMIN AKPISAAVKE FFGSSQLSQF MDQNNPLSEI THKRRISALG PGGLTRERAG FEVRDVHPTH YGRVCP IET PEGPNIGLIN SLSVYAQTNE YGFLETPYRK VTDGVVTDEI HYLSAIEEGN YVIAQANSNL DEEGHFVEDL VTCRSKG ES SLFSRDQVDY MDVSTQQVVS VGASLIPFLE HDDANRALMG ANMQRQAVPT LRADKPLVGT GMERAVAVDS GVTAVAKR G GVVQYVDASR IVIKVNEDEM YPGEAGIDIY NLTKYTRSNQ NTCINQMPCV SLGEPVERGD VLADGPSTDL GELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTP KGETQLTPEE KLLRAIFGEK ASDVKDSSLR VPNGVSGTVI DVQVFTRDGV EKDKRALEIE EMQLKQAKKD L SEELQILE AGLFSRIRAV LVAGGVEAEK LDKLPRDRWL ELGLTDEEKQ NQLEQLAEQY DELKHEFEKK LEAKRRKITQ GD DLAPGVL KIVKVYLAVK RRIQPGDKMA GRHGNKGVIS KINPIEDMPY DENGTPVDIV LNPLGVPSRM NIGQILETHL GMA AKGIGD KINAMLKQQQ EVAKLREFIQ RAYDLGADVR QKVDLSTFSD EEVMRLAENL RKGMPIATPV FDGAKEAEIK ELLK LGDLP TSGQIRLYDG RTGEQFERPV TVGYMYMLKL NHLVDDKMHA RSTGSYSLVT QQPLGGKAQF GGQRFGEMEV WALEA YGAA YTLQEMLTVK SDDVNGRTKM YKNIVDGNHQ MEPGMPESFN VLLKEIRSLG INIELEDE UniProtKB: DNA-directed RNA polymerase subunit beta |
-Macromolecule #5: DNA-directed RNA polymerase subunit beta'
Macromolecule | Name: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 155.366781 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA ...String: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR ERMGHIELAS PTAHIWFLKS LPSRIGLLLD MPLRDIERVL YFESYVVIEG GMTNLERQQI L TEEQYLDA LEEFGDEFDA KMGAEAIQAL LKSMDLEQEC EQLREELNET NSETKRKKLT KRIKLLEAFV QSGNKPEWMI LT VLPVLPP DLRPLVPLDG GRFATSDLND LYRRVINRNN RLKRLLDLAA PDIIVRNEKR MLQEAVDALL DNGRRGRAIT GSN KRPLKS LADMIKGKQG RFRQNLLGKR VDYSGRSVIT VGPYLRLHQC GLPKKMALEL FKPFIYGKLE LRGLATTIKA AKKM VEREE AVVWDILDEV IREHPVLLNR APTLHRLGIQ AFEPVLIEGK AIQLHPLVCA AYNADFDGDQ MAVHVPLTLE AQLEA RALM MSTNNILSPA NGEPIIVPSQ DVVLGLYYMT RDCVNAKGEG MVLTGPKEAE RLYRSGLASL HARVKVRITE YEKDAN GEL VAKTSLKDTT VGRAILWMIV PKGLPYSIVN QALGKKAISK MLNTCYRILG LKPTVIFADQ IMYTGFAYAA RSGASVG ID DMVIPEKKHE IISEAEAEVA EIQEQFQSGL VTAGERYNKV IDIWAAANDR VSKAMMDNLQ TETVINRDGQ EEKQVSFN S IYMMADSGAR GSAAQIRQLA GMRGLMAKPD GSIIETPITA NFREGLNVLQ YFISTHGARK GLADTALKTA NSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCD TDFGVCAHCY GRDLARGHII NKGEAIGVIA AQSIGEPGTQ LTMRTFHIGG AASRAAAESS IQVKNKGSIK L SNVKSVVN SSGKLVITSR NTELKLIDEF GRTKESYKVP YGAVLAKGDG EQVAGGETVA NWDPHTMPVI TEVSGFVRFT DM IDGQTIT RQTDELTGLS SLVVLDSAER TAGGKDLRPA LKIVDAQGND VLIPGTDMPA QYFLPGKAIV QLEDGVQISS GDT LARIPQ ESGGTKDITG GLPRVADLFE ARRPKEPAIL AEISGIVSFG KETKGKRRLV ITPVDGSDPY EEMIPKWRQL NVFE GERVE RGDVISDGPE APHDILRLRG VHAVTRYIVN EVQDVYRLQG VKINDKHIEV IVRQMLRKAT IVNAGSSDFL EGEQV EYSR VKIANRELEA NGKVGATYSR DLLGITKASL ATESFISAAS FQETTRVLTE AAVAGKRDEL RGLKENVIVG RLIPAG TGY AYHQDRMRRR AAGEAPAAPQ VTAEDASASL AELLNAGLGG SDNE UniProtKB: DNA-directed RNA polymerase subunit beta' |
-Macromolecule #6: DNA-directed RNA polymerase subunit omega
Macromolecule | Name: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 10.249547 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR UniProtKB: DNA-directed RNA polymerase subunit omega |
-Macromolecule #7: RNA polymerase sigma factor RpoD
Macromolecule | Name: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 70.352242 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP DADDLMLAEN TADEDAAEAA AQVLSSVES EIGRTTDPVR MYMREMGTVE LLTREGEIDI AKRIEDGINQ VQCSVAEYPE AITYLLEQYD RVEAEEARLS D LITGFVDP ...String: MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP DADDLMLAEN TADEDAAEAA AQVLSSVES EIGRTTDPVR MYMREMGTVE LLTREGEIDI AKRIEDGINQ VQCSVAEYPE AITYLLEQYD RVEAEEARLS D LITGFVDP NAEEDLAPTA THVGSELSQE DLDDDEDEDE EDGDDDSADD DNSIDPELAR EKFAELRAQY VVTRDTIKAK GR SHATAQE EILKLSEVFK QFRLVPKQFD YLVNSMRVMM DRVRTQERLI MKLCVEQCKM PKKNFITLFT GNETSDTWFN AAI AMNKPW SEKLHDVSEE VHRALQKLQQ IEEETGLTIE QVKDINRRMS IGEAKARRAK KEMVEANLRL VISIAKKYTN RGLQ FLDLI QEGNIGLMKA VDKFEYRRGY KFSTYATWWI RQAITRSIAD QARTIRIPVH MIETINKLNR ISRQMLQEMG REPTP EELA ERMLMPEDKI RKVLKIAKEP ISMETPIGDD EDSHLGDFIE DTTLELPLDS ATTESLRAAT HDVLAGLTAR EAKVLR MRF GIDMNTDYTL EEVGKQFDVT RERIRQIEAK ALRKLRHPSR SEVLRSFLDD UniProtKB: RNA polymerase sigma factor RpoD |
-Macromolecule #8: DNA-binding transcriptional regulator BasR
Macromolecule | Name: DNA-binding transcriptional regulator BasR / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella pneumoniae JM45 (bacteria) |
Molecular weight | Theoretical: 25.477045 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKILVIEDDA LLLQGLILAM QSEGYVCDGV STAHEAALSL ASNHYSLIVL DLGLPDEDGL HFLSRMRREK MTQPVLILTA RDTLEDRIS GLDTGADDYL VKPFALEELN ARIRALLRRH NNQGDNEISV GNLRLNVTRR LVWLGETALD LTPKEYALLS R LMMKAGSP ...String: MKILVIEDDA LLLQGLILAM QSEGYVCDGV STAHEAALSL ASNHYSLIVL DLGLPDEDGL HFLSRMRREK MTQPVLILTA RDTLEDRIS GLDTGADDYL VKPFALEELN ARIRALLRRH NNQGDNEISV GNLRLNVTRR LVWLGETALD LTPKEYALLS R LMMKAGSP VHREILYNDI YSGDNEPATN TLEVHIHNLR EKIGKSRIRT VRGFGYMLAN NDDTEHLE UniProtKB: DNA-binding transcriptional regulator BasR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.1 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8jo2: |