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- EMDB-9786: Cryo-EM structure of Xanthomonos oryzae transcription elongation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9786
TitleCryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7
Map data
Sample
  • Complex: Xoo transcription elongation complex with P7(P7-TEC)
    • 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
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • RNA: RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
    • Protein or peptide: 45L
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNA polymerase / transcription termination / anti-termination / RNAP clamp / phage / transcription initiation / P7 / Xanthomonos oryzae / Xp10 / transcription
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Xanthomonas phage Xp10 Transcription regulator P7 / : / 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 ...Xanthomonas phage Xp10 Transcription regulator P7 / : / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega / RNA polymerase inhibitor p7
Similarity search - Component
Biological speciesXanthomonas oryzae (bacteria) / Xanthomonas oryzae pv. oryzae PXO99A (bacteria) / Xanthomonas oryzae pv. oryzae MAFF 311018 (bacteria) / Xanthomonas oryzae pv. oryzae (bacteria) / Xanthomonas virus Xp10 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsYou LL / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822001 China
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for transcription antitermination at bacterial intrinsic terminator.
Authors: Linlin You / Jing Shi / Liqiang Shen / Lingting Li / Chengli Fang / Chengzhi Yu / Wenbo Cheng / Yu Feng / Yu Zhang /
Abstract: Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein- ...Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation-in particular transcription antitermination-is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation.
History
DepositionJan 22, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
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  • Surface view with fitted model
  • Atomic models: PDB-6j9f
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9786.png

Downloads & links

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Map

FileDownload / File: emd_9786.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.049584664 - 0.084427685
Average (Standard dev.)0.00017693116 (±0.0021583955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z304.200304.200304.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0500.0840.000

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Supplemental data

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Half map: #2

Fileemd_9786_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_9786_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Xoo transcription elongation complex with P7(P7-TEC)

EntireName: Xoo transcription elongation complex with P7(P7-TEC)
Components
  • Complex: Xoo transcription elongation complex with P7(P7-TEC)
    • 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
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • RNA: RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
    • Protein or peptide: 45L
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Xoo transcription elongation complex with P7(P7-TEC)

SupramoleculeName: Xoo transcription elongation complex with P7(P7-TEC) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Xanthomonas oryzae (bacteria) / Strain: PXO99A
Molecular weightTheoretical: 427 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 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Xanthomonas oryzae pv. oryzae PXO99A (bacteria)
Molecular weightTheoretical: 38.030168 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMTVTAN QVLRPRGPQI ERLTDNRAKV VIEPLERGYG HTLGNALRRV LLSSIPGFAI TEVEIDGVLH EYTTVEGLQ EDVLDVLLNL KDVAIRMHSG DSATLSLSKQ GPGTVTAADI RTDHNVEIIN GDHVICHLTK DTALNMRLKI E RGFGYQPA ...String:
MGSSHHHHHH SQDPMTVTAN QVLRPRGPQI ERLTDNRAKV VIEPLERGYG HTLGNALRRV LLSSIPGFAI TEVEIDGVLH EYTTVEGLQ EDVLDVLLNL KDVAIRMHSG DSATLSLSKQ GPGTVTAADI RTDHNVEIIN GDHVICHLTK DTALNMRLKI E RGFGYQPA AARRRPDEET RTIGRLMLDA SFSPVRRVAY AVEAARVEQR TDLDKLVIDI ETNGTIDAEE AVRTAADILS DQ LSVFGDF THRDRGAAKP AASGVDPVLL RPIDDLELTV RSANCLKAES IYYIGDLIQK TEVELLKTPN LGKKSLTEIK EVL AQRGLA LGMKLENWPP AGVAQHGMLG

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 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Xanthomonas oryzae pv. oryzae MAFF 311018 (bacteria)
Strain: MAFF 311018
Molecular weightTheoretical: 154.471719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTSYSFTEKK RIRKDFGKQR SILEVPFLLA IQVDSYREFL QEDVESTKRK DLGLHAALKS VFPISSYSGN AALEYVGYKL GQPVFDERE CRQRGMSYGA PLRVTVRLVI YDRESSTKAI KYVKEQEVYL GEIPLMTGNG TFIVNGTERV IVSQLHRSPG V FFDHDRGK ...String:
MTSYSFTEKK RIRKDFGKQR SILEVPFLLA IQVDSYREFL QEDVESTKRK DLGLHAALKS VFPISSYSGN AALEYVGYKL GQPVFDERE CRQRGMSYGA PLRVTVRLVI YDRESSTKAI KYVKEQEVYL GEIPLMTGNG TFIVNGTERV IVSQLHRSPG V FFDHDRGK THSSGKLLYS ARIIPYRGSW LDFEFDPKDA LFTRIDRRRK LPVSILLRAL GYNNEEMLAE FFEINTFHIN PD EGVQLEL VPERLRGETL NFDLADGDKV IVEAGKRITA RHVKQLEAAG VAALAVPDDY LVGRILSHDV VDGSTGELLA NAN DEISED QLTAFRKAGV DAVGTLWVND LDRGPYLSNT LRIDPTKTQL EALVEIYRMM RPGEPPTKEA AQNLFHNLFF TFER YDLST VGRMKFNRRV GRKDVLGESV LYDKKYFAER NDEESKRLVA EHTDTSDILE VIKVLTEIRN GRGVVDDIDH LGNRR VRSV GEMAENVFRV GLVRVERAVK ERLSMAESEG LTPQELINAK PVAAAIKEFF GSSQLSQFMD QNNPLSEVTH KRRVSA LGP GGLTRERAGF EVRDVHPTHY GRVCTIETPE GPNIGLINSL AVFARTNQYG FLETPYRKVL DGKVSDDVEY LSAIEEN EY VIAQANALTD AKNMLTEQFV PCRFQGESLL KPPSEVHFMD VSPMQTVSVA AALVPFLEHD DANRALMGAN MQRQAVPT L RSQKPLVGTG IERAVARDSG VTVNALRGGV IEQIDAARIV VKVNEAEIGG GTDAGVDIYN LIKYTRSNQN TCINQRPLV NVGDVIARGD VLADGPSTDI GELALGQNML IAFMPWNGYN FEDSILLSER VVEEDRYTTI HIEELTCVAR DTKLGPEEIS ADIPNVSEQ ALNRLDESGV VYIGAEVRAG DIMVGKVTPK GESQLTPEEK LLRAIFGEKA SDVKDSSLRV PPGMDGTVID V QVFTRDGI EKDKRARQIE ENEIKRVKKD FDDQFRILEA AIYARLRSQI VGKVANGGAN LKKGDSVTDA YLDGLKKSDW FQ LRMKDED AADAIERAQK QIQAHEKEFE ARFADKRGKI TQGDDLAPGV LKMVKVFLAV KRRIQPGDKM AGRHGNKGVV SNV VPVEDM PYMATGESVD IVLNPLGVPS RMNIGQILEV HLGWAAKGLG RKIQRMLEAQ AAVSELRKFL DDIYNHDNAI NAQR VDLSQ FSDEELLNLG KNLIDGVPMA TPVFDGASEA EIKRMLELAD LPQSGQTQLY DGRTGEAFDR KTTVGYMHYL KLNHL VDDK MHARSTGPYS LVTQQPLGGK AQFGGQRFGE MEVWALEAYG AAYTLQEMLT VKSDDVQGRN QMYKNIVDGE HEMVAG MPE SFNVLVKEIR SLAIHMELEE

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 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Xanthomonas oryzae pv. oryzae PXO99A (bacteria)
Molecular weightTheoretical: 155.444609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDLLNLFNQ QRQTLDFDAI KIALASPDLI RSWSYGEVKK PETINYRTFK PERDGLFCAA IFGPIKDYEC LCGKYKRMKH RGVVCEKCG TEVTLAKVRR ERMGHIDLAS PVAHIWFLKS LPSRIGLMLD MTLRDIERVL YFEAYVVTEP GLTPLERRQL L TEEQYLTA ...String:
MKDLLNLFNQ QRQTLDFDAI KIALASPDLI RSWSYGEVKK PETINYRTFK PERDGLFCAA IFGPIKDYEC LCGKYKRMKH RGVVCEKCG TEVTLAKVRR ERMGHIDLAS PVAHIWFLKS LPSRIGLMLD MTLRDIERVL YFEAYVVTEP GLTPLERRQL L TEEQYLTA RQEYNDDFDA AMGAEAVYEL LRTIDLQSEM TRLREEIAST GSETKLKRLT KRIKLIEAFL ESGNRPEWMV MT VLPVLPP DLRPLVPLDG GRFATSDLND LYRRVINRNN RLRRLLELNA PDIIVRNEKR MLQESVDALL DNGRRGRAIT GTN KRPLKS LADMIKGKQG RFRQNLLGKR VDYSGRSVIT VGPYLKLHQC GLPKKMALEL FKPFVFAKLQ RRGLATTIKA AKKL VEREE AEVWDILEEV IREHPVLLNR APTLHRLGIQ AFEPVLIEGK AIQLHPLVCT AFNADFDGDQ MAVHVPLSLE AQLEA RALM MSTNNILSPA NGEPIIVPSQ DVVLGLYYMS RALENKKGEG MVFANTSEVK RAYDNRVVEL HAKVKVRITQ VDVDAV DGK RTSGTSIVDT TVGRALLSEI LPEGLPFQLA NTEMTKKNIS RLINSSYRLL GLKDTVVFAD KLMYTGYAYA TRAGVSI GI DDMLIPDEKK GILTEAEAEV LEIQEQYQSG LVTAGERYNK VVDIWSRTSE RIAKAMMDTI GTEKVENAKG ETIDQKSM N SLYIMADSGA RGSQAQIRQL AGMRGLMARP DGSIIETPIK ANFREGLNVQ EYFNSTHGAR KGLADTALKT ANSGYLTRR LVDVAQDVVI TEIDCGTTEG LIMTPIVEGG DVVEPLKERV LGRVVAEDVY LPGNDEEPIV TRNTLLDEAW VAKLEDASVQ SVKVRSTIS CESSFGVCAR CYGRDLARGH QVNIGEAVGV IAAQSIGEPG TQLTMRTFHI GGAASRAAAV DNITVKTTGS V KFNNLKSV AHASGSLVAV SRSGELSVLD GHGRERERYK LPYGATITAK DGDAVKAGQS VANWDPHNHP IVSEVAGFIR FI DFVDGVT VIEKTDELTG LASREITDPK RRGAHAKELR PIVRIVDGKG NDLTIPNTDL PAQYLLPPRS IVNLQDGAAV GVG DVVAKI PQEASKTRDI TGGLPRVADL FEARKPKDPA ILAERSGIIS FGKDTKGKQR LIIKDTDGSE HEELIPKYRQ IIVF EGEHV TKGETVVDGE PSPQDILRLL GVEPLAAYLV KEIQDVYRLQ GVKINDKHIE VITRQMLRKV EIVDQGNSKF LNGEQ VERQ RVIEENARLV KRNELPAKYD PVLLGITKAS LATESFISAA SFQETTRVLT EAAVRGTRDN LRGLKENVIV GRLIPA GTG LAYHAGRRKA SGLTDSEMET LSGKPAGAEP VAALADAGAD EE

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 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Xanthomonas oryzae pv. oryzae (bacteria)
Molecular weightTheoretical: 11.112536 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARITVEDCL EVVNNRFELV MMASKRARQL ANGVQPLIEN AAASDKPTVM ALREIAARRI DNALIDEVEK AERERAEREA LEWAAAEVV ADEDMSKNDD

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #8: 45L

MacromoleculeName: 45L / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas virus Xp10
Molecular weightTheoretical: 8.519374 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GAMAMNEFTQ ISGYVNAFGS QRGSVLTVKV ENDEGWTLVE EDFDRADYGS DPEFVAEVSS YLKRNGGIKD LTKVLTR

UniProtKB: RNA polymerase inhibitor p7

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Macromolecule #5: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.813646 KDa
SequenceString:
(DG)(DG)(DG)(DT)(DA)(DT)(DT)(DC)(DG)(DC) (DC)(DG)(DT)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DA)(DG)(DC)(DC)(DC)

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Macromolecule #6: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.840689 KDa
SequenceString:
(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DG)(DA)(DC)(DG)(DG) (DC)(DG)(DA)(DA)(DT)(DA)(DC)(DC)(DC)

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Macromolecule #7: RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.509968 KDa
SequenceString:
GCAUUCAAAG CGGAGAGGUA

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration9.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHepesHepes
50.0 mMKCLPotassium Chloride
5.0 mMMgCL2Magnesium chloride
3.0 mMDTTDL-Dithiothreitol
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 8 seconds before plunging.
DetailsThis sample was monodisperse

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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 / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 2.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2271 / Average exposure time: 8.0 sec. / Average electron dose: 1.675 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Particle selectionNumber selected: 410547
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5upc
PDB Unreleased entry


Details: CryoEM structure of E.coli RNA polymerase elongation complex
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 555 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 319613
Image processing ID1
FSC plot (resolution estimation)

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Image processing #2

Particle selectionNumber selected: 410547
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5upc
PDB Unreleased entry


Details: CryoEM structure of E.coli RNA polymerase elongation complex
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 555 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 319613
Image processing ID2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5upc
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model

2mc6

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6j9f:
Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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