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- EMDB-6986: RNA polymerase II elongation complex stalled at SHL(-1) of the nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-6986
TitleRNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Map datawhole, postprocessed
Sample
  • Complex: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
    • Protein or peptide: x 16 types
    • RNA: x 1 types
    • DNA: x 4 types
  • Ligand: x 2 types
Function / homology
Function and homology information


regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / muscle cell differentiation / oocyte maturation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / RPB4-RPB7 complex / inner kinetochore / pericentric heterochromatin formation / muscle cell differentiation / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nucleus organization / spermatid development / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / transcription elongation by RNA polymerase I / protein localization to CENP-A containing chromatin / RNA polymerase III complex / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / CENP-A containing nucleosome / : / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / innate immune response in mucosa / DNA-directed RNA polymerase activity / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / lipopolysaccharide binding / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / ribonucleoside binding / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / : / : / : / : / : / : / DNA-directed RNA polymerase / Transcriptional regulation of granulopoiesis / antimicrobial humoral immune response mediated by antimicrobial peptide / HCMV Early Events / male gonad development
Similarity search - Function
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 ...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 / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / S1 RNA binding domain / S1 domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit ...DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii (fungus) / Yeast (brewer's yeast) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsKujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of ScienceJP15H04344 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101082 Japan
RIKEN Dynamic Structural Biology project Japan
CitationJournal: Science / Year: 2018
Title: Structural basis of the nucleosome transition during RNA polymerase II passage.
Authors: Tomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo- ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
History
DepositionJun 25, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6inq
  • Surface level: 0.05
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6986.png

Downloads & links

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Map

FileDownload / File: emd_6986.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationwhole, postprocessed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 240 pix.
= 357.6 Å		1.49 Å/pix.
x 240 pix.
= 357.6 Å		1.49 Å/pix.
x 240 pix.
= 357.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.052211598 - 0.1518552
Average (Standard dev.)0.00090830715 (±0.008049498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 357.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.491.491.49
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z357.600357.600357.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0520.1520.001

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Supplemental data

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Additional map: nucleosome, postprocessed

Fileemd_6986_additional.map
Annotationnucleosome, postprocessed
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 II elongation complex stalled at SHL(-1) of the nu...

EntireName: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Components
  • Complex: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: RNA polymerase II third largest subunit B44, part of central core
    • Protein or peptide: RNA polymerase II subunit B32
    • Protein or peptide: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
    • Protein or peptide: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
    • Protein or peptide: RNA polymerase II subunit
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
    • Protein or peptide: RNA polymerase II subunit B12.5
    • Protein or peptide: RNA polymerase subunit ABC10-alpha
    • RNA: RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')
    • DNA: DNA (198-MER)
    • DNA: DNA (198-MER)
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A, Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B, Histone H2B type 1-J
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA polymerase II elongation complex stalled at SHL(-1) of the nu...

SupramoleculeName: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 194.107422 KDa
SequenceString: MSQFPYSSAP LRSVKEVQFG LLSPEEIRAI SVVKIEYPEI MDESRQRPRE GGLNDPKLGS IDRNFKCQTC GEGMAECPGH FGHMELAKP VFHIGFIPKI KKVCECICMN CGKLLLDETN PTMAQAIRIR DPKKRFNAVW QLCKTKMVCE ADAPVDEYSE Q KVVSRGGC ...String:
MSQFPYSSAP LRSVKEVQFG LLSPEEIRAI SVVKIEYPEI MDESRQRPRE GGLNDPKLGS IDRNFKCQTC GEGMAECPGH FGHMELAKP VFHIGFIPKI KKVCECICMN CGKLLLDETN PTMAQAIRIR DPKKRFNAVW QLCKTKMVCE ADAPVDEYSE Q KVVSRGGC GNTQPVVRKD GMKLWGTWKK SGFSDRDAQP ERKLLTPGEI LNVFKHISPE DCFRLGFNED YARPEWMIIT VL PVPPPQV RPSIAMDETT QGQDDLTHKL SDILKANINV QKLEMDGSPQ HIINEVEQLL QFHVATYMDN DIAGQPQALQ KSG RPVKAI RARLKGKEGR LRGNLMGKRV DFSARTVISG DPNLELDQVG VPISIAKTLS YPETVTQYNI HRLTEYVRNG PNEH PGAKY VIRDNGDRID LRYHKRAGDI VLQYGWKVER HLMDDDPVLF NRQPSLHKMS MMAHRVKVMP YSTFRLNLSV TSPYN ADFD GDEMNLHVPQ SEETRAELSQ LCAVPLQIVS PQSNKPVMGI VQDTLCGVRK MTLRDTFIEY EQVMNMLFWV PSWDGV VPQ PAILKPKPLW TGKQLLSIAI PSGIHLQRTD GGNSLLSPKD NGMLIVDGKV MFGVVDKKTV GSGGGGLIHT VMREKGP KI CAELFGNIQK VVNYWLLHNG FSIGIGDAIA DASTMKEITH AISSAKEQVQ EIIYKAQHNE LELKPGMTLR ESFEGEVS R TLNDARDSAG RSAEMNLKDL NNVKQMVSAG SKGSFINIAQ MSACVGQQMV EGKRIAFGFA DRSLPHFTKD DFSPESKGF VENSYLRGLT PQEFFFHAMA GREGLIDTAV KTAETGYIQR RLVKALEDIM VHYDGTTRNS LGDIIQFLYG EDGLDGTQVE RQTIDTIPG SDKAFHKRYY VDLMDEKNSI KPDVIEYAAD ILGDVELQKE LNSEYEQLVS DRKFLREIVF VNGDHNWPLP V NLRRIIQN AQQIFHLDRA KASDLTIPEI IHGVRDLCKK LFVLRGENEL IKEAQQNATS LFQCLVRARL ATRRILEEFR LN RDAFEWV LGTIEAQFQR SLVHPGEMVG VIAAQSIGEP ATQMTLNTFH YAGVSSKNVT LGVPRLKEIL NVAKNIKTPA LTV YLDREI ALDIEKAKVI QSSIEYTTLK NVTSATEIYY DPDPTSTVIE EDFDTVEAYF SIPDEKVEET IDKQSPWLLR LELD RARML DKQLTMNQVA DKISEVFSDD LFVMWSEDNA DKLIIRCRVI RDPKAMDEEL EAEEDQMLKR IEAHMLDLIA LRGIP GISK VYMVKHKVSV PDESGEYKNE ELWALETDGI NLAEVMAVPG VDSSRTYSNS FVEILSVLGI EATRSSLYKE ILNVIA FDG SYVNYRHMAL LVDVMTSRGY LMAITRHGIN RADTGALMRC SFEETVEILF EAGAAAELDD CRGVSENVML GQLAPMG TG AFDVMIDEKL LTSLPADYAP TMPLFKGKAT QGSATPYDNN AQYDDEFNHD DVADVMFSPM AETGSGDDRS GGLTEYAG I QSPYQPTSPG LSATSPGFAP TSPGFAPTSP RYSPTSPGYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPQY SPTSPQYSPT SPQYSPTSPQ YSPTSPQYSP TSPQYSPTSP QYSPTSPQYS PTSPQYSPT SPQYSPTSPQ YSPTSPQYSP TSPQYSPTSP QYSPASPQYS PSRHSPNGES KEGE

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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: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 139.746094 KDa
SequenceString: MSYDPYSIDD TITTEDCWTV ISAFFEEKGL VSQQLDSFDE FMETSIQDLV WEEPRLILDQ PAQHTNEKDN INKRYEIRFG KIYLSRPTM TEADGTTHAM FPQEARLRNL TYSSPVYLDM EKSMFTSIDD EGNPNATLDW QQVHEPIKDG VEEGNKVHIG K VPIMLRSK ...String:
MSYDPYSIDD TITTEDCWTV ISAFFEEKGL VSQQLDSFDE FMETSIQDLV WEEPRLILDQ PAQHTNEKDN INKRYEIRFG KIYLSRPTM TEADGTTHAM FPQEARLRNL TYSSPVYLDM EKSMFTSIDD EGNPNATLDW QQVHEPIKDG VEEGNKVHIG K VPIMLRSK FCSLRTLDEV DLYKMKECPY DMGGYFVING SEKVLIAQER SAANIVQVFK KAAPSPISHV AEIRSALEKG SR LISTMQI KLYGREDKGT GRTIKATLPY VKQDIPIVIV FRALGVVPDG EILQHICYDE NDWQMLEMLK PCIEEGFVIQ DKE VALDFI GRRGSAALGI RREKRIQYAK DILQKELLPH ITQEEGFETR KTFFLGYMVN RLLLCALERK DQDDRDHFGK KRLD LAGPL LANLFRILFR KLTREIYRYM QRCIETDRDF NLNLAVKSTT ITSGLKYSLA TGNWGEQKKA MSSRAGVSQV LNRYT YSST LSHLRRTNTP IGRDGKLAKP RQLHNTHWGL VCPAETPEGQ ACGLVKNLSL LSGISIGSPS EPIINFLEEW GMEPLE DYD PAQHTKSTRI FVNGVWTGIH RDPSMLVSTM RDLRRSGAIS PEVSIIRDIR EREFKIFTDV GRVYRPLFIV EDDESKD NK GELRITKEHI RKIQQGYDDD AMNDDSEEQE QDVYGWSSLV TSGVIEYVDG EEEETIMIAM TPEDLQTRSL EQKEIDLN D TAKRIKPEMS TSSHHTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLAKTQAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKRFGISI VEEFEKPTRA TTLRLKHGT YEKLDEDGLI APGVRVSGDD IIIGKTTPIP PDTEELGQRT KYHTKRDAST PLRSTENGIV DQVLLTTNQE G LKFVKVRM RTTKVPQIGD KFASRHGQKG TIGVTYRHED MPFSAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVGSIR GY EGDATPF TDLTVDAVSN LLRDNGYQSR GFEVMYNGHT GKKLMAQVFF GPTYYQRLRH MVDDKIHARA RGPVQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAAGF LKERLMEASD AFRVHVCGIC GLMSVIANLK KNQFECRSCK NKTNIYQLHI PYAA KLLFQ ELMAMNIAPR LYTERSGVSM RS

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Macromolecule #3: RNA polymerase II third largest subunit B44, part of central core

MacromoleculeName: RNA polymerase II third largest subunit B44, part of central core
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 34.216293 KDa
SequenceString: MSKEPKVNII NAQDDEVELM LSDVNLSLAN SLRRTMLAEV PTLAIDLVEI KMNTSVLADE FISHRLGLIP LVSEDVEEMK YSRDCTCED YCDECSVVLE LSARHEGEEG TTDVYSSSLI KVSGPGNLNV GEPVRRDDYD QGILLCKLRN HQELNIRCIA K KGIAKEHA ...String:
MSKEPKVNII NAQDDEVELM LSDVNLSLAN SLRRTMLAEV PTLAIDLVEI KMNTSVLADE FISHRLGLIP LVSEDVEEMK YSRDCTCED YCDECSVVLE LSARHEGEEG TTDVYSSSLI KVSGPGNLNV GEPVRRDDYD QGILLCKLRN HQELNIRCIA K KGIAKEHA KWSPCSAIAF EYDPHNKLKH TDFWFEVDAK KEWPDSKYAT WEEPPKPGEV FDYKAKPNRF YMTVETTGSL KA NQVFSRG IKTLQEKLAN VLFELENSRP ANTTAYGGAT AYGGQTVYGR ETSYGGNTNY GDYNAPY

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Macromolecule #4: RNA polymerase II subunit B32

MacromoleculeName: RNA polymerase II subunit B32 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 20.62298 KDa
SequenceString:
MNVSTSTVGA RRRRAKQQVD DEENATLLRL GPEFALKQYD HDGNEHDLIA LSLSESRLLI REALKARSRA RNGGVDIESS NGEIDDDEL AKVTSGAVAN GVVKKTLDYL NTFARFKDEE TCTAVDQLLH NSSDCSVLHP FEIAQLSSLG CEDVDEAITL I PSLAAKKE VNLQRILDEL NRLEDPYK

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Macromolecule #5: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III

MacromoleculeName: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 24.96268 KDa
SequenceString: MEDNNRIISR LWRSFRTVKE MAADRGYFIS QEEMDQSLEE FRSKICDSMG NPQRKLMSFL ANPTPEALEK YSDLGTLWVE FCDEPSVGI KTMRNFCLRI QEKNFSTGIF IYQNNITPSA NKMIPTVSPA IIETFQESDL VVNITHHELV PKHIRLSDGE K SQLLQRYK ...String:
MEDNNRIISR LWRSFRTVKE MAADRGYFIS QEEMDQSLEE FRSKICDSMG NPQRKLMSFL ANPTPEALEK YSDLGTLWVE FCDEPSVGI KTMRNFCLRI QEKNFSTGIF IYQNNITPSA NKMIPTVSPA IIETFQESDL VVNITHHELV PKHIRLSDGE K SQLLQRYK LKESQLPRIQ REDPVARYLG LKRGQVVKII RRSETSGRYA SYRICL

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Macromolecule #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

MacromoleculeName: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 17.803588 KDa
SequenceString:
MSEDEAFNEQ TENFENFEDE HFSDDNFEDR STQPEDYAVG VTADGRQIIN GDGIQEVNGT IKAHRKRSNK ELAILKEERT TTPYLTKYE RARILGTRAL QISMNAPVLV DIEGETDPLQ IAMKELSQRK IPLVIRRYLP DGSYEDWGCD ELIVDN

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Macromolecule #7: RNA polymerase II subunit

MacromoleculeName: RNA polymerase II subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 18.802625 KDa
SequenceString:
MFFLKDLSLI LTLHPSYFGP QMNQYLREKL LTDVEGTCTG QFGYIVTVLD GMNIDVGKGR IIPGSGSAEF EVKYRAVVWK PFKGEVVDA IVSNVSPIGF FADVGPLNVF VSTRLIPDNL VYNPSNSPPA YMSNDELITK GSKVRLKVVG TRTDVNEIYA I GSIKEDFL GAI

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Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 16.24922 KDa
SequenceString:
MSSALFDDIF TVQTVDNGRY NKVSRIIGIS TTNSAIKLTL DINNEMFPVS QDDSLTVTLA NSLSLDGEDE SANFSKSWRP PKPTDKSLA DDYDYVMFGT VYKFEEGDED KIKVYVSFGG LLMCLEGGYK SLASLKQDNL YILIRR

+
Macromolecule #9: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 13.61232 KDa
SequenceString:
MASFRFCLEC NNMLYPKEDK ENQRLLYSCR NCDYTELAED PKVYRHELIT NIGETAGIVD DIGQDPTLPR SDKECPECHS RDCVFFQSQ QRRKDTNMTL FYVCLNCKKT FRDESE

+
Macromolecule #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...

MacromoleculeName: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 8.554064 KDa
SequenceString:
MIIPVRCFSC GKVVGDKWDA YLRLLEEGKQ EGDALDELKL KRYCCRRMVL THVDLIEKFL RYNPLEKKDF DS

+
Macromolecule #11: RNA polymerase II subunit B12.5

MacromoleculeName: RNA polymerase II subunit B12.5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 13.832896 KDa
SequenceString:
MNAPDRFELF ILPDDVPKLK ITPDSRVPNC IIIKFEREDH TLANLLREEL ALYPDVTFVA YKVEHPLFAN FVMRLQTEEG TRPKQALER ACASIINKLK TLDHKFNEEW NIKNFSLND

+
Macromolecule #12: RNA polymerase subunit ABC10-alpha

MacromoleculeName: RNA polymerase subunit ABC10-alpha / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yeast (brewer's yeast) / Strain: GS115 / ATCC 20864
Molecular weightTheoretical: 7.862048 KDa
SequenceString:
MSREGFVAPS GTDLAAAASG VAPNKHYGVK YTCGACAHNF SLNKSDPVRC KECGHRVIYK ARTKRMIQFD AR

+
Macromolecule #16: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.643262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPSTGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SAAIGALQEA SEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

+
Macromolecule #17: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

+
Macromolecule #18: Histone H2A, Histone H2A type 1-B/E

MacromoleculeName: Histone H2A, Histone H2A type 1-B/E / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

+
Macromolecule #19: Histone H2B, Histone H2B type 1-J

MacromoleculeName: Histone H2B, Histone H2B type 1-J / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

+
Macromolecule #13: RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3') / type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.517082 KDa
SequenceString:
GUGUCUUGGG U

+
Macromolecule #14: DNA (198-MER)

MacromoleculeName: DNA (198-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 38.379488 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DA)(DC) (DA)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)

+
Macromolecule #15: DNA (198-MER)

MacromoleculeName: DNA (198-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 61.381906 KDa
SequenceString: (DG)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DT) (DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG) (DG)(DG)(DT)(DG)(DG)(DT) ...String:
(DG)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DT) (DT)(DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG) (DG)(DG)(DT)(DG)(DG)(DT)(DG)(DG) (DC)(DC)(DG)(DT)(DT)(DT)(DT)(DC)(DG)(DT) (DT)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT) (DC)(DT)(DG)(DT)(DC)(DT)(DC)(DG)(DT)(DG) (DC)(DC)(DT) (DG)(DG)(DT)(DG)(DT)(DC) (DT)(DT)(DG)(DG)(DG)(DT)(DG)(DT)(DA)(DA) (DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA) (DT)(DT)(DC)(DT)(DG)(DA)(DT)

+
Macromolecule #20: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.544222 KDa
SequenceString:
(DC)(DC)(DA)(DA)(DG)(DA)(DC)(DA)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DG)(DA) (DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DC)

+
Macromolecule #21: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 21 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.52007 KDa
SequenceString:
(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT) (DG)(DT)(DC)(DT)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DG)(DG)(DT)(DG)(DT)(DC)(DT)(DT) (DG)(DG)

+
Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #23: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Software - details: per-particle CTF
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xog

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 28961
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6inq:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)

+
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