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- EMDB-36253: RNA polymerase II elongation complex containing 60 bp upstream DN... -

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Basic information

Entry
Database: EMDB / ID: EMD-36253
TitleRNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome
Map data
Sample
  • Complex: RNA polymerase II - nucleosome complex
    • Complex: RNA polymerase II
    • Complex: Histones
    • Complex: DNA
    • Complex: RNA
    • Protein or peptide: x 16 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsTranscription-DNA-RNA COMPLEX / RNAPII
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 / pericentric heterochromatin formation / inner kinetochore / 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 / pericentric heterochromatin formation / inner kinetochore / 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 / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase I complex / transcription elongation by RNA polymerase I / 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 / CENP-A containing nucleosome / tRNA transcription by RNA polymerase III / : / 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 / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / 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 / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAkatsu M / Fujita R / Ogasawara M / Ehara H / Kujirai T / Takizawa Y / Sekine S / Kurumizaka H
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15711 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: J Biol Chem / Year: 2023
Title: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
Authors: Munetaka Akatsu / Haruhiko Ehara / Tomoya Kujirai / Risa Fujita / Tomoko Ito / Ken Osumi / Mitsuo Ogasawara / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the ...RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.
History
DepositionMay 22, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36253.png

Downloads & links

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Map

FileDownload / File: emd_36253.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Contour LevelBy AUTHOR: 0.0149
Minimum - Maximum-0.026737252 - 0.08243265
Average (Standard dev.)0.00036999313 (±0.0024697583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #3

Fileemd_36253_additional_1.map
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Additional map: #2

Fileemd_36253_additional_2.map
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Additional map: #1

Fileemd_36253_additional_3.map
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Half map: #2

Fileemd_36253_half_map_1.map
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Half map: #1

Fileemd_36253_half_map_2.map
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Sample components

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Entire : RNA polymerase II - nucleosome complex

EntireName: RNA polymerase II - nucleosome complex
Components
  • Complex: RNA polymerase II - nucleosome complex
    • Complex: RNA polymerase II
    • Complex: Histones
    • Complex: DNA
    • Complex: RNA
    • 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: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • 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
    • DNA: DNA (198-MER)
    • RNA: RNA (5'-R(P*GP*UP*CP*UP*UP*GP*GP*GP*UP*GP)-3')
    • DNA: DNA (198-MER)
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA polymerase II - nucleosome complex

SupramoleculeName: RNA polymerase II - nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Komagataella phaffii (fungus)

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: RNA

SupramoleculeName: RNA / type: complex / ID: 5 / Parent: 1

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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: Komagataella phaffii (fungus)
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

UniProtKB: DNA-directed RNA polymerase subunit

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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: Komagataella phaffii (fungus)
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

UniProtKB: DNA-directed RNA polymerase subunit beta

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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: Komagataella phaffii (fungus)
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

UniProtKB: RNA polymerase II third largest subunit B44, part of central core

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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: Komagataella phaffii (fungus)
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

UniProtKB: RNA polymerase II subunit B32

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Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
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

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 17.803588 KDa
SequenceString:
MSEDEAFNEQ TENFENFEDE HFSDDNFEDR STQPEDYAVG VTADGRQIIN GDGIQEVNGT IKAHRKRSNK ELAILKEERT TTPYLTKYE RARILGTRAL QISMNAPVLV DIEGETDPLQ IAMKELSQRK IPLVIRRYLP DGSYEDWGCD ELIVDN

UniProtKB: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

+
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: Komagataella phaffii (fungus)
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

UniProtKB: DNA-directed RNA polymerase subunit

+
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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 16.24922 KDa
SequenceString:
MSSALFDDIF TVQTVDNGRY NKVSRIIGIS TTNSAIKLTL DINNEMFPVS QDDSLTVTLA NSLSLDGEDE SANFSKSWRP PKPTDKSLA DDYDYVMFGT VYKFEEGDED KIKVYVSFGG LLMCLEGGYK SLASLKQDNL YILIRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 13.61232 KDa
SequenceString:
MASFRFCLEC NNMLYPKEDK ENQRLLYSCR NCDYTELAED PKVYRHELIT NIGETAGIVD DIGQDPTLPR SDKECPECHS RDCVFFQSQ QRRKDTNMTL FYVCLNCKKT FRDESE

UniProtKB: DNA-directed RNA polymerase subunit

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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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 8.554064 KDa
SequenceString:
MIIPVRCFSC GKVVGDKWDA YLRLLEEGKQ EGDALDELKL KRYCCRRMVL THVDLIEKFL RYNPLEKKDF DS

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 13.832896 KDa
SequenceString:
MNAPDRFELF ILPDDVPKLK ITPDSRVPNC IIIKFEREDH TLANLLREEL ALYPDVTFVA YKVEHPLFAN FVMRLQTEEG TRPKQALER ACASIINKLK TLDHKFNEEW NIKNFSLND

UniProtKB: RNA polymerase II subunit B12.5

+
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: Komagataella phaffii (fungus)
Molecular weightTheoretical: 7.862048 KDa
SequenceString:
MSREGFVAPS GTDLAAAASG VAPNKHYGVK YTCGACAHNF SLNKSDPVRC KECGHRVIYK ARTKRMIQFD AR

UniProtKB: RNA polymerase subunit ABC10-alpha

+
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: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

+
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: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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

MacromoleculeName: 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: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

+
Macromolecule #19: Histone H2B type 1-J

MacromoleculeName: 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: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

+
Macromolecule #13: DNA (198-MER)

MacromoleculeName: DNA (198-MER) / type: dna / ID: 13 / 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 #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: 60.869977 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)(DA)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DC)(DA) (DA)(DC)(DG) (DA)(DA)(DA)(DA)(DC)(DG)(DG)(DC)(DC)(DA) (DC)(DC)(DA)(DC)(DC)(DC)(DA) (DA)(DA) (DC)(DA)(DC)(DA)(DC)(DC)(DA)(DA)(DA)(DC) (DA)(DC)(DA)(DA)(DG)(DA)(DG)(DC) (DT) (DA)(DA)(DT)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC)(DG)(DT)(DA)(DA)(DG)(DC)

+
Macromolecule #14: RNA (5'-R(P*GP*UP*CP*UP*UP*GP*GP*GP*UP*GP)-3')

MacromoleculeName: RNA (5'-R(P*GP*UP*CP*UP*UP*GP*GP*GP*UP*GP)-3') / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.210917 KDa
SequenceString:
GUCUUGGGUG

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Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.09144 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH(pH7.5)
50.0 mMPotassium acetateCH3COOK
200.0 nMZinc acetate(CH3COO)2Zn
0.1 mMTCEP-HCl

Details: 20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
DetailsdsDNA concentration is 0.09144 mg/mL. This sample contains 0.005% Tween20.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsRNAPII-nucleosome complex
Startup modelType of model: EMDB MAP
EMDB ID:

9713

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97768
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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