EMDB-64226: RNA polymerase II elongation complex stalled at SHL(-0.5) of the ...

Basic information

Entry

Database: EMDB / ID: EMD-64226

• Title: RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)

Sample

• Complex: RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)
  • Complex: RNA Polymerase II elongation complex
    • Protein or peptide: x 12 types
  • Complex: H3-H4 tetrasome
    • Protein or peptide: x 2 types
  • Complex: DNA,RNAA
    • DNA: x 2 types
    • RNA: x 1 types

• Keywords: RNAPII / subnucleosome / H3-H4 tetrasome / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex

Function / homology

Function:

regulation of septum digestion after cytokinesis / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / siRNA-mediated pericentric heterochromatin formation / RPB4-RPB7 complex / intracellular phosphate ion homeostasis / chromatin-protein adaptor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / nuclear-transcribed mRNA catabolic process / pericentric heterochromatin / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / negative regulation of megakaryocyte differentiation / translesion synthesis / transcription by RNA polymerase I / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / transcription-coupled nucleotide-excision repair / translation initiation factor binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / epigenetic regulation of gene expression / telomere organization / Interleukin-7 signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / P-body / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / ribonucleoside binding / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / DNA-directed RNA polymerase / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / DNA-directed RNA polymerase activity / nucleosome / nucleosome assembly / single-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / transcription by RNA polymerase II / Estrogen-dependent gene expression / nucleic acid binding / chromosome, telomeric region / protein dimerization activity

Domain/homology:

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 / Rpb4/RPC9 superfamily / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / 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 / HRDC-like superfamily / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / 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 / 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 Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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

Component:

DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / 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 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Histone H4 / Histone H3.1

• Biological species: Komagataella phaffii GS115 (fungus) / Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 6.54 Å
• Authors: Ho C-H / Nozawa K / Nishimura M / Oi M / Kujirai T / Ogasawara M / Ehara H / Sekine S / Takizawa Y / Kurumizaka H

Funding support

Japan, 9 items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP20H03201	Japan
Japan Society for the Promotion of Science (JSPS)	JP20H05690	Japan
Japan Society for the Promotion of Science (JSPS)	JP22K15033	Japan
Japan Society for the Promotion of Science (JSPS)	JP23K17392	Japan
Japan Society for the Promotion of Science (JSPS)	JP22K06098	Japan
Japan Society for the Promotion of Science (JSPS)	JP23H05475	Japan
Japan Society for the Promotion of Science (JSPS)	JP24H02328	Japan
Japan Science and Technology	JPMJER1901	Japan
Japan Agency for Medical Research and Development (AMED)	JP24ama121009	Japan

• Citation: Journal: J Biol Chem / Year: 2026; Title: Structural basis of RNA polymerase II transcription on the histone H3-H4 octasome.; Authors: Cheng-Han Ho / Kayo Nozawa / Masahiro Nishimura / Mayuko Oi / Tomoya Kujirai / Mitsuo Ogasawara / Haruhiko Ehara / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka / ; Abstract: The histone H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each histone (H3-H4) tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNA polymerase II (RNAPII) transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL(-4)) in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-EM analysis revealed that two (H3-H4) tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal (H3-H4) tetramer was disassembled, but the distal (H3-H4) tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise (H3-H4) tetramer disassembly.

History

Deposition	Apr 17, 2025	-
Header (metadata) release	Apr 15, 2026	-
Map release	Apr 15, 2026	-
Update	Apr 15, 2026	-
Current status	Apr 15, 2026	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_64226.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.06 Å

Density

Contour Level	By AUTHOR: 0.004
Minimum - Maximum	-0.008489729 - 0.017235935
Average (Standard dev.)	0.000093671595 (±0.0007380735)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 381.59998 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_64226_half_map_1.map

Half map: #1

• File: emd_64226_half_map_2.map

Sample components

Entire : RNA polymerase II elongation complex stalled at SHL(-0.5) of the ...

• Entire: Name: RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)

Components

• Complex: RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)
  • Complex: RNA Polymerase II elongation complex
    • 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
  • Complex: H3-H4 tetrasome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
  • Complex: DNA,RNAA
    • DNA: DNA (198-MER)
    • DNA: DNA (198-MER)
    • RNA: RNA (5'-R(P*CP*UP*UP*GP*GP*GP*UP*GP*UP*UP*U)-3')

Supramolecule #1: RNA polymerase II elongation complex stalled at SHL(-0.5) of the ...

• Supramolecule: Name: RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome); type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17

Supramolecule #2: RNA Polymerase II elongation complex

• Supramolecule: Name: RNA Polymerase II elongation complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#14
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)

Supramolecule #3: H3-H4 tetrasome

• Supramolecule: Name: H3-H4 tetrasome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #16-#17
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #4: DNA,RNAA

• Supramolecule: Name: DNA,RNAA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1-#2, #15

Macromolecule #1: DNA (198-MER)

• Macromolecule: Name: DNA (198-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 61.372891 KDa

Sequence

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)(DT)(DT) (DA)(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 #2: DNA (198-MER)

• Macromolecule: Name: DNA (198-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 60.878992 KDa

Sequence

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)(DT)(DA)(DA)(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 #3: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 194.107422 KDa

Sequence

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

Macromolecule #4: DNA-directed RNA polymerase subunit beta

• Macromolecule: Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 139.746094 KDa

Sequence

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

Macromolecule #5: RNA polymerase II third largest subunit B44, part of central core

• Macromolecule: Name: RNA polymerase II third largest subunit B44, part of central core; type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 34.216293 KDa

Sequence

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: DNA-directed RNA polymerase II subunit RPB3

Macromolecule #6: RNA polymerase II subunit B32

• Macromolecule: Name: RNA polymerase II subunit B32 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 20.62298 KDa

Sequence

String:

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

Macromolecule #7: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III

• Macromolecule: Name: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III; type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 24.96268 KDa

Sequence

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

Macromolecule #8: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

• Macromolecule: Name: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III; type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 17.803588 KDa

Sequence

String:

MSEDEAFNEQ TENFENFEDE HFSDDNFEDR STQPEDYAVG VTADGRQIIN GDGIQEVNGT IKAHRKRSNK ELAILKEERT TTPYLTKYE RARILGTRAL QISMNAPVLV DIEGETDPLQ IAMKELSQRK IPLVIRRYLP DGSYEDWGCD ELIVDN

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

Macromolecule #9: RNA polymerase II subunit

• Macromolecule: Name: RNA polymerase II subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 18.802625 KDa

Sequence

String:

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

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC3; type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 16.24922 KDa

Sequence

String:

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 #11: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 13.61232 KDa

Sequence

String:

MASFRFCLEC NNMLYPKEDK ENQRLLYSCR NCDYTELAED PKVYRHELIT NIGETAGIVD DIGQDPTLPR SDKECPECHS RDCVFFQSQ QRRKDTNMTL FYVCLNCKKT FRDESE

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #12: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...

• Macromolecule: Name: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III; type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 8.554064 KDa

Sequence

String:

MIIPVRCFSC GKVVGDKWDA YLRLLEEGKQ EGDALDELKL KRYCCRRMVL THVDLIEKFL RYNPLEKKDF DS

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

Macromolecule #13: RNA polymerase II subunit B12.5

• Macromolecule: Name: RNA polymerase II subunit B12.5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 13.832896 KDa

Sequence

String:

MNAPDRFELF ILPDDVPKLK ITPDSRVPNC IIIKFEREDH TLANLLREEL ALYPDVTFVA YKVEHPLFAN FVMRLQTEEG TRPKQALER ACASIINKLK TLDHKFNEEW NIKNFSLND

UniProtKB: RNA polymerase II subunit B12.5

Macromolecule #14: RNA polymerase subunit ABC10-alpha

• Macromolecule: Name: RNA polymerase subunit ABC10-alpha / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Komagataella phaffii GS115 (fungus)
• Molecular weight: Theoretical: 7.862048 KDa

Sequence

String:

MSREGFVAPS GTDLAAAASG VAPNKHYGVK YTCGACAHNF SLNKSDPVRC KECGHRVIYK ARTKRMIQFD AR

UniProtKB: RNA polymerase subunit ABC10-alpha

Macromolecule #16: Histone H3.1

• Macromolecule: Name: Histone H3.1 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.719445 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

Macromolecule #17: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.676703 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

Macromolecule #15: RNA (5'-R(P*CP*UP*UP*GP*GP*GP*UP*GP*UP*UP*U)-3')

• Macromolecule: Name: RNA (5'-R(P*CP*UP*UP*GP*GP*GP*UP*GP*UP*UP*U)-3') / type: rna / ID: 15 / Number of copies: 1
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 3.478042 KDa

Sequence

String:

CUUGGGUGUU U

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Specialist optics: Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 36878 / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: INSILICO MODEL / In silico model: 3D Initial model / Details: 3D initial model generated in RELION.
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 6.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: 3Dflex / Details: CryoSPARC 3D flex reconstruction / Number images used: 5000
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD