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- EMDB-34415: RNA polymerase II transcribing a chromatosome (type I) -

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Basic information

Entry
Database: EMDB / ID: EMD-34415
TitleRNA polymerase II transcribing a chromatosome (type I)
Map data
Sample
  • Complex: RNA polymerase II transcribing a chromatosome (type I)
    • Complex: RNA polymerase II
      • Protein or peptide: x 12 types
    • Complex: DNA,RNA
      • RNA: x 1 types
      • DNA: x 2 types
    • Complex: Histone
      • Protein or peptide: x 5 types
  • Ligand: x 2 types
Keywordschromatin / nucleosome / TRANSCRIPTION
Function / homology
Function and homology information


regulation of septum digestion after cytokinesis / histone H3K27me3 reader activity / siRNA-mediated pericentric heterochromatin formation / facultative heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding ...regulation of septum digestion after cytokinesis / histone H3K27me3 reader activity / siRNA-mediated pericentric heterochromatin formation / facultative heterochromatin formation / negative regulation of DNA recombination / RPB4-RPB7 complex / Apoptosis induced DNA fragmentation / chromosome condensation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleosomal DNA binding / termination of RNA polymerase II transcription / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / protein localization to CENP-A containing chromatin / transcription by RNA polymerase I / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / translation initiation factor binding / Packaging Of Telomere Ends / transcription-coupled nucleotide-excision repair / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / transcription initiation at RNA polymerase II promoter / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / P-body / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / chromatin DNA binding / 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 / Transcriptional regulation of granulopoiesis / DNA-directed RNA polymerase / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / DNA-directed RNA polymerase activity / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / 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 / HRDC-like superfamily / 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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
Similarity search - Domain/homology
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 ...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 H2A type 1-B/E / Histone H2B type 1-J / Histone H1.2 / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesKomagataella phaffii (fungus) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHirano R / Ehara H / Tomoya K / Takizawa Y / Sekine S / Kurumizaka H
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1.
Authors: Rina Hirano / Haruhiko Ehara / Tomoya Kujirai / Tamami Uejima / Yoshimasa Takizawa / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in ...In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.
History
DepositionSep 30, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34415.png

Downloads & links

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Map

FileDownload / File: emd_34415.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.030894665 - 0.08429674
Average (Standard dev.)0.00025994107 (±0.0038852044)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: RNAP reconstruction

Fileemd_34415_additional_1.map
AnnotationRNAP reconstruction
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Additional map: Nucleosome reconstruction

Fileemd_34415_additional_2.map
AnnotationNucleosome reconstruction
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Half map: #1

Fileemd_34415_half_map_1.map
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Half map: #2

Fileemd_34415_half_map_2.map
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Sample components

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Entire : RNA polymerase II transcribing a chromatosome (type I)

EntireName: RNA polymerase II transcribing a chromatosome (type I)
Components
  • Complex: RNA polymerase II transcribing a chromatosome (type I)
    • Complex: RNA polymerase II
      • 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
    • Complex: DNA,RNA
      • RNA: RNA (5'-R(P*AP*GP*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*U)-3')
      • DNA: DNA (261-MER)
      • DNA: DNA (261-MER)
    • Complex: Histone
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Histone H1.2
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNA polymerase II transcribing a chromatosome (type I)

SupramoleculeName: RNA polymerase II transcribing a chromatosome (type I)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Komagataella phaffii (fungus)

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Supramolecule #3: DNA,RNA

SupramoleculeName: DNA,RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13-#15

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Supramolecule #4: Histone

SupramoleculeName: Histone / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #16-#20
Source (natural)Organism: Homo sapiens (human)

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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: DNA-directed RNA polymerase II subunit RPB3

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

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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: 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

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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: 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

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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

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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

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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

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Macromolecule #16: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

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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

UniProtKB: Histone H4

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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: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

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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: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #20: Histone H1.2

MacromoleculeName: Histone H1.2 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.15684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSETAPAAPA AAPPAEKAPV KKKAAKKAGG TPRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK VKKAGGTKPK KPVGAAKKPK KAAGGATPKK SAKKTPKKAK K PAAATVTK ...String:
MSETAPAAPA AAPPAEKAPV KKKAAKKAGG TPRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK VKKAGGTKPK KPVGAAKKPK KAAGGATPKK SAKKTPKKAK K PAAATVTK KVAKSPKKAK VAKPKKAAKS AAKAVKPKAA KPKVVKPKKA APKKKLEVLF Q

UniProtKB: Histone H1.2

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

MacromoleculeName: RNA (5'-R(P*AP*GP*CP*AP*AP*UP*AP*GP*GP*AP*GP*CP*UP*U)-3')
type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.510755 KDa
SequenceString:
AGCAAUAGGA GCUU

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Macromolecule #14: DNA (261-MER)

MacromoleculeName: DNA (261-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 80.851555 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC) ...String:
(DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA) (DG)(DG)(DG)(DA)(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)(DA) (DT)(DT)(DC)(DC)(DC)(DA)(DA)(DA)(DC)(DA) (DC)(DA)(DC)(DC)(DA)(DA)(DA)(DC) (DA) (DC)(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DC)(DC) (DG)(DT)(DA)(DA)(DG)(DC)(DT)(DC)(DC) (DT)(DA)(DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA) (DA)(DA)(DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG) (DA)(DC)(DA)(DA)(DA)(DC)(DA)(DC)(DG) (DT)(DC)(DC)(DG)(DG)(DA)(DA)(DT)(DG)(DA) (DG) (DA)(DG)(DC)(DT)(DA)(DA)(DT)(DT) (DT)(DG)(DG)(DT)(DA)(DT)(DT)(DT)(DA)(DA) (DG)(DA) (DA)

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Macromolecule #15: DNA (261-MER)

MacromoleculeName: DNA (261-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 80.329078 KDa
SequenceString: (DT)(DT)(DC)(DT)(DT)(DA)(DA)(DA)(DT)(DA) (DC)(DC)(DA)(DA)(DA)(DT)(DT)(DA)(DG)(DC) (DT)(DC)(DT)(DC)(DA)(DT)(DT)(DC)(DC) (DG)(DG)(DA)(DC)(DG)(DT)(DG)(DT)(DT)(DT) (DG) (DT)(DC)(DC)(DT)(DC)(DT) ...String:
(DT)(DT)(DC)(DT)(DT)(DA)(DA)(DA)(DT)(DA) (DC)(DC)(DA)(DA)(DA)(DT)(DT)(DA)(DG)(DC) (DT)(DC)(DT)(DC)(DA)(DT)(DT)(DC)(DC) (DG)(DG)(DA)(DC)(DG)(DT)(DG)(DT)(DT)(DT) (DG) (DT)(DC)(DC)(DT)(DC)(DT)(DG)(DC) (DC)(DT)(DT)(DT)(DA)(DA)(DA)(DG)(DC)(DA) (DA)(DT) (DA)(DG)(DG)(DA)(DG)(DC)(DT) (DT)(DA)(DC)(DG)(DG)(DT)(DC)(DC)(DA)(DC) (DT)(DT)(DG) (DT)(DG)(DT)(DT)(DT)(DG) (DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)(DG) (DG)(DA)(DA)(DT) (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)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DC)(DA)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DC) (DT) (DT)(DG)(DT)(DG)(DT)(DC)(DG)(DC) (DG)(DA)(DA)(DA)(DT)(DT)(DC)(DA)(DT)(DA) (DG)(DA) (DT)

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #22: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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