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- EMDB-60593: RNA polymerase II elongation complex stalled at SHL(-1) of the nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-60593
TitleRNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B
Map data
Sample
  • Complex: RNA polymerase II - nucleosome complex
    • Complex: RNA polymerase II
      • Protein or peptide: x 13 types
    • Complex: Histones
      • Protein or peptide: x 4 types
    • Complex: DNA
      • DNA: x 2 types
    • Complex: RNA
      • RNA: x 1 types
    • Protein or peptide: x 2 types
  • Ligand: x 2 types
KeywordsTranscription-DNA-RNA COMPLEX / RNAPII / TRANSCRIPTION
Function / homology
Function and homology information


negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of septum digestion after cytokinesis / regulation of transcription-coupled nucleotide-excision repair / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / siRNA-mediated pericentric heterochromatin formation / RNA polymerase I core binding / DSIF complex / regulation of rRNA processing / intracellular mRNA localization ...negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of septum digestion after cytokinesis / regulation of transcription-coupled nucleotide-excision repair / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / siRNA-mediated pericentric heterochromatin formation / RNA polymerase I core binding / DSIF complex / regulation of rRNA processing / intracellular mRNA localization / RNA polymerase I general transcription initiation factor binding / rDNA heterochromatin / transcription elongation factor complex / intracellular phosphate ion homeostasis / transcription elongation-coupled chromatin remodeling / snRNP binding / U4 snRNA binding / transcription elongation factor activity / chromatin-protein adaptor activity / kinetochore assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / spliceosomal complex assembly / RNA polymerase II complex binding / termination of RNA polymerase II transcription / U5 snRNA binding / termination of RNA polymerase I transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / chromosome, centromeric region / transcription initiation at RNA polymerase I promoter / positive regulation of translational initiation / mitotic metaphase chromosome alignment / U2 snRNA binding / nuclear-transcribed mRNA catabolic process / U6 snRNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / U1 snRNA binding / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / negative regulation of megakaryocyte differentiation / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / protein localization to CENP-A containing chromatin / transcription by RNA polymerase I / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / transcription-coupled nucleotide-excision repair / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of autophagy / telomere organization / 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 / translesion synthesis / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / 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 / Meiotic synapsis / 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 / positive regulation of transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / transcription initiation at RNA polymerase II promoter / P-body / euchromatin / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription elongation by RNA polymerase II / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / transcription by RNA polymerase II
Similarity search - Function
Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / : ...Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / : / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / 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 Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / S1 domain profile. / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / 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
Similarity search - Domain/homology
Transcription elongation factor 1 homolog / 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 / Transcription elongation factor SPT5 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit ...Transcription elongation factor 1 homolog / 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 / Transcription elongation factor SPT5 / 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 / Transcription elongation factor SPT4 / Histone H2B type 1-J / Histone H2A-Bbd type 2/3 / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii (fungus) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAkatsu M / Kujirai T / Rina H / Ehara H / 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)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 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)JP23K17392 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
CitationJournal: EMBO J / Year: 2025
Title: Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B.
Authors: Munetaka Akatsu / Rina Hirano / Tomoya Kujirai / Mitsuo Ogasawara / Haruhiko Ehara / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka /
Abstract: H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that ...H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.
History
DepositionJun 19, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60593.png

Downloads & links

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Map

FileDownload / File: emd_60593.map.gz / Format: CCP4 / Size: 178 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.)
1.06 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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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00843
Minimum - Maximum-0.022489788 - 0.052126758
Average (Standard dev.)0.00025803674 (±0.00176177)
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: #4

Fileemd_60593_additional_1.map
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Additional map: #2

Fileemd_60593_additional_2.map
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Additional map: #1

Fileemd_60593_additional_3.map
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Additional map: #3

Fileemd_60593_additional_4.map
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Half map: #2

Fileemd_60593_half_map_1.map
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Half map: #1

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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
      • 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
      • Protein or peptide: Transcription elongation factor 1 homolog
    • Complex: Histones
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A-Bbd type 2/3
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA
      • DNA: DNA (198-MER)
      • DNA: DNA (198-MER)
    • Complex: RNA
      • RNA: RNA (5'-R(P*CP*CP*CP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
    • Protein or peptide: Transcription elongation factor SPT4
    • Protein or peptide: Transcription elongation factor SPT5
  • 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-#22

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Supramolecule #2: RNA polymerase II

SupramoleculeName: RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13
Source (natural)Organism: Komagataella phaffii (fungus)

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Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #19-#22
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14, #16
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: RNA

SupramoleculeName: RNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #15
Source (natural)Organism: synthetic construct (others)

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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

+
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

+
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

+
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 #13: Transcription elongation factor 1 homolog

MacromoleculeName: Transcription elongation factor 1 homolog / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 12.395677 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGKRKSSARK PAPKIKQKLE TQFTCLFCNH DNSVVCTLDK KNSIGLLECK KCNLSFQAPI NSLSQPIDIY SDWIDACEAV AEENADVNG DNFIENDGAD REQDDDYDDE F

UniProtKB: Transcription elongation factor 1 homolog

+
Macromolecule #17: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 12.62726 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTNKGVRER ACMLCGIVLP GRVFMQNGCP NCDSVLNLRD SDQATVNECT SSSFEGLVAV GDNEHSWVAK WLRVDRFQPG LYAVRVDGR LPSDIVAALE QYGVYYRPRD GSVID

UniProtKB: Transcription elongation factor SPT4

+
Macromolecule #18: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella phaffii (fungus)
Molecular weightTheoretical: 101.248188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSETHKNQLD KVSTVSPDGP SEAVKEHSLQ SKDLSKNDGQ FIVPLDRNVI EQEEHKQVKS SAQAHNTTGD AADNEIEDGV PSEDVEFDK FKEDDYDEDD EVEEEGDIRS RKRRRHNQFL DVEAEVDDEE DDDDDDDDVE LKHDFIQDDH IQHETQNEGF I AGHVDDDR ...String:
MSETHKNQLD KVSTVSPDGP SEAVKEHSLQ SKDLSKNDGQ FIVPLDRNVI EQEEHKQVKS SAQAHNTTGD AADNEIEDGV PSEDVEFDK FKEDDYDEDD EVEEEGDIRS RKRRRHNQFL DVEAEVDDEE DDDDDDDDVE LKHDFIQDDH IQHETQNEGF I AGHVDDDR LHRKLDQSRE KIADQDAQEL ADEFKQRYGR SASSKYMGSA STTAPQRLLI PTVDDPGIWG VKVRLGKEKD VV RQILKKK LAREGTKNPL EIYSAFQRDS FKGHVYIEAR KAEAINDALK GNVNVFSNNS KFLVGIVEYK DLLRPVKSSD VKL TRGSYV RVKNGKFKGD LAQVDEVLEN GLEARLKLVP RLDYGKDLSH LSTSSSVDST KNRRKFYTSK FRPAQRLFSE AEAR VHEPT IRRDRDGFVT YGGEEYYEGF LYKTFRLQNL IVNSINPTLN ELSLFQSNEE STTIDLSTIA DSLKETAKNL VSFQP GDNV EIINGELNHL TGTVSSVNQS TIVSVRLHSD DDTINSETVE IPTSDLRKIF NVGDHVRVIH GKHTDDTGLI VEVNGD KVE FISNQTKRTV IVFSNYLIKS TDSTVSINES GRFELHDLVQ VNSDLVGIVI RAQKDSFDVL CSDGKLLSLP PVSIYSK LN LNPNQQIAID SNGVEVKVGD TVREFTGERR QGTILHVYRN FLFLRSREIV ENQGVFVTSS NRVKTITSKS NGTGGQIS G PDLSRMNPSR VIPPPSIPVA NQRMTGRDPT LNKTVKIRQG GYKGKIGIVK EANGDRFRVE LHNPNKTIPI PCSFLLIES THGWVPYEDF VASDRRGGNI PRHEISGHVQ QPQHGRAPAW GSGGKTPAWG SGGKTPAWGS GGSGGKTPAW GSGGKTPTWG SGAKTPAWG SGSKTPAWSG LDEEDRRDF

UniProtKB: Transcription elongation factor SPT5

+
Macromolecule #19: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 19 / 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 #20: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 20 / 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 #21: Histone H2A-Bbd type 2/3

MacromoleculeName: Histone H2A-Bbd type 2/3 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.732389 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRRRRRRGS SGAGGRGRTC SRTVRAELSF SVSQVERSLR EGHYAQRLSR TAPVYLAAVI EYLTAKVLEL AGNEAQNSGE RNITPLLLD MVVHNDRLLS TLFNTTTISQ VAPGED

UniProtKB: Histone H2A-Bbd type 2/3

+
Macromolecule #22: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 22 / Number of copies: 1 / 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 #14: DNA (198-MER)

MacromoleculeName: DNA (198-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 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 #16: DNA (198-MER)

MacromoleculeName: DNA (198-MER) / type: dna / ID: 16 / 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 #15: RNA (5'-R(P*CP*CP*CP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.12304 KDa
SequenceString:
CCCGGUGUCU UGGGUG

+
Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #24: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 24 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH(pH7.5)
200.0 nMZinc acetate(CH3COO)2Zn
0.1 mMTCEP-HCl

Details: 20 mM HEPES-KOH(pH7.5), 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 0.06 mg/mL. This sample contains 0.003% NP-40.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.4 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

9713

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 297456
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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