[English] 日本語
Yorodumi
- EMDB-48043: RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48043
TitleRNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream
Map data
Sample
  • Complex: SETD2 downstream complex
    • Protein or peptide: x 28 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsSETD2 / Transcription / H3K36me3 / TRANSFERASE-RNA-DNA complex
Function / homology
Function and homology information


mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / blastocyst growth / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / positive regulation of mRNA 3'-end processing / Ski complex / [histone H3]-lysine36 N-trimethyltransferase ...mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / blastocyst growth / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / positive regulation of mRNA 3'-end processing / Ski complex / [histone H3]-lysine36 N-trimethyltransferase / mRNA decay by 3' to 5' exoribonuclease / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity / Cdc73/Paf1 complex / negative regulation of DNA-templated transcription, elongation / inner cell mass cell differentiation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / pericardium development / regulation of mRNA export from nucleus / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / DSIF complex / positive regulation of cell cycle G1/S phase transition / stem cell development / trophectodermal cell differentiation / blastocyst hatching / regulation of transcription elongation by RNA polymerase II / histone H3K36 methyltransferase activity / regulation of mRNA processing / nucleosome organization / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / response to type I interferon / protein-lysine N-methyltransferase activity / embryonic cranial skeleton morphogenesis / positive regulation of ossification / nuclear lumen / response to alkaloid / mRNA 3'-end processing / regulation of protein localization to chromatin / positive regulation of DNA-templated transcription, elongation / response to metal ion / Abortive elongation of HIV-1 transcript in the absence of Tat / histone H3 methyltransferase activity / poly(A)+ mRNA export from nucleus / regulation of double-strand break repair via homologous recombination / transcription elongation-coupled chromatin remodeling / stem cell population maintenance / transcription factor TFIID complex / interleukin-6-mediated signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of gene expression, epigenetic / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / endodermal cell differentiation / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of interferon-alpha production / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of Wnt signaling pathway / cell surface receptor signaling pathway via JAK-STAT / alpha-tubulin binding / Tat-mediated elongation of the HIV-1 transcript / transcription by RNA polymerase III / transcription by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / : / forebrain development / RNA Polymerase II Transcription Elongation / negative regulation of fibroblast proliferation
Similarity search - Function
Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / : / Histone-lysine N-methyltransferase SETD2, animal / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin ...Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / : / Histone-lysine N-methyltransferase SETD2, animal / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / : / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Tetratricopeptide repeat / Transcription initiation Spt4 / Spt4 superfamily / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / TFIIS N-terminal domain profile. / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Tetratricopeptide repeat / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / DNA-directed RNA polymerase II subunit Rpb4-like / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Tetratricopeptide repeat / WW domain / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 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.
Similarity search - Domain/homology
Histone H3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / RNA polymerase Rpb4/RPC9 core domain-containing protein / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11-a ...Histone H3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / RNA polymerase Rpb4/RPC9 core domain-containing protein / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Histone H2B 1.1 / Histone H2A type 1 / Transcription elongation factor A protein 1 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Transcription elongation factor SPT4 / Parafibromin / RNA polymerase-associated protein CTR9 homolog / RNA polymerase-associated protein RTF1 homolog / Protein IWS1 homolog / Histone-lysine N-methyltransferase SETD2 / Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMarkert J / Farnung L
Funding support United States, 4 items
OrganizationGrant numberCountry
Richard and Susan Smith Family Foundation United States
Damon Runyon Cancer Research Foundation United States
Rita Allen Foundation United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Science / Year: 2025
Title: Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription.
Authors: Jonathan W Markert / Jelly H Soffers / Lucas Farnung
Abstract: During transcription, RNA polymerase II traverses through chromatin, and posttranslational modifications including histone methylations mark regions of active transcription. Histone protein H3 lysine ...During transcription, RNA polymerase II traverses through chromatin, and posttranslational modifications including histone methylations mark regions of active transcription. Histone protein H3 lysine 36 trimethylation (H3K36me3), which is established by the histone methyltransferase SET domain containing 2 (SETD2), suppresses cryptic transcription, regulates splicing, and serves as a binding site for transcription elongation factors. The mechanism by which the transcription machinery coordinates the deposition of H3K36me3 is not well understood. Here we provide cryo-electron microscopy structures of mammalian RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome elongation complexes, revealing that the transcription machinery regulates H3K36me3 deposition by SETD2 on downstream and upstream nucleosomes. SPT6 binds the exposed H2A-H2B dimer during transcription, and the SPT6 death-like domain mediates an interaction with SETD2 bound to a nucleosome upstream of RNA polymerase II.
History
DepositionNov 21, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48043.png

Downloads & links

-
Map

FileDownload / File: emd_48043.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.19129011 - 0.54141814
Average (Standard dev.)-0.000038297916 (±0.0142409885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 550.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : SETD2 downstream complex

EntireName: SETD2 downstream complex
Components
  • Complex: SETD2 downstream complex
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: RNA polymerase Rpb4/RPC9 core domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerase II subunit E
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
    • Protein or peptide: DNA-directed RNA polymerase I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-a
    • Protein or peptide: RNA polymerase II subunit K
    • Protein or peptide: Transcription elongation factor SPT6
    • DNA: Non-template DNA
    • Protein or peptide: Protein IWS1 homolog
    • RNA: RNA
    • Protein or peptide: RNA polymerase-associated protein CTR9 homolog
    • Protein or peptide: RNA polymerase-associated protein RTF1 homolog
    • Protein or peptide: Transcription elongation factor A protein 1
    • DNA: Template DNA
    • Protein or peptide: RNA polymerase-associated protein LEO1
    • Protein or peptide: RNA polymerase II-associated factor 1 homolog
    • Protein or peptide: Superkiller complex protein 8, N-terminally processed
    • Protein or peptide: Parafibromin
    • Protein or peptide: Transcription elongation factor SPT4
    • Protein or peptide: Transcription elongation factor SPT5
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone-lysine N-methyltransferase SETD2
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: SETD2 downstream complex

SupramoleculeName: SETD2 downstream complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Homo sapiens (human)

+
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: Sus scrofa (pig)
Molecular weightTheoretical: 173.530125 KDa
SequenceString: DSACPLRTIK RVQFGVLSPD ELKRMSVTEG GIKYPETTEG GRPKLGGLMD PRQGVIERTG RCQTCAGNMT ECPGHFGHIE LAKPVFHVG FLVKTMKVLR CVCFFCSKLL VDSNNPKIKD ILAKSKGQPK KRLTHVYDLC KGKNICEGGE EMDNKFGVEQ P EGDEDLTK ...String:
DSACPLRTIK RVQFGVLSPD ELKRMSVTEG GIKYPETTEG GRPKLGGLMD PRQGVIERTG RCQTCAGNMT ECPGHFGHIE LAKPVFHVG FLVKTMKVLR CVCFFCSKLL VDSNNPKIKD ILAKSKGQPK KRLTHVYDLC KGKNICEGGE EMDNKFGVEQ P EGDEDLTK EKGHGGCGRY QPRIRRSGLE LYAEWKHVNE DSQEKKILLS PERVHEIFKR ISDEECFVLG MEPRYARPEW MI VTVLPVP PLSVRPAVVM QGSARNQDDL THKLADIVKI NNQLRRNEQN GAAAHVIAED VKLLQFHVAT MVDNELPGLP RAM QKSGRP LKSLKQRLKG KEGRVRGNLM GKRVDFSART VITPDPNLSI DQVGVPRSIA ANMTFAEIVT PFNIDRLQEL VRRG NSQYP GAKYIIRDNG DRIDLRFHPK PSDLHLQTGY KVERHMCDGD IVIFNRQPTL HKMSMMGHRV RILPWSTFRL NLSVT TPYN ADFDGDEMNL HLPQSLETRA EIQELAMVPR MIVTPQSNRP VMGIVQDTLT AVRKFTKRDV FLERGEVMNL LMFLST WDG KVPQPAILKP RPLWTGKQIF SLIIPGHINC IRTHSTHPDD EDSGPYKHIS PGDTKVVVEN GELIMGILCK KSLGTSA GS LVHISYLEMG HDITRLFYSN IQTVINNWLL IEGHTIGIGD SIADSKTYQD IQNTIKKAKQ DVIEVIEKAH NNELEPTP G NTLRQTFENQ VNRILNDARD KTGSSAQKSL SEYNNFKSMV VSGAKGSKIN ISQVIAVVGQ QNVEGKRIPF GFKHRTLPH FIKDDYGPES RGFVENSYLA GLTPTEFFFH AMGGREGLID TAVKTAETGY IQRRLIKSME SVMVKYDATV RNSINQVVQL RYGEDGLAG ESVEFQNLAT LKPSNKAFEK KFRFDYTNER ALRRTLQEDL VKDVLSNAHI QNELEREFER MREDREVLRV I FPTGDSKV VLPCNLLRMI WNAQKIFHIN PRLPSDLHPI KVVEGVKELS KKLVIVNGDD PLSRQAQENA TLLFNIHLRS TL CSRRMAE EFRLSGEAFD WLLGEIESKF NQAIAHPGEM VGALAAQSLG EPATQMTLNT FHYAGVSAKN VTLGVPRLKE LIN ISKKPK TPSLTVFLLG QSARDAERAK DILCRLEHTT LRKVTANTAI YYDPNPQSTV VAEDQEWVNV YYEMPDFDVA RISP WLLRV ELDRKHMTDR KLTMEQIAEK INAGFGDDLN CIFNDDNAEK LVLRIRIMNS DENKMQEEEE VVDKMDDDVF LRCIE SNML TDMTLQGIEQ ISKVYMHLPQ TDNKKKIIIT EDGEFKALQE WILETDGVSL MRVLSEKDVD PVRTTSNDIV EIFTVL GIE AVRKALEREL YHVISFDGSY VNYRHLALLC DTMTCRGHLM AITRHGVNRQ DTGPLMKCSF EETVDVLMEA AAHGESD PM KGVSENIMLG QLAPAGTGCF DLLLDAEKCK YGMEIPTNIP GLGAAGPTGM FFGSAPSPMG GISPAMTPWN QGA(TPO) PAYGA WSPSVGSGMT PGAAGF(SEP)PSA ASD

UniProtKB: DNA-directed RNA polymerase subunit

+
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: Sus scrofa (pig)
Molecular weightTheoretical: 132.189656 KDa
SequenceString: EITPDLWQEA CWIVISSYFD EKGLVRQQLD SFDEFIQMSV QRIVEDAPPI DLQAEAQHAS GEVEEPPRYL LKFEQIYLSK PTHWERDGA PSPMMPNEAR LRNLTYSAPL YVDITKTVIK EGEEQLQTQH QKTFIGKIPI MLRSTYCLLN GLTDRDLCEL N ECPLDPGG ...String:
EITPDLWQEA CWIVISSYFD EKGLVRQQLD SFDEFIQMSV QRIVEDAPPI DLQAEAQHAS GEVEEPPRYL LKFEQIYLSK PTHWERDGA PSPMMPNEAR LRNLTYSAPL YVDITKTVIK EGEEQLQTQH QKTFIGKIPI MLRSTYCLLN GLTDRDLCEL N ECPLDPGG YFIINGSEKV LIAQEKMATN TVYVFAKKDS KYAYTGECRS CLENSSRPTS TIWVSMLARG GQGAKKSAIG QR IVATLPY IKQEVPIIIV FRALGFVSDR DILEHIIYDF EDPEMMEMVK PSLDEAFVIQ EQNVALNFIG SRGAKPGVTK EKR IKYAKE VLQKEMLPHV GVSDFCETKK AYFLGYMVHR LLLAALGRRE LDDRDHYGNK RLDLAGPLLA FLFRGMFKNL LKEV RIYAQ KFIDRGKDFN LELAIKTRII SDGLKYSLAT GNWGDQKKAH QARAGVSQVL NRLTFASTLS HLRRLNSPIG RDGKL AKPR QLHNTLWGMV CPAETPEGHA VGLVKNLALM AYISVGSQPS PILEFLEEWS MENLEEISPA AIADATKIFV NGCWVG IHK DPEQLMNTLR KLRRQMDIIV SEVSMIRDIR EREIRIYTDA GRICRPLLIV EKQKLLLKKR HIDQLKEREY NNYSWQD LV ASGVVEYIDT LEEETVMLAM TPDDLQEKEV AYCSTYTHCE IHPSMILGVC ASIIPFPDHN QSPRNTYQSA MGKQAMGV Y ITNFHVRMDT LAHVLYYPQK PLVTTRSMEY LRFRELPAGI NSIVAIASYT GYNQEDSVIM NRSAVDRGFF RSVFYRSYK EQESKKGFDQ EEVFEKPTRE TCQGMRHAIY DKLDDDGLIA PGVRVSGDDV IIGKTVTLPE NEDELEGTNR RYTKRDCSTF LRTSETGIV DQVMVTLNQE GYKFCKIRVR SVRIPQIGDK FASRHGQKGT CGIQYRQEDM PFTCEGITPD IIINPHAIPS R MTIGHLIE CLQGKVSANK GEIGDATPFN DAVNVQKISN LLSDYGYHLR GNEVLYNGFT GRKITSQIFI GPTYYQRLKH MV DDKIHSR ARGPIQILNR QPMEGRSRDG GLRFGEMERD CQIAHGAAQF LRERLFEASD PYQVHVCNLC GIMAIANTRT HTY ECRGCR NKTQISLVRM PYACKLLFQE LMSMSIAPRM MSV

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 30.76723 KDa
SequenceString: PYANQPTVRI TELTDENVKF IIENTDLAVA NSIRRVFIAE VPIIAIDWVQ IDANSSVLHD EFIAHRLGLI PLTSDDIVDK LQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR L RAYAKKGF ...String:
PYANQPTVRI TELTDENVKF IIENTDLAVA NSIRRVFIAE VPIIAIDWVQ IDANSSVLHD EFIAHRLGLI PLTSDDIVDK LQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL ISNSPRVIPV TSRNRDNDPS DYVEQDDILI VKLRKGQELR L RAYAKKGF GKEHAKWNPT AGVAFEYDPD NALRHTVYPK PEEWPKSEYS ELDEDESQAP YDPNGKPERF YYNVESCGSL RP ETIVLSA LSGLKKKLSD LQTQLSHEIQ SD

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

+
Macromolecule #4: RNA polymerase Rpb4/RPC9 core domain-containing protein

MacromoleculeName: RNA polymerase Rpb4/RPC9 core domain-containing protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.70649 KDa
SequenceString:
EEDASQLIFP KEFETAETLL NSEVHMLLEH RKQQNESAED EQELSEVFMK TLNYTARFSR FKNRETIASV RSLLLQKKLH KFELACLAN LCPETAEESK ALIPSLEGRF EDEELQQILD DIQTKRS

UniProtKB: RNA polymerase Rpb4/RPC9 core domain-containing protein

+
Macromolecule #5: DNA-directed RNA polymerase II subunit E

MacromoleculeName: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 24.513119 KDa
SequenceString: DDEEETYRLW KIRKTIMQLC HDRGYLVTQD ELDQTLEEFK AQFGDKPSEG RPRRTDLTVL VAHNDDPTDQ MFVFFPEEPK VGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL A RYKLRENQ ...String:
DDEEETYRLW KIRKTIMQLC HDRGYLVTQD ELDQTLEEFK AQFGDKPSEG RPRRTDLTVL VAHNDDPTDQ MFVFFPEEPK VGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD MAPKYILEQF LQQELLINIT EHELVPEHVV MTKEEVTELL A RYKLRENQ LPRIQAGDPV ARYFGIKRGQ VVKIIRPSET AGRYITYRLV Q

UniProtKB: DNA-directed RNA polymerase II subunit E

+
Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 8.978591 KDa
SequenceString:
KRITTPYMTK YERARVLGTR ALQIAMCAPV MVELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

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

+
Macromolecule #7: DNA-directed RNA polymerase subunit

MacromoleculeName: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 19.227205 KDa
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLV

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: Sus scrofa (pig)
Molecular weightTheoretical: 17.031076 KDa
SequenceString:
AGILFEDIFD VKDIDPEGKK FDRVSRLHCE SESFKMDLIL DVNIQIYPVD LGDKFRLVIA STLYEDGTLD DGEYNPTDDR PSRADQFEY VMYGKVYRIE GDETSTEAAT RLSAYVSYGG LLMRLQGDAN NLHGFEVDSR VYLLMKKLAF

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

+
Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.521151 KDa
SequenceString:
GFVGIRFCQE CNNMLYPKED KENRILLYAC RNCDYQQEAD NSCIYVNKIT HEVDELTQII ADVSQDPTLP RTEDHPCQKC GHKEAVFFQ SHSARAEDAM RLYYVCTAPH CGHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

+
Macromolecule #10: DNA-directed RNA polymerase I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerase I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 7.525943 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLE

+
Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.068013 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEG

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

+
Macromolecule #12: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.747791 KDa
SequenceString:
QQPMIYICGE CHTENEIKSR DPIRCRECGY RIMYKKRTKR LVVFDAR

UniProtKB: RNA polymerase II subunit K

+
Macromolecule #13: Transcription elongation factor SPT6

MacromoleculeName: Transcription elongation factor SPT6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.027672 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DQDNEIRATD LPERFQLRSI PVKGAEDDEL EEEADWIYRN AFATPTISLS RKGPSTIQKI KEALGFMRNQ HFEVPFIAFY RKEYVEPEL HINDLWRVWQ WDEKWTQLRI RKENLTRLFE KMQAYQYEQI SAIRALDTTD MERLKDVQSM DELKDVYNHF L LYYGRDIP ...String:
DQDNEIRATD LPERFQLRSI PVKGAEDDEL EEEADWIYRN AFATPTISLS RKGPSTIQKI KEALGFMRNQ HFEVPFIAFY RKEYVEPEL HINDLWRVWQ WDEKWTQLRI RKENLTRLFE KMQAYQYEQI SAIRALDTTD MERLKDVQSM DELKDVYNHF L LYYGRDIP KKFGLTPEQF GENLRDSYQR HETEQFPAEP LELAKDTPEA VLEGARYMVA LQIAREPLVR QVLRQTFQER AK LNITPTK KGRKDVDEAH YAYSFKYLKN KPVKELRDDQ FLKICLAEDE GLLTTDISID LKGTYFEEIK QFYYRDEFSH QVQ EWNRQR TMAIERALQQ FLYVQMAKEL KNKLLAEAKE YVIKACSRKL YNWLRVAPYR PDQQQGKGIR VLGIAFSSAR DHPV FCALV NGEGEVTDFL RLPHFTEERE KKAQDIETLK KFLLNKKPHV VTVAGENRDA QMLIEDVKRI VHELDQGQQL SSIGV ELVD NELAILYMNS KKSEAEFRDY PPVLRQAVSL ARRIQDPLIE FAQVCSEDIL CLKFHPLQEH VVKEELLNAL YCEFIN RVN EVGVDVNRAI AHPYSQALIQ YVCGLGPRKG THLLKILKQN NTRLESRTQL VTMCHMGPKV FMNCAGFLKI DTEVLDG SR VHPETYEWAR KMAVDALEYD ESAEDANPAG ALEEILENPE RLKDLDLDAF AEELERQGYG DKHITLYDIR AELSCRYK D LRTAYRSPNT EEIFNMLTKE TPETFYIGKL IICNVTGIAH IGVKTRLDNG VTGFIPTKFL SDKVVKRPEE RVKVGMTVH CRIMKIDIEK FSADLTCRTS DLMIAHPSFH NINFKQAEKM METMDQGDVI IRPSSKGENH LTVTWKVSDG IYQHVDVRAT LWINSEEFE DLDEIVARYV QPMASFARDL LNHKYYQDCS GGDRKKLEEL LIKTKKEKPT FIPYFICACK ELPGKFLLGY Q PRGKPRIE YVTVTPEGFR YRGQIFPTVN GLFRWFKDHY QDPV

+
Macromolecule #15: Protein IWS1 homolog

MacromoleculeName: Protein IWS1 homolog / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.972472 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SDADDVVSAM IVKMNEAAEE DRQLNNQKKP ALKKLTLLPA VVMHLKKQDL KETFIDSGVM SAIKEWLSPL PDRSLPALKI REELLKILQ ELPSVSQETL KHSGIGRAVM YLYKHPKESR SNKDMAGKLI NEW

UniProtKB: Protein IWS1 homolog

+
Macromolecule #17: RNA polymerase-associated protein CTR9 homolog

MacromoleculeName: RNA polymerase-associated protein CTR9 homolog / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.85907 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RGSIEIPLRD TDEVIELDFD QLPEGDEVIS ILKQEHTQLH IWIALALEYY KQGKTEEFVK LLEAARIDGN LDYRDHEKDQ MTCLDTLAA YYVQQARKEK NKDNKKDLIT QATLLYTMAD KIIMYDQNHL LGRACFCLLE GDKMDQADAQ FHFVLNQSPN N IPALLGKA ...String:
RGSIEIPLRD TDEVIELDFD QLPEGDEVIS ILKQEHTQLH IWIALALEYY KQGKTEEFVK LLEAARIDGN LDYRDHEKDQ MTCLDTLAA YYVQQARKEK NKDNKKDLIT QATLLYTMAD KIIMYDQNHL LGRACFCLLE GDKMDQADAQ FHFVLNQSPN N IPALLGKA CISFNKKDYR GALAYYKKAL RTNPGCPAEV RLGMGHCFVK LNKLEKARLA FSRALELNSK CVGALVGLAV LE LNNKEAD SIKNGVQLLS RAYTIDPSNP MVLNHLANHF FFKKDYSKVQ HLALHAFHNT EVEAMQAESC YQLARSFHVQ EDY DQAFQY YYQATQFASS SFVLPFFGLG QMYIYRGDKE NASQCFEKVL KAYPNNYETM KILGSLYAAS EDQEKRDIAK GHLK KVTEQ YPDDVEAWIE LAQILEQTDI QGALSAYGTA TRILQEKVQA DVPPEILNNV GALHFRLGNL GEAKKYFLAS LDRAK AEAE HDEHYYNAIS VTTSYNLARL YEAMCEFHEA EKLYKNILRE HPNYVDCYLR LGAMARDKGN FYEASDWFKE ALQINQ DHP DAWSLIGNLH LAKQEWGPGQ KKFERILKQP STQSDTYSML ALGNVWLQTL HQPTRDREKE KRHQDRALAI YKQVLRN DA KNLYAANGIG AVLAHKGYFR EARDVFAQVR EATADISDVW LNLAHIYVEQ KQYISAVQMY ENCLRKFYKH QNTEVVLY L ARALFKCGKL QECKQTLLKA RHVAPSDTVL MFNVALVLQR LATSVLKDEK SNLKEVLNAV KELELAHRYF SYLSKVGDK MRFDLALAAT EARQCSDLLS QAQYHVARAR KQDEEERELR AKQEQEKELL RQKLLKEQEE KRLREKEEQK KLLEQRAQYV EKTKNILMF T

UniProtKB: RNA polymerase-associated protein CTR9 homolog

+
Macromolecule #18: RNA polymerase-associated protein RTF1 homolog

MacromoleculeName: RNA polymerase-associated protein RTF1 homolog / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.128234 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VSLPEELNRV RLSRHKLERW CHMPFFAKTV TGCFVRIGIG NHNSKPVYRV AEITGVVETA KVYQLGGTRT NKGLQLRHGN DQRVFRLEF VSNQEFTESE FMKWKEAMFS AGMQLPTLDE INKKELSIKE ALNYKFNDQD IEEIVKEKER FRKAPPNYAM K KTQLLKEK ...String:
VSLPEELNRV RLSRHKLERW CHMPFFAKTV TGCFVRIGIG NHNSKPVYRV AEITGVVETA KVYQLGGTRT NKGLQLRHGN DQRVFRLEF VSNQEFTESE FMKWKEAMFS AGMQLPTLDE INKKELSIKE ALNYKFNDQD IEEIVKEKER FRKAPPNYAM K KTQLLKEK AMAEDLGDQD KAKQIQDQLN ELEERAEALD RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MD PFTRRQC K

UniProtKB: RNA polymerase-associated protein RTF1 homolog

+
Macromolecule #19: Transcription elongation factor A protein 1

MacromoleculeName: Transcription elongation factor A protein 1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.371117 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RAPSTSDSVR LKCREMLAAA LRTGDDYIAI GADEEELGSQ IEEAIYQEIR NTDMKYKNRV RSRISNLKDA KNPNLRKNVL CGNIPPDLF ARMTAEEMAS DELKEMRKNL TKEAIREHQM AKTGGTQTDL FTCGKCKKKN CTYTQVQTRS ADEPMTTFVV C NECGNRWK FC

UniProtKB: Transcription elongation factor A protein 1

+
Macromolecule #21: RNA polymerase-associated protein LEO1

MacromoleculeName: RNA polymerase-associated protein LEO1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.451314 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GNDLYFVKLP NFLSVEPRPF DPQYYEDEFE EEGRTRLKLK VENNARIVKW SDGSMSLHLG NEVFDVYKAP LQGDHNHLFI RQGTGLQGQ AVFKTKLTFR PHSTDSATHR KMTLSLADRC SKTQKI

+
Macromolecule #22: RNA polymerase II-associated factor 1 homolog

MacromoleculeName: RNA polymerase II-associated factor 1 homolog / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.991545 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ERSGVVCRVK YCNSLPDIPF DPKFITYPFD QNRFVQYKAT SLEKQHKHDL LTEPDLGVTI DLINPDTYRI DPNVLLDPAD EKLLEEEIQ RSQQHAKVVP WMRKTEYIST EFNKDRDSQI TAIEKTFEDA QKSISQHYSK PRVTPVEVMP VSQAMIRGMM D EEGNQFVA ...String:
ERSGVVCRVK YCNSLPDIPF DPKFITYPFD QNRFVQYKAT SLEKQHKHDL LTEPDLGVTI DLINPDTYRI DPNVLLDPAD EKLLEEEIQ RSQQHAKVVP WMRKTEYIST EFNKDRDSQI TAIEKTFEDA QKSISQHYSK PRVTPVEVMP VSQAMIRGMM D EEGNQFVA YFLPVEETLK KRKRDQEEEM DYAPDDVYDY KIAREYNWNV KNKASKGYEE NYFFIFREGD GVYYNELETR VR LSKR

+
Macromolecule #23: Superkiller complex protein 8, N-terminally processed

MacromoleculeName: Superkiller complex protein 8, N-terminally processed / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.029781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: YGILFKQEQA HDDAIWSVAW GTNKKENSET VVTGSLDDLV KVWKWRDERL DLQWSLEGHQ LGVVSVDISH TLPIAASSSL DAHIRLWDL ENGKQIKSID AGPVDAWTLA FSPDSQYLAT GTHVGKVNIF GVESGKKEYS LDTRGKFILS IAYSPDGKYL A SGAIDGII ...String:
YGILFKQEQA HDDAIWSVAW GTNKKENSET VVTGSLDDLV KVWKWRDERL DLQWSLEGHQ LGVVSVDISH TLPIAASSSL DAHIRLWDL ENGKQIKSID AGPVDAWTLA FSPDSQYLAT GTHVGKVNIF GVESGKKEYS LDTRGKFILS IAYSPDGKYL A SGAIDGII NIFDIATGKL LHTLEGHAMP IRSLTFSPDS QLLVTASDDG YIKIYDVQHA NLAGTLSGHA SWVLNVAFCP DD THFVSSS SDKSVKVWDV GTRTCVHTFF DHQDQVWGVK YNGNGSKIVS VGDDQEIHIY DCP

UniProtKB: Superkiller complex protein 8

+
Macromolecule #24: Parafibromin

MacromoleculeName: Parafibromin / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.029778 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
VDVTRDIVSR ERVWRTRTTI LQSTGKNFSK NIFAILQSVK ARE

UniProtKB: Parafibromin

+
Macromolecule #25: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.079004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALETVPKDLR HLRACLLCSL VKTIDQFEYD GCDNCDAYLQ MKGNREMVYD CTSSSFDGII AMMSPEDSWV SKWQRVSNFK PGVYAVSVT GRLPQGIVRE LKSRGVAYKS RDTAIKT

UniProtKB: Transcription elongation factor SPT4

+
Macromolecule #26: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.815262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPNLWTVKCK IGEERATAIS LMRKFIAYQF TDTPLQIKSV VAPEHVKGYI YVEAYKQTHV KQAIEGVGNL RLGYWNQQMV PIKEMTDVL KVVKANLKPK SWVRLKRGIY KDDIAQVDYV EPSQNTISLK MIPRIDYDRI KAPPQRLFDA EKIRSLGGDV A SDGDFLIF ...String:
DPNLWTVKCK IGEERATAIS LMRKFIAYQF TDTPLQIKSV VAPEHVKGYI YVEAYKQTHV KQAIEGVGNL RLGYWNQQMV PIKEMTDVL KVVKANLKPK SWVRLKRGIY KDDIAQVDYV EPSQNTISLK MIPRIDYDRI KAPPQRLFDA EKIRSLGGDV A SDGDFLIF EGNRYSRKGF LFKSFAMSAV ITEGVKPTLS ELEKFREHNF QPGDNVEVCE GELINLQGKI LSVDGNKITI MP KHEDLKD MLEFPAQELR KYFKMGDHVK VIAGRFEGDT GLIVRVEENF VILFSDLTMH ELKVLPRDLQ LCSETASGVD VGG QHEWGE LVQLDPQTVG VIVRLERETF QVLNMYGKVV TVRHQAVTRK KDNRFAVALD SEQNNIHVKD IVKVIDGPHS GREG EIRHL FRSFAFLHCK KLVENGGMFV CKTRHLVLAN ELIGQTVRIS QGPYKGYIGV VKDATESTAR VELHSTCQTI SVDRQ RLTT VGSRRPGGMT STYGRYGSQ(TPO) PMYGSG

+
Macromolecule #27: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.437144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVMKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

+
Macromolecule #28: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 8.853342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFG

UniProtKB: Histone H4

+
Macromolecule #29: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 29 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A type 1

+
Macromolecule #30: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 30 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

+
Macromolecule #31: Histone-lysine N-methyltransferase SETD2

MacromoleculeName: Histone-lysine N-methyltransferase SETD2 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine36 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.3785 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDCL NRLLMIECSS RCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK ARVKEYARNK NIHYYFMALK N DEIIDATQ ...String:
DDFRDPQRWK ECAKQGKMPC YFDLIEENVY LTERKKNKSH RDIKRMQCEC TPLSKDERAQ GEIACGEDCL NRLLMIECSS RCPNGDYCS NRRFQRKQHA DVEVILTEKK GWGLRAAKDL PSNTFVLEYC GEVLDHKEFK ARVKEYARNK NIHYYFMALK N DEIIDATQ KGNCSRFMNH SCEPNCETQK WTVNGQLRVG FFTTKLVPSG SELTFDYQFQ RYGKEAQKCF CGSANCRGYL GG ENRVSIR AAGGKMKKER SRKKDSVDGE LEALMENGEG LSDKNQVLSL SRLMVRIETL EQKLTCLELI QNTHSQSCLK SFL ERHGLS LLWIWMAELG DGRESNQKLQ EEIIKTLEHL PIPTKNMLEE SKVLPIIQRW SQTKTAVPPL SEGDGYSSEN TSRA HTPLN TPDPSTKLST EADTDTPKKL MFRRLKIISE NSMDSAISDA TSELEGKDGK EDLDQLENVP VEEEEELQSQ QLLPQ QLPE CKVDSETNIE ASKLPTSEPE ADAEIEPKES NGTKLEEPIN EETPSQDEEE GVSDVESERS QEQPDKTVDI SDLATK LLD SWKDLKEVYR IPKKSQTEKE NTTTER

UniProtKB: Histone-lysine N-methyltransferase SETD2

+
Macromolecule #14: Non-template DNA

MacromoleculeName: Non-template DNA / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.348324 KDa
SequenceString: (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) ...String:
(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)(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) (DG)(DA)(DT) (DA)(DA)(DC)(DG)(DG)(DC)(DC)(DA)(DG)(DT) (DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG)(DG) (DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG)

+
Macromolecule #20: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.053766 KDa
SequenceString: (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)(DG)(DC)(DC)(DG)(DT)(DT)(DA) (DT) (DC)(DG)(DA)(DT)(DG)(DT) ...String:
(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)(DG)(DC)(DC)(DG)(DT)(DT)(DA) (DT) (DC)(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)(DG)(DA)(DT)(DT)(DC)(DT) (DG)

+
Macromolecule #16: RNA

MacromoleculeName: RNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.475138 KDa
SequenceString:
AAAAUUAGCU C

+
Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / 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: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121657
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more