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- EMDB-12967: Structure of active transcription elongation complex Pol II-DSIF-... -

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Basic information

Entry
Database: EMDB / ID: EMD-12967
TitleStructure of active transcription elongation complex Pol II-DSIF-ELL2-EAF1, Map 6, Focused map for the stalk of Pol II
Map dataFocused map for the stalk region of Pol II (map6), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model).
Sample
  • Complex: Transcription elongation complex of RNA polymerase II with elongation factors DSIF, ELL2 and EAF1
    • Complex: RNA Polymerase
      • Protein or peptide: x 12 types
    • Complex: Elongation and association factor
      • Protein or peptide: x 2 types
    • Complex: DNA and RNA
      • DNA: x 2 types
      • RNA: x 1 types
    • Complex: Transcription elongation factor
      • Protein or peptide: x 2 types
Function / homology
Function and homology information


super elongation complex / negative regulation of DNA-templated transcription, elongation / : / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...super elongation complex / negative regulation of DNA-templated transcription, elongation / : / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / 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 / transcription elongation factor activity / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / intercellular bridge / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / organelle membrane / RNA polymerase III activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / cis-regulatory region sequence-specific DNA binding / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Cajal body / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / positive regulation of RNA splicing / transcription elongation factor complex / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / nuclear body / protein dimerization activity / hydrolase activity / nuclear speck / protein heterodimerization activity / RNA-directed RNA polymerase / intracellular membrane-bounded organelle
Similarity search - Function
Transcription elongation factor Eaf, N-terminal / EAF family / RNA polymerase II transcription elongation factor / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / E3 ubiquitin-protein ligase ELL-like ...Transcription elongation factor Eaf, N-terminal / EAF family / RNA polymerase II transcription elongation factor / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / E3 ubiquitin-protein ligase ELL-like / Spt5, KOW domain repeat 6 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / 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 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / RNA-binding domain, S1 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / 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 II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4
Similarity search - Domain/homology
RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E ...RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / RNA polymerase II elongation factor ELL2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / ELL-associated factor 1
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human) / HIV whole-genome vector AA1305#18 (others) / pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsChen Y / Vos SM / Dienemann C / Ninov M / Urlaub H / Cramer P
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)Advanced Grant CHROMATRANS 693023 Germany
German Research Foundation (DFG)SFB1286 Germany
CitationJournal: Mol Cell / Year: 2021
Title: Allosteric transcription stimulation by RNA polymerase II super elongation complex.
Authors: Ying Chen / Seychelle M Vos / Christian Dienemann / Momchil Ninov / Henning Urlaub / Patrick Cramer /
Abstract: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we ...The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
History
DepositionMay 18, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateSep 1, 2021-
Current statusSep 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12967.png

Downloads & links

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Map

FileDownload / File: emd_12967.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map for the stalk region of Pol II (map6), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.16425082 - 0.25136623
Average (Standard dev.)-8.377867e-06 (±0.0028168585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z315.000315.000315.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1640.251-0.000

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Supplemental data

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Mask #1

Fileemd_12967_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 for the focused map of the Stalk region of Pol II (map6)

Fileemd_12967_half_map_1.map
Annotationhalf map 1 for the focused map of the Stalk region of Pol II (map6)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 for the focused map of the Stalk region of Pol II (map6)

Fileemd_12967_half_map_2.map
Annotationhalf map 2 for the focused map of the Stalk region of Pol II (map6)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transcription elongation complex of RNA polymerase II with elonga...

EntireName: Transcription elongation complex of RNA polymerase II with elongation factors DSIF, ELL2 and EAF1
Components
  • Complex: Transcription elongation complex of RNA polymerase II with elongation factors DSIF, ELL2 and EAF1
    • Complex: RNA Polymerase
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
      • Protein or peptide: DNA-directed RNA polymerase subunit beta
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
      • Protein or peptide: RNA polymerase II subunit D
      • Protein or peptide: RNA polymerase II subunit E
      • Protein or peptide: RNA polymerase II subunit F
      • Protein or peptide: RNA polymerase II subunit G
      • 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 polymerases 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
    • Complex: Elongation and association factor
      • Protein or peptide: RNA polymerase II elongation factor ELL2
      • Protein or peptide: ELL-associated factor 1
    • Complex: DNA and RNA
      • DNA: Template DNA
      • DNA: Non-template DNA
      • RNA: RNA
    • Complex: Transcription elongation factor
      • Protein or peptide: Transcription elongation factor SPT5
      • Protein or peptide: Transcription elongation factor SPT4

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Supramolecule #1: Transcription elongation complex of RNA polymerase II with elonga...

SupramoleculeName: Transcription elongation complex of RNA polymerase II with elongation factors DSIF, ELL2 and EAF1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19

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Supramolecule #2: RNA Polymerase

SupramoleculeName: RNA Polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: Elongation and association factor

SupramoleculeName: Elongation and association factor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13-#14
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: DNA and RNA

SupramoleculeName: DNA and RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #15-#17
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
Recombinant expressionOrganism: HIV whole-genome vector AA1305#18 (others)

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Supramolecule #5: Transcription elongation factor

SupramoleculeName: Transcription elongation factor / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #18-#19
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMT ECPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK R LTHVYDLC KGKNICEGGE EMDNKFGVEQ ...String:
MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMT ECPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK R LTHVYDLC KGKNICEGGE EMDNKFGVEQ PEGDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQ EKKILLS PERVHEIFKR ISDEECFVLG MEPRYARPEW MIVTVLPVPP LSVRPAVVMQ GSARNQDDLT HKL ADIVKI NNQLRRNEQN GAAAHVIAED VKLLQFHVAT MVDNELPGLP RAMQKSGRPL KSLKQRLKGK EGRV RGNLM GKRVDFSART VITPDPNLSI DQVGVPRSIA ANMTFAEIVT PFNIDRLQEL VRRGNSQYPG AKYII RDNG DRIDLRFHPK PSDLHLQTGY KVERHMCDGD IVIFNRQPTL HKMSMMGHRV RILPWSTFRL NLSVTT PYN ADFDGDEMNL HLPQSLETRA EIQELAMVPR MIVTPQSNRP VMGIVQDTLT AVRKFTKRDV FLERGEV MN LLMFLSTWDG KVPQPAILKP RPLWTGKQIF SLIIPGHINC IRTHSTHPDD EDSGPYKHIS PGDTKVVV E NGELIMGILC KKSLGTSAGS LVHISYLEMG HDITRLFYSN IQTVINNWLL IEGHTIGIGD SIADSKTYQ DIQNTIKKAK QDVIEVIEKA HNNELEPTPG NTLRQTFENQ VNRILNDARD KTGSSAQKSL SEYNNFKSMV VSGAKGSKI NISQVIAVVG QQNVEGKRIP FGFKHRTLPH FIKDDYGPES RGFVENSYLA GLTPTEFFFH A MGGREGLI DTAVKTAETG YIQRRLIKSM ESVMVKYDAT VRNSINQVVQ LRYGEDGLAG ESVEFQNLAT LK PSNKAFE KKFRFDYTNE RALRRTLQED LVKDVLSNAH IQNELEREFE RMREDREVLR VIFPTGDSKV VLP CNLLRM IWNAQKIFHI NPRLPSDLHP IKVVEGVKEL SKKLVIVNGD DPLSRQAQEN ATLLFNIHLR STLC SRRMA EEFRLSGEAF DWLLGEIESK FNQAIAHPGE MVGALAAQSL GEPATQMTLN TFHYAGVSAK NVTLG VPRL KELINISKKP KTPSLTVFLL GQSARDAERA KDILCRLEHT TLRKVTANTA IYYDPNPQST VVAEDQ EWV NVYYEMPDFD VARISPWLLR VELDRKHMTD RKLTMEQIAE KINAGFGDDL NCIFNDDNAE KLVLRIR IM NSDENKMQEE EEVVDKMDDD VFLRCIESNM LTDMTLQGIE QISKVYMHLP QTDNKKKIII TEDGEFKA L QEWILETDGV SLMRVLSEKD VDPVRTTSND IVEIFTVLGI EAVRKALERE LYHVISFDGS YVNYRHLAL LCDTMTCRGH LMAITRHGVN RQDTGPLMKC SFEETVDVLM EAAAHGESDP MKGVSENIML GQLAPAGTGC FDLLLDAEK CKYGMEIPTN IPGLGAAGPT GMFFGSAPSP MGGISPAMTP WNQGATPAYG AWSPSVGSGM T PGAAGFSP SAASDASGFS PGYSPAWSPT PGSPGSPGPS SPYIPSPGGA MSPSYSPTSP AYEPRSPGGY TP QSPSYSP TSPSYSPTSP SYSPTSPNYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSP TSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP NYSP TSPNY TPTSPSYSPT SPSYSPTSPN YTPTSPNYSP TSPSYSPTSP SYSPTSPSYS PSSPRYTPQS PTYTP SSPS YSPSSPSYSP TSPKYTPTSP SYSPSSPEYT PTSPKYSPTS PKYSPTSPKY SPTSPTYSPT TPKYSP TSP TYSPTSPVYT PTSPKYSPTS PTYSPTSPKY SPTSPTYSPT SPKGSTYSPT SPGYSPTSPT YSLTSPA IS PDDSDEEN

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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 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString: MCSTNLSQAL AYFRAGANLT AASLWAGFRG SRRIFWERRK RKSLCLALRP GGACWRWLLA VSCVSLRGL GAPGSCANMY DADEDMQYDE DDDEITPDLW QEACWIVISS YFDEKGLVRQ Q LDSFDEFI QMSVQRIVED APPIDLQAEA QHASGEVEEP PRYLLKFEQI ...String:
MCSTNLSQAL AYFRAGANLT AASLWAGFRG SRRIFWERRK RKSLCLALRP GGACWRWLLA VSCVSLRGL GAPGSCANMY DADEDMQYDE DDDEITPDLW QEACWIVISS YFDEKGLVRQ Q LDSFDEFI QMSVQRIVED APPIDLQAEA QHASGEVEEP PRYLLKFEQI YLSKPTHWER DG APSPMMP NEARLRNLTY SAPLYVDITK TVIKEGEEQL QTQHQKTFIG KIPIMLRSTY CLL NGLTDR DLCELNECPL DPGGYFIING SEKVLIAQEK MATNTVYVFA KKDSKYAYTG ECRS CLENS SRPTSTIWVS MLARGGQGAK KSAIGQRIVA TLPYIKQEVP IIIVFRALGF VSDRD ILEH IIYDFEDPEM MEMVKPSLDE AFVIQEQNVA LNFIGSRGAK PGVTKEKRIK YAKEVL QKE MLPHVGVSDF CETKKAYFLG YMVHRLLLAA LGRRELDDRD HYGNKRLDLA GPLLAFL FR GMFKNLLKEV RIYAQKFIDR GKDFNLELAI KTRIISDGLK YSLATGNWGD QKKAHQAR A GVSQVLNRLT FASTLSHLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLV KNLALMAYIS VGSQPSPILE FLEEWSMENL EEISPAAIAD ATKIFVNGCW VGIHKDPEQL MNTLRKLRR QMDIIVSEVS MIRDIREREI RIYTDAGRIC RPLLIVEKQK LLLKKRHIDQ L KEREYNNY SWQDLVASGV VEYIDTLEEE TVMLAMTPDD LQEKEVAYCS TYTHCEIHPS MI LGVCASI IPFPDHNQSP RNTYQSAMGK QAMGVYITNF HVRMDTLAHV LYYPQKPLVT TRS MEYLRF RELPAGINSI VAIASYTGYN QEDSVIMNRS AVDRGFFRSV FYRSYKEQES KKGF DQEEV FEKPTRETCQ GMRHAIYDKL DDDGLIAPGV RVSGDDVIIG KTVTLPENED ELEGT NRRY TKRDCSTFLR TSETGIVDQV MVTLNQEGYK FCKIRVRSVR IPQIGDKFAS RHGQKG TCG IQYRQEDMPF TCEGITPDII INPHAIPSRM TIGHLIECLQ GKVSANKGEI GDATPFN DA VNVQKISNLL SDYGYHLRGN EVLYNGFTGR KITSQIFIGP TYYQRLKHMV DDKIHSRA R GPIQILNRQP MEGRSRDGGL RFGEMERDCQ IAHGAAQFLR ERLFEASDPY QVHVCNLCG IMAIANTRTH TYECRGCRNK TQISLVRMPY ACKLLFQELM SMSIAPRMMS V

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLG LIPLTSDDIV DKLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD L ISNSPRVI PVTSRNRDND PSDYVEQDDI LIVKLRKGQE LRLRAYAKKG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLG LIPLTSDDIV DKLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD L ISNSPRVI PVTSRNRDND PSDYVEQDDI LIVKLRKGQE LRLRAYAKKG FGKEHAKWNP TA GVAFEYD PDNALRHTVY PKPEEWPKSE YSELDEDESQ APYDPNGKPE RFYYNVESCG SLR PETIVL SALSGLKKKL SDLQTQLSHE IQSDVLTIN

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Macromolecule #4: RNA polymerase II subunit D

MacromoleculeName: RNA polymerase II subunit D / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MWGPAQPYSD SALSPKPRPF RAVFRGSALP FPAVRVEVRG RSMAAGGSDP RAGDVEEDAS QLIFPKEFE TAETLLNSEV HMLLEHRKQQ NESAEDEQEL SEVFMKTLNY TARFSRFKNR E TIASVRSL LLQKKLHKFE LACLANLCPE TAEESKALIP SLEGRFEDEE LQQILDDIQT KR SFQY

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Macromolecule #5: RNA polymerase II subunit E

MacromoleculeName: RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPT DQMFVFFPEE PKVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV D MAPKYILE QFLQQELLIN ITEHELVPEH VVMTKEEVTE LLARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPT DQMFVFFPEE PKVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV D MAPKYILE QFLQQELLIN ITEHELVPEH VVMTKEEVTE LLARYKLREN QLPRIQAGDP VA RYFGIKR GQVVKIIRPS ETAGRYITYR LVQ

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Macromolecule #6: RNA polymerase II subunit F

MacromoleculeName: RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTR ALQIAMCAPV MVELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG V DELIISD

+
Macromolecule #7: RNA polymerase II subunit G

MacromoleculeName: RNA polymerase II subunit G / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYP VKYKAIVFRP FKGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF D PNSNPPCY KTMDEDIVIQ QDDEIRLKIV GTRVDKNDIF AIGSLMDDYL GLVS

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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 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGT LDDGEYNPTD DRPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG G LLMRLQGD ANNLHGFEVD SRVYLLMKKL AF

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQII ADVSQDPTLP RTEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC G HRWTE

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

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

+
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 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEH KIIIRVQTTP DYSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

+
Macromolecule #12: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

+
Macromolecule #13: RNA polymerase II elongation factor ELL2

MacromoleculeName: RNA polymerase II elongation factor ELL2 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAGGTGGLR EEQRYGLSCG RLGQDNITVL HVKLTETAIR ALETYQSHKN LIPFRPSIQF QGLHGLVKI PKNDPLNEVH NFNFYLSNVG KDNPQGSFDC IQQTFSSSGA SQLNCLGFIQ D KITVCATN DSYQMTRERM TQAEEESRNR STKVIKPGGP YVGKRVQIRK ...String:
MAAGGTGGLR EEQRYGLSCG RLGQDNITVL HVKLTETAIR ALETYQSHKN LIPFRPSIQF QGLHGLVKI PKNDPLNEVH NFNFYLSNVG KDNPQGSFDC IQQTFSSSGA SQLNCLGFIQ D KITVCATN DSYQMTRERM TQAEEESRNR STKVIKPGGP YVGKRVQIRK APQAVSDTVP ER KRSTPMN PANTIRKTHS SSTISQRPYR DRVIHLLALK AYKKPELLAR LQKDGVNQKD KNS LGAILQ QVANLNSKDL SYTLKDYVFK ELQRDWPGYS EIDRRSLESV LSRKLNPSQN AAGT SRSES PVCSSRDAVS SPQKRLLDSE FIDPLMNKKA RISHLTNRVP PTLNGHLNPT SEKSA AGLP LPPAAAAIPT PPPLPSTYLP ISHPPQIVNS NSNSPSTPEG RGTQDLPVDS FSQNDS IYE DQQDKYTSRT SLETLPPGSV LLKCPKPMEE NHSMSHKKSK KKSKKHKEKD QIKKHDI ET IEEKEEDLKR EEEIAKLNNS SPNSSGGVKE DCTASMEPSA IELPDYLIKY IAIVSYEQ R QNYKDDFNAE YDEYRALHAR METVARRFIK LDAQRKRLSP GSKEYQNVHE EVLQEYQKI KQSSPNYHEE KYRCEYLHNK LAHIKRLIGE FDQQQAESWS

+
Macromolecule #14: ELL-associated factor 1

MacromoleculeName: ELL-associated factor 1 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNGTANPLLD REEHCLRLGE SFEKRPRASF HTIRYDFKPA SIDTSCEGEL QVGKGDEVTI TLPHIPGST PPMTVFKGNK RPYQKDCVLI INHDTGEYVL EKLSSSIQVK KTRAEGSSKI Q ARMEQQPT RPPQTSQPPP PPPPMPFRAP TKPPVGPKTS PLKDNPSPEP ...String:
MNGTANPLLD REEHCLRLGE SFEKRPRASF HTIRYDFKPA SIDTSCEGEL QVGKGDEVTI TLPHIPGST PPMTVFKGNK RPYQKDCVLI INHDTGEYVL EKLSSSIQVK KTRAEGSSKI Q ARMEQQPT RPPQTSQPPP PPPPMPFRAP TKPPVGPKTS PLKDNPSPEP QLDDIKRELR AE VDIIEQM SSSSGSSSSD SESSSGSDDD SSSSGGEDNG PASPPQPSHQ QPYNSRPAVA NGT SRPQGS NQLMNTLRND LQLSESGSDS DD

+
Macromolecule #18: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKK PRHGGFILDE ADVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR S GARRLQNL WRDQREEELG EYYMKKYAKS SVGETVYGGS DELSDDITQQ ...String:
MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKK PRHGGFILDE ADVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR S GARRLQNL WRDQREEELG EYYMKKYAKS SVGETVYGGS DELSDDITQQ QLLPGVKDPN LW TVKCKIG EERATAISLM RKFIAYQFTD TPLQIKSVVA PEHVKGYIYV EAYKQTHVKQ AIE GVGNLR LGYWNQQMVP IKEMTDVLKV VKEVANLKPK SWVRLKRGIY KDDIAQVDYV EPSQ NTISL KMIPRIDYDR IKARMSLKDW FAKRKKFKRP PQRLFDAEKI RSLGGDVASD GDFLI FEGN RYSRKGFLFK SFAMSAVITE GVKPTLSELE KFEDQPEGID LEVVTESTGK EREHNF QPG DNVEVCEGEL INLQGKILSV DGNKITIMPK HEDLKDMLEF PAQELRKYFK MGDHVKV IA GRFEGDTGLI VRVEENFVIL FSDLTMHELK VLPRDLQLCS ETASGVDVGG QHEWGELV Q LDPQTVGVIV RLERETFQVL NMYGKVVTVR HQAVTRKKDN RFAVALDSEQ NNIHVKDIV KVIDGPHSGR EGEIRHLFRS FAFLHCKKLV ENGGMFVCKT RHLVLAGGSK PRDVTNFTVG GFAPMSPRI SSPMHPSAGG QRGGFGSPGG GSGGMSRGRG RRDNELIGQT VRISQGPYKG Y IGVVKDAT ESTARVELHS TCQTISVDRQ RLTTVGSRRP GGMTSTYGRT PMYGSQTPMY GS GSRTPMY GSQTPLQDGS RTPHYGSQTP LHDGSRTPAQ SGAWDPNNPN TPSRAEEEYE YAF DDEPTP SPQAYGGTPN PQTPGYPDPS SPQVNPQYNP QTPGTPAMYN TDQFSPYAAP SPQG SYQPS PSPQSYHQVA PSPAGYQNTH SPASYHPTPS PMAYQASPSP SPVGYSPMTP GAPSP GGYN PHTPGSGIEQ NSSDWVTTDI QVKVRDTYLD TQVVGQTGVI RSVTGGMCSV YLKDSE KVV SISSEHLEPI TPTKNNKVKV ILGEDREATG VLLSIDGEDG IVRMDLDEQL KILNLRF LG KLLEA

+
Macromolecule #19: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 19 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MALETVPKDL RHLRACLLCS LVKTIDQFEY DGCDNCDAYL QMKGNREMVY DCTSSSFDGI IAMMSPEDS WVSKWQRVSN FKPGVYAVSV TGRLPQGIVR ELKSRGVAYK SRDTAIKT

+
Macromolecule #15: Template DNA

MacromoleculeName: Template DNA / type: dna / ID: 15 / Classification: DNA
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
SequenceString:
GGCAAGCTTT ATTGAGGCTT AAGCAGTGGG TTCAAGGTAC TAGTGTAC

+
Macromolecule #16: Non-template DNA

MacromoleculeName: Non-template DNA / type: dna / ID: 16 / Classification: DNA
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
SequenceString:
GTACACTAGT ACCTACTCGA GTGACCTTAA GCCTCAATAA AGCTTGCC

+
Macromolecule #17: RNA

MacromoleculeName: RNA / type: rna / ID: 17
Details: The last nucleotide (A47) was extended at the 3' of the original synthetic RNA scaffold (46-mer) during complex assembly in the presence of ATP.
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
SequenceString:
ACCAGAUCUG AGCCUGGGAG CUCUCUGGCU AACUAGGGAA CCCACUA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 43.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Ab initio model created by CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107918
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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