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- EMDB-57673: Cryo-EM structure of the yeast RNA polymerase II elongation compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-57673
TitleCryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in State III (TL-open), in the presence of substrate ATP
Map dataCryoEM map of Yeast RNA polymerase II elongation complex ( 19 mer RNA) with ATP_open state
Sample
  • Complex: Yeast RNA polymerase II elongation complex
    • Protein or peptide: x 10 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsCryoEM / RNA Polymerase / Transcription
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsYi G / Li Q / Zhang P / Wang D
Funding support United Kingdom, United States, 6 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148476 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147652 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI170791-7522 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)CA280467 United States
CitationJournal: bioRxiv / Year: 2026
Title: Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle.
Authors: Gangshun Yi / Qingrong Li / Hannah Holmberg / Shisheng Li / Daniel K Clare / Dong Wang / Peijun Zhang
Abstract: RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post- ...RNA polymerase II (RNAPII) drives gene expression through iterative nucleotide addition cycles (NACs) comprising translocation, substrate binding, and catalysis. The lack of pre-catalysis and post-catalysis intermediates has precluded a complete mechanistic understanding of the NAC. Here we present 43 cryo-EM structures capturing distinct stages of the RNAPII elongation complex (EC) NAC, including previously intractable transition intermediates. We establish a continuous spectrum of RNAPII EC structural dynamics during the NAC, which can be divided into two coordinated phases: a substrate-induced EC tightening phase and a post-catalysis EC relaxation phase. For the substrate-induced EC tightening phase, the substrate binding initiates allosteric conformational changes across the entire RNAPII EC, including TL folding, funnel closure, clamp closure, transcription bubble ordering, and precise alignment of the RNA 3'-end with substrate to form a catalysis-competent configuration. For the post-catalysis EC relaxation phase, we captured the long-sought, short-lived post-catalysis product state and identified a series of intermediates that reveal a reverse conformational transition that facilitates rapid translocation. Together, our findings define a comprehensive structural and dynamic framework for RNAPII NAC, yielding a "molecular movie" of RNAPII in action and revealing a fundamental principle by which the enzyme balances speed and fidelity through coordinated conformational dynamics.
History
DepositionApr 22, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57673.png

Downloads & links

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Map

FileDownload / File: emd_57673.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Yeast RNA polymerase II elongation complex ( 19 mer RNA) with ATP_open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.40374056 - 0.91538775
Average (Standard dev.)-0.00059819006 (±0.024990765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B of cryoEM structure of Yeast...

Fileemd_57673_half_map_1.map
AnnotationHalf map B of cryoEM structure of Yeast RNA polymerase II elongation complex ( 19 mer RNA) with ATP_open state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryoEM structure of Yeast...

Fileemd_57673_half_map_2.map
AnnotationHalf map A of cryoEM structure of Yeast RNA polymerase II elongation complex ( 19 mer RNA) with ATP_open state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast RNA polymerase II elongation complex

EntireName: Yeast RNA polymerase II elongation complex
Components
  • Complex: Yeast RNA polymerase II elongation complex
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • 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
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • DNA: DNA (74-MER)
    • RNA: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')
    • DNA: DNA (74-MER)
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Yeast RNA polymerase II elongation complex

SupramoleculeName: Yeast RNA polymerase II elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#13, #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 513 KDa

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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 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 191.821578 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG ...String:
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG NTQPTIRKDG LKLVGSWKKD RATGDADEPE LRVLSTEEIL NIFKHISVKD FTSLGFNEVF SRPEWMILTC LP VPPPPVR PSISFNESQR GEDDLTFKLA DILKANISLE TLEHNGAPHH AIEEAESLLQ FHVATYMDND IAGQPQALQK SGR PVKSIR ARLKGKEGRI RGNLMGKRVD FSARTVISGD PNLELDQVGV PKSIAKTLTY PEVVTPYNID RLTQLVRNGP NEHP GAKYV IRDSGDRIDL RYSKRAGDIQ LQYGWKVERH IMDNDPVLFN RQPSLHKMSM MAHRVKVIPY STFRLNLSVT SPYNA DFDG DEMNLHVPQS EETRAELSQL CAVPLQIVSP QSNKPCMGIV QDTLCGIRKL TLRDTFIELD QVLNMLYWVP DWDGVI PTP AIIKPKPLWS GKQILSVAIP NGIHLQRFDE GTTLLSPKDN GMLIIDGQII FGVVEKKTVG SSNGGLIHVV TREKGPQ VC AKLFGNIQKV VNFWLLHNGF STGIGDTIAD GPTMREITET IAEAKKKVLD VTKEAQANLL TAKHGMTLRE SFEDNVVR F LNEARDKAGR LAEVNLKDLN NVKQMVMAGS KGSFINIAQM SACVGQQSVE GKRIAFGFVD RTLPHFSKDD YSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGS DAAFEKRYRV DLLNTDHTLD PSLLESGSEI LGDLKLQVLL DEEYKQLVKD RKFLREVFVD GEANWPLPVN I RRIIQNAQ QTFHIDHTKP SDLTIKDIVL GVKDLQENLL VLRGKNEIIQ NAQRDAVTLF CCLLRSRLAT RRVLQEYRLT KQ AFDWVLS NIEAQFLRSV VHPGEMVGVL AAQSIGEPAT QMTLNTFHFA GVASKKVTSG VPRLKEILNV AKNMKTPSLT VYL EPGHAA DQEQAKLIRS AIEHTTLKSV TIASEIYYDP DPRSTVIPED EEIIQLHFSL LDEEAEQSFD QQSPWLLRLE LDRA AMNDK DLTMGQVGER IKQTFKNDLF VIWSEDNDEK LIIRCRVVRP KSLDAETEAE EDHMLKKIEN TMLENITLRG VENIE RVVM MKYDRKVPSP TGEYVKEPEW VLETDGVNLS EVMTVPGIDP TRIYTNSFID IMEVLGIEAG RAALYKEVYN VIASDG SYV NYRHMALLVD VMTTQGGLTS VTRHGFNRSN TGALMRCSFE ETVEILFEAG ASAELDDCRG VSENVILGQM APIGTGA FD VMIDEESLVK YMPEQKITEI EDGQDGGVTP YSNESGLVNA DLDVKDELMF SPLVDSGSND AMAGGFTAYG GADYGEAT S PFGAYGEAPT SPGFGVSSPG FSPTSPTYSP TSPAYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSY SPTSPNYSPT SPSYSPTSPG YSPGSPAYSP KQDEQKHNEN ENSR

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 138.937297 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG ...String:
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG RLPIMLRSKN CYLSEATESD LYKLKECPFD MGGYFIINGS EKVLIAQERS AGNIVQVFKK AAPSPISHVA EI RSALEKG SRFISTLQVK LYGREGSSAR TIKATLPYIK QDIPIVIIFR ALGIIPDGEI LEHICYDVND WQMLEMLKPC VED GFVIQD RETALDFIGR RGTALGIKKE KRIQYAKDIL QKEFLPHITQ LEGFESRKAF FLGYMINRLL LCALDRKDQD DRDH FGKKR LDLAGPLLAQ LFKTLFKKLT KDIFRYMQRT VEEAHDFNMK LAINAKTITS GLKYALATGN WGEQKKAMSS RAGVS QVLN RYTYSSTLSH LRRTNTPIGR DGKLAKPRQL HNTHWGLVCP AETPEGQACG LVKNLSLMSC ISVGTDPMPI ITFLSE WGM EPLEDYVPHQ SPDATRVFVN GVWHGVHRNP ARLMETLRTL RRKGDINPEV SMIRDIREKE LKIFTDAGRV YRPLFIV ED DESLGHKELK VRKGHIAKLM ATEYQDIEGG FEDVEEYTWS SLLNEGLVEY IDAEEEESIL IAMQPEDLEP AEANEEND L DVDPAKRIRV SHHATTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGT YDKLDDDGLI APGVRVSGED VIIGKTTPIS PDEEELGQRT AYHSKRDAST PLRSTENGIV DQVLVTTNQD G LKFVKVRV RTTKIPQIGD KFASRHGQKG TIGITYRRED MPFTAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVAALS GN EGDASPF TDITVEGISK LLREHGYQSR GFEVMYNGHT GKKLMAQIFF GPTYYQRLRH MVDDKIHARA RGPMQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAASF LKERLMEASD AFRVHICGIC GLMTVIAKLN HNQFECKGCD NKIDIYQIHI PYAA KLLFQ ELMAMNITPR LYTDRSRDF

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.330457 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA ...String:
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA KWGPAAAIEF EYDPWNKLKH TDYWYEQDSA KEWPQSKNCE YEDPPNEGDP FDYKAQADTF YMNVESVGSI PV DQVVVRG IDTLQKKVAS ILLALTQMDQ DKVNFASGDN NTASNMLGSN EDVMMTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.117094 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.931834 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

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

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Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.525363 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

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

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Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.308161 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #8: 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: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.290732 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

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

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Macromolecule #9: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.633493 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.729969 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #11: DNA (74-MER)

MacromoleculeName: DNA (74-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.851645 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT)(DA) (DT)(DT)(DA)(DA)(DT)(DG)(DA)(DA)(DT)(DT) (DC)(DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA) (DT)(DC)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DC) (DC) (DA)(DT)(DT)(DC)(DC)(DT) ...String:
(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT)(DA) (DT)(DT)(DA)(DA)(DT)(DG)(DA)(DA)(DT)(DT) (DC)(DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA) (DT)(DC)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DC) (DC) (DA)(DT)(DT)(DC)(DC)(DT)(DA)(DC) (DT)(DT)(DG)(DG)(DG)(DA)(DG)(DA)(DA)(DG) (DG)(DA) (DG)(DC)(DA)(DG)(DA)(DG)(DC) (DG)(DG)(DG)(DA)(DT)(DC)(DC)

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Macromolecule #13: DNA (74-MER)

MacromoleculeName: DNA (74-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.582428 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DG)(DG)(DA)(DT)(DC) (DC)(DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC) (DT)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DC)(DC) (DA) (DT)(DC)(DC)(DT)(DC)(DT) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DG)(DG)(DA)(DT)(DC) (DC)(DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC) (DT)(DC)(DC)(DT)(DT)(DC)(DT)(DC)(DC)(DC) (DA) (DT)(DC)(DC)(DT)(DC)(DT)(DC)(DG) (DA)(DT)(DG)(DG)(DC)(DT)(DA)(DT)(DG)(DA) (DG)(DA) (DT)(DC)(DA)(DA)(DC)(DT)(DA) (DG)(DG)(DA)(DA)(DT)(DT)(DC)

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Macromolecule #12: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*AP*UP*CP*GP*AP*GP*AP*GP*...

MacromoleculeName: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*CP*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')
type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.995506 KDa
SequenceString:
UUUUUUUUUC AUCGAGAGG

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Macromolecule #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #16: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2e2h


Details: 2E2H and 8U9R
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: UCSF Chimera, UCSF ChimeraX, PHENIX) / Number images used: 66728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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