EMDB-61965: A cryo-EM structure of B. oleracea RNA polymerase V in complex wi...

Basic information

Entry

Database: EMDB / ID: EMD-61965

• Title: A cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom

Sample

• Complex: DNA-directed RNA polymerase V in complex with 4U scaffold
  • Complex: DNA-directed RNA polymerase V
    • Protein or peptide: x 7 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Complex: DNA-RNA
    • Protein or peptide: x 3 types
• Ligand: x 2 types

• Keywords: DNA-dependent RNA polymerase V / TRANSCRIPTION / plant

Function / homology

Function:

RNA polymerase IV complex / RNA polymerase V complex / nuclear DNA-directed RNA polymerase complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding

Domain/homology:

Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Nucleic acid-binding, OB-fold

Component:

Uncharacterized protein / DNA-directed RNA polymerase subunit / Uncharacterized protein / Uncharacterized protein / DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein / Uncharacterized protein

• Biological species: Brassica oleracea (wild cabbage)
• Method: single particle reconstruction / cryo EM / Resolution: 3.32 Å
• Authors: Xie G / Du X / Du J

Funding support

1 items

Organization	Grant number	Country
Other government

• Citation: Journal: EMBO J / Year: 2026; Title: A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.; Authors: Guohui Xie / Xuan Du / Yifang Tan / Yuxing Zhou / Cheng Chi / Sixian Zhou / Colette L Picard / Songge Chai / Lei Wu / Danling Zhu / Jun Zhao / Yan Xue / Sisi Li / Steven E Jacobsen / Zhe Wu / Jiamu Du / ; Abstract: DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3'-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNA). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNA, which subsequently defines the DNA methylation landscape in plants. A-rich-DNA successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNA show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.

History

Deposition	Oct 16, 2024	-
Header (metadata) release	Apr 15, 2026	-
Map release	Apr 15, 2026	-
Update	Apr 15, 2026	-
Current status	Apr 15, 2026	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_61965.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.095 Å

Density

Contour Level	By AUTHOR: 0.0112
Minimum - Maximum	-0.052204285 - 0.11772316
Average (Standard dev.)	0.00025640565 (±0.0026770628)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 300 300 300 Spacing 300 300 300
Cell	A=B=C: 328.5 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_61965_msk_1.map

Half map: #1

• File: emd_61965_half_map_1.map

Half map: #2

• File: emd_61965_half_map_2.map

Sample components

Entire : DNA-directed RNA polymerase V in complex with 4U scaffold

• Entire: Name: DNA-directed RNA polymerase V in complex with 4U scaffold

Components

• Complex: DNA-directed RNA polymerase V in complex with 4U scaffold
  • Complex: DNA-directed RNA polymerase V
    • Protein or peptide: DNA-directed RNA polymerase II, IV and V subunit 10
    • Protein or peptide: DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerase II, IV and V subunit 12
    • Protein or peptide: DNA-directed RNA polymerase II, IV and V subunit 8
    • Protein or peptide: DNA-directed RNA polymerase subunit
    • Protein or peptide: RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerase IV and V subunit 2
    • DNA: DNA (34-MER)
    • DNA: DNA (34-MER)
    • RNA: RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*UP*U)-3')
  • Complex: DNA-RNA
    • Protein or peptide: DNA-directed RNA polymerase V largest subunit
    • Protein or peptide: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION

Supramolecule #1: DNA-directed RNA polymerase V in complex with 4U scaffold

• Supramolecule: Name: DNA-directed RNA polymerase V in complex with 4U scaffold; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
• Source (natural): Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence

Supramolecule #2: DNA-directed RNA polymerase V

• Supramolecule: Name: DNA-directed RNA polymerase V / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4-#13

Supramolecule #3: DNA-RNA

• Supramolecule: Name: DNA-RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#3

Macromolecule #1: DNA-directed RNA polymerase V largest subunit

• Macromolecule: Name: DNA-directed RNA polymerase V largest subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 222.876891 KDa

Sequence

String:

MEEASSSDIL EAEIVGISFA LATHRQIRLA SISDAGINHA SQLSNAFLGL PLEFGKCEAC GATEPDKCEG HFGYIHLPVP IYHPAHVSE LKQMLSLLCL KCLKIKKIKS TSSGLAERLL GVCCEEASNI TIKDKSSDGA SYLQLKLPSR TRLQEGFWNF L ERYGYRYG SDHTRPLLAR EVKEILRRIP EETRKKLTAK GHIPQEGYIL EYLPVPPNCL SVPEVSDGSN SMSVDPSRIE LK DVLRKVV AINNSRSGET NFESHRAEAN EMFRVVDTYL QVRGTAKPTR NIDMRFGVSK ISDSSSSKAW TEKMRTLFIR KGS GFSSRS VITGDAFRNV NEVGIPMEIA HRITFEERVS VHNIGYLQEL VDNKMCLSYT QGSTTYSLRD GSKGHTVLKP GQIV HRRVM DGDVVFINRP PTTHKHSLQA LRVYVHEDNT VKINPLMCGP LSADFDGDCV HLFYPQSLTA KAEVLELFSV DKQLR SSHT GQLILQLGLD SLLSLRVMME QVFLDKASAQ QLAMYGSRSL PSPAVVKSSK SGPAWTFFQI LQLAFPERLS CRGDGF IVG GSDLLSFDFG VDALASIING IVTGIMVEKG PKEALAFFDS LQPLLMEHLD PQGFSLSLED LSMSREDMGV IHNLIVR EI SPMVSRLRLS YEDELQLENS IQKVKEVAAN FMLKSYSMRN LIDIKSNSAI NKLVQQIGFL GLQLSDKKKL YTKTLVED M AQFYKKKYVS TSSSGDFGIV KGCFFHGLDP YEEMAHSVAA REVIVRSSRG LAEPGTLFKN LMAVLRDIVI TNDGTVRNT CSNSIVQFKY ELSSDNENQG LFEAGDPVGV LAATAMSNPA YKAVLDSSPN SNSSWELMKE VLLCKVNFQN TTNDRRVILY LNECRCGKK YCQENSAYTV RNKLKKVSLK DTAVEFLVEY RKQQAISEIF GMDICLHGHI HLNKTLLEGW NISMQDILQR C EDAINSLV QKKKKKAEDF KKMNLSVSEC CSFRGPGSSK DSDMPCLMFS SYNATDPDLE RTLDVLCNTI YPVLLETVIK GD PRIASAN IIWNSPETTT WIRSLHASRR GEWVLDVTVE KSDVKQSGDA WRVVIDSCLS VLHLIDTKRS IPYSIKQVQE LLG LSCAFE QAVQRLSASV RKVSKGVLKE HIILVANNMT CSGDMLGFNY GGYKALTRSL NIKAPFTEAT LIAPRKCFEK AAEK CHKDS LSTVVGSCSW GKRVDVGTGS QFELLWNKKE TGLENDDETD VFSFLQMVRS TKTADAYVSS PGFDVTEEEM AEWAE SPER DSALGEPKFD DSAEFQNLLD EGKASESKWD NGSLWENGCS SGSEWGVSKN AGGEENTQSG WGKAANVENE DASSGW NSK KDAQEATNTD SWGAWGSKTK DDAENATPNW GTKPAQNDSV VIENGEPSSD VWGPKAVSDK PWGKKNSETE PAPAAWG KT NSESESAAAA WGSDDEKNTG TESDAAGWGS TYKKNPETEL NAAAWGSGAK MNKETEPAPA AWGSWGKKSS ETVSGGAD W GNRGKRVSET ESGAGGWASR NRSLENQSGG ATWGSRDKSK FETESGGAAW GSQAKNNSET EPGSGAAALG TWDKKKPET ETGGGGAAWG SQAKNNSETE SGSGAAAWGT WDKKKSETES GGGAWGSQAK KNSETESGAG ASTWGAWDKK KPETESGGGG AAWGSQAKN NSETESGSGA AAWGSQAKKN SESQLGTANW GSKDTNNSEN GSDSAAWGKK KNSEAEPTSV AWCSWGQPSP P ASDKDAQE DDGNPWVSLK ATSSGDKEGN ETSQWGVPNK RYPSAGSQSQ GGGGGADWKR NRPPRTPGSE SILGPMFTAT RQ RVDMFTS EEQELLSDVD PVMRRLRKIM HQSGYTDGEP ISDEDKTYVL EQILNYHPDK DAKLGPGLDF ITVDKHTTFT ESR CFFVVS TDGTKQDFSY RKCINNYLVE KHPNLAEEFI AKYFRKRDNE NRDKNSQEAT PPGEQESQTQ PIDNGSQDSQ PQPI GNEGG DTQPQSQIED IQPIGNGGED SQTEPQA

Macromolecule #2: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein

• Macromolecule: Name: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 35.48407 KDa

Sequence

String:

MDTGATYQRF PKVKIRELKD DYAKFELRDT DVSMANALRR VMISEVPTVA IDLVEIEVNS SVLNDEFIAH RLGLIPLTSE RAMSMRFSR DCDACDGDGQ CEFCSVEFRL SAKCVTDQTL DVTSKDLYSA DPTVTPVDFG DSSGADSSEQ RGIIIVKLRR G QELKLRAI ARKGIGKDHA KWSPAATVTF MYEPDIIINE DMMDTLTDDE KIDLIESSPT KVFDFDAVTR QVVVVDPEAY TY DEEVIKK AEAMGKQGLI EIRPKDDSFI FTVESTGAVK ASQLVLNAID LLKQKLDAVR LSDDTVEADD QFGELGAHMR GG

UniProtKB: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein

Macromolecule #3: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein

• Macromolecule: Name: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein; type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 16.686348 KDa

Sequence

String:

MAEDDYNEVD DLGYEDEPAE PEIEEGIEED ADMKDNDDIN GEPLETEDKV ETEPVQRPRK TSKFMTKYER ARILGTRALQ ISMNAPVMV ELEGETDPLE IAMKELRQRK IPFTIRRYLP DGSFEEWGVD ELIVEDSWKR QVGGD

UniProtKB: Uncharacterized protein

Macromolecule #4: DNA-directed RNA polymerase II, IV and V subunit 10

• Macromolecule: Name: DNA-directed RNA polymerase II, IV and V subunit 10 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 8.167508 KDa

Sequence

String:

MIIPVRCFTC GKVIGNKWDT YLDLLQADYT EGDALDAIGL VRYCCRRMLM THVDLIEKLL NYNTLEKSDA N

UniProtKB: Uncharacterized protein

Macromolecule #5: DNA-directed RNA polymerase RBP11-like dimerisation domain-contai...

• Macromolecule: Name: DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein; type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 13.538273 KDa

Sequence

String:

MNAPDRYERF VVPEGTKKVS YERDTKIINA ASFTIEREDH TIGNIVRMQL HRDENVLFAG YQLPHPLKYK IIVRIHTTSQ SSPMQAYNQ AINDLDKELD FLKSQFEAEV AKFSNPY

UniProtKB: DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein

Macromolecule #6: DNA-directed RNA polymerase II, IV and V subunit 12

• Macromolecule: Name: DNA-directed RNA polymerase II, IV and V subunit 12 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 5.983796 KDa

Sequence

String:

MDQQSEPVTY VCGDCGQENT LKSGDVIQCR ECGYRILYKK RTRRVVQYEA R

UniProtKB: Uncharacterized protein

Macromolecule #7: DNA-directed RNA polymerase II, IV and V subunit 8

• Macromolecule: Name: DNA-directed RNA polymerase II, IV and V subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 16.607275 KDa

Sequence

String:

MASSIIMFED IFVVDKLDPD GKKFDKVTRI EATSHNLDMF MHLDVNTEVY PMAVGDKFTL AMAPTLNLDG TPDTGYFTPG AKKTLADKY EYVMHGKLYK ITERDGQTPK AEMYVSFGGL LMLLRGDPAH ISHFELDQRL FLLMRKL

UniProtKB: Uncharacterized protein

Macromolecule #8: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 13.12378 KDa

Sequence

String:

MSTMKFCREC NNILYPKEDR EQSILLYACR NCDHQEAADD NCVYRNEVHH SVSEQTQILS DVASDPTLPR TKAVRCAKCQ HGEAVFFQA TARGEEGMTL FFVCCNPNCG HRWRE

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #9: RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein

• Macromolecule: Name: RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein; type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 26.260105 KDa

Sequence

String:

MEGIGNDKSS CSSSSTVPSP CLSKYVDPSS EESHRYYLAR RNALEMLRDR GYEVSLEDIN LSLQDFRTVY GERPDVDRLR ISAHHRSDS SNKVKVVFFG TGKVKVNTIR SVAAEILSQE TITGLILVLQ NQVTDKALKA IELFTFKVEI FQITDLLVNL T KHVLSLRH RVLTDGEKKA LLKQFNIEEK QLPRISKKDA VVRYYGLEKG QIVKVSYRGE LTESYVAYRC VW

UniProtKB: RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein

Macromolecule #10: DNA-directed RNA polymerase IV and V subunit 2

• Macromolecule: Name: DNA-directed RNA polymerase IV and V subunit 2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 132.377766 KDa

Sequence

String:

MTDIDIEEIE AAGEVDLRDL GEPFLQSFCK KAATSFFDEY GLVSHQLNSY NFFIEHGLQS VFESSGEMLV EPSFDPTKNK DHEWRYATV KFGEVSVDKP TLYSDDKELV FLPWHARLQN MTYSARMKVN VDVEVFVKKV VKRDKFKTGQ DEYVEKQILS K KTQDIPIG RIPVMVKSVL CNTTEKGKNG ESYRKGECAF DQGGYFVIKG AEKVFIAQEQ ICTKRLWISN SPWTVSYRSE TK RNRFIVR LSENQKAEDF KRKEKVLTVY FLSTEIPVWV LFFALGVASD KEAVDLIAFD GGDASITNSV VASIQEADSV CED FRHGRN ALAYVEQQIK GTKFPPGESV DECLSLYLFP GLKSLTQKAR FLGYMVKCLF SAYAGKRKCE NRDNFRNKRI ELAG ELLER ELRVHLAHAR RTMTKAMQRH LTGDGDLKPI EHYLDASIIT NGLSRAFSTG AWCHPFRKME RVSGVVANLG RANPL QSLI DLRRTRQQVL YTGRVGDARY PHPSHWGRLC FLSTPDGENC GLVKNLSLLG LVSTQIMEPV VEELFDSGME ELMDDT STP LSGKHKVLLN GDWVGVCSDS DYFVADLKSR RRQSELPRQM EIKLDKDDKE VRIFTDAGRL LRPLLVVENL HKLKQSK PS KYTFEHLLDQ GILELIGIEE EEDCTTAWGT KQLLKQQKSY THCELDLSFL LGVSCAIVPF ANHDHGRRVL YQSQKHCQ Q AIGFCSTNPN IRCDTLSQQL FYPQRPLFKT MASECLQKDV LFNGQNAIVA VNVHLGFNQE DSIVMNKASL ERGMFRSEQ IRSYKADVDS KDSEKRKKMD EVVQFGKTHS KIGRVDSLDD DGFPFVGANM HSGDIVIGRC TESGTDHSVK LKHTERGIVQ KVVLSSNDD GKNYATVSLR QVRSPCLGDK FSSMHGQKGV LGYIEEQENF AFTNQGIVPD IVINPHAFPS RQTPGQLLEA A LSKGIACP MQKKKGKSDA YSKVTRHATP FSTPSVDDIT DQLHRAGFSR SGNERVYNGR TGEMMRSLIF MGPNFYQRLI HM SEDKVKF RNTGPVHPLT RQPVADRKRF GGIKFGEMER DCLIAHGASA NLHERLFTLS DSSQMHICRN CKSAANVIER VAS SGRRIR GPYCRLCESP DYVVMVNVPY GAKLLYQELF SMGICLNFET NLC

Macromolecule #11: DNA (34-MER)

• Macromolecule: Name: DNA (34-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 10.467806 KDa

Sequence

String:

(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT) (DA)(DC)(DT)(DT)(DA)(DA)(DA)(DA)(DA)(DA) (DT)(DC)(DG)(DC)(DA)(DT)(DT)(DA)(DC) (DG)(DA)(DG)(DT)(DA)

Macromolecule #12: DNA (34-MER)

• Macromolecule: Name: DNA (34-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 10.433726 KDa

Sequence

String:

(DT)(DA)(DC)(DT)(DC)(DG)(DT)(DA)(DA)(DG) (DT)(DG)(DC)(DC)(DT)(DA)(DG)(DC)(DA)(DC) (DA)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DG) (DA)(DG)(DC)(DT)(DT)

Macromolecule #13: RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*...

• Macromolecule: Name: RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*UP*U)-3'); type: rna / ID: 13 / Number of copies: 1
• Source (natural): Organism: Brassica oleracea (wild cabbage)
• Molecular weight: Theoretical: 6.393832 KDa

Sequence

String:

UAUAUGCAGA AAGCGAUUUU

Macromolecule #14: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #15: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 15 / Number of copies: 6 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.1 mg/mL
• Buffer: pH: 7.8
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K

Electron microscopy

• Microscope: FEI TALOS ARCTICA
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3423 / Average exposure time: 2.9975 sec. / Average electron dose: 1.5625 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: OTHER
• Electron optics: Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Talos Arctica / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 2295354
• CTF correction: Software - Name: RELION (ver. 3.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 39800
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: OTHER

Output model

PDB-9k15:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom