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- EMDB-34820: A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-34820
TitleA cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom
Map data
Sample
  • Complex: DNA-directed RNA polymerase V
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
KeywordsDNA-dependent RNA polymerase V / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase V complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / 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 ...RNA polymerase V complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / 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 / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing 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 / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesBrassica oleracea (wild cabbage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsDu X / Xie G / Hu H / Du J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Science / Year: 2023
Title: Structure and mechanism of the plant RNA polymerase V.
Authors: Guohui Xie / Xuan Du / Hongmiao Hu / Sisi Li / Xiaofeng Cao / Steven E Jacobsen / Jiamu Du /
Abstract: In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation ...In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation pathway in plants. Here, we report on the structures of cauliflower Pol V in the free and elongation conformations. A conserved tyrosine residue of NRPE2 stacks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation by inducing transcription stalling. The nontemplate DNA strand is captured by NRPE2 to enhance backtracking, thereby increasing 3'-5' cleavage, which likely underpins Pol V's high fidelity. The structures also illuminate the mechanism of Pol V transcription stalling and enhanced backtracking, which may be important for Pol V's retention on chromatin to serve its function in tethering downstream factors for RNA-directed DNA methylation.
History
DepositionNov 20, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34820.png

Downloads & links

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Map

FileDownload / File: emd_34820.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 328.5 Å		1.1 Å/pix.
x 300 pix.
= 328.5 Å		1.1 Å/pix.
x 300 pix.
= 328.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.051074114 - 0.11121769
Average (Standard dev.)0.00028326802 (±0.0028528809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 328.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34820_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_34820_half_map_2.map
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Sample components

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Entire : DNA-directed RNA polymerase V

EntireName: DNA-directed RNA polymerase V
Components
  • Complex: DNA-directed RNA polymerase V
    • Protein or peptide: DNA-directed RNA polymerase V largest subunit
    • Protein or peptide: DNA-dependent RNA polymerase IV and V subunit 2
    • Protein or peptide: RPOLD domain-containing protein
    • 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 subunit
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: RNA_pol_L_2 domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 12
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DNA-directed RNA polymerase V

SupramoleculeName: DNA-directed RNA polymerase V / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence

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

MacromoleculeName: 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) / Tissue: inflorescence
Molecular weightTheoretical: 222.800797 KDa
SequenceString: MEEASSSDIL EAEIVGISFA LATHRQIRLA SISDAGINHA SQLSNAFLGL PLEFGKCEAC GATEPDKCEG HFGYIHLPVP IYHPAHVSE LKQMLSLLCL KCLKIKKIKS TSSGLAERLL GVCCEEASNI TIKDKSSDGA SYLQLKLPSR TRLQEGFWNF L ERYGYRYG ...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 CSGDMLGFNS 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

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

MacromoleculeName: DNA-dependent RNA polymerase IV and V subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 132.377766 KDa
SequenceString: MTDIDIEEIE AAGEVDLRDL GEPFLQSFCK KAATSFFDEY GLVSHQLNSY NFFIEHGLQS VFESSGEMLV EPSFDPTKNK DHEWRYATV KFGEVSVDKP TLYSDDKELV FLPWHARLQN MTYSARMKVN VDVEVFVKKV VKRDKFKTGQ DEYVEKQILS K KTQDIPIG ...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

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Macromolecule #3: RPOLD domain-containing protein

MacromoleculeName: RPOLD domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 35.48407 KDa
SequenceString: MDTGATYQRF PKVKIRELKD DYAKFELRDT DVSMANALRR VMISEVPTVA IDLVEIEVNS SVLNDEFIAH RLGLIPLTSE RAMSMRFSR DCDACDGDGQ CEFCSVEFRL SAKCVTDQTL DVTSKDLYSA DPTVTPVDFG DSSGADSSEQ RGIIIVKLRR G QELKLRAI ...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

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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: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 26.260105 KDa
SequenceString: MEGIGNDKSS CSSSSTVPSP CLSKYVDPSS EESHRYYLAR RNALEMLRDR GYEVSLEDIN LSLQDFRTVY GERPDVDRLR ISAHHRSDS SNKVKVVFFG TGKVKVNTIR SVAAEILSQE TITGLILVLQ NQVTDKALKA IELFTFKVEI FQITDLLVNL T KHVLSLRH ...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

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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: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 16.686348 KDa
SequenceString:
MAEDDYNEVD DLGYEDEPAE PEIEEGIEED ADMKDNDDIN GEPLETEDKV ETEPVQRPRK TSKFMTKYER ARILGTRALQ ISMNAPVMV ELEGETDPLE IAMKELRQRK IPFTIRRYLP DGSFEEWGVD ELIVEDSWKR QVGGD

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

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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: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 16.607275 KDa
SequenceString:
MASSIIMFED IFVVDKLDPD GKKFDKVTRI EATSHNLDMF MHLDVNTEVY PMAVGDKFTL AMAPTLNLDG TPDTGYFTPG AKKTLADKY EYVMHGKLYK ITERDGQTPK AEMYVSFGGL LMLLRGDPAH ISHFELDQRL FLLMRKL

UniProtKB: Uncharacterized protein

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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: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 13.12378 KDa
SequenceString:
MSTMKFCREC NNILYPKEDR EQSILLYACR NCDHQEAADD NCVYRNEVHH SVSEQTQILS DVASDPTLPR TKAVRCAKCQ HGEAVFFQA TARGEEGMTL FFVCCNPNCG HRWRE

UniProtKB: DNA-directed RNA polymerase subunit

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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: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 8.167508 KDa
SequenceString:
MIIPVRCFTC GKVIGNKWDT YLDLLQADYT EGDALDAIGL VRYCCRRMLM THVDLIEKLL NYNTLEKSDA N

UniProtKB: Uncharacterized protein

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Macromolecule #9: RNA_pol_L_2 domain-containing protein

MacromoleculeName: RNA_pol_L_2 domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 13.538273 KDa
SequenceString:
MNAPDRYERF VVPEGTKKVS YERDTKIINA ASFTIEREDH TIGNIVRMQL HRDENVLFAG YQLPHPLKYK IIVRIHTTSQ SSPMQAYNQ AINDLDKELD FLKSQFEAEV AKFSNPY

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

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Macromolecule #10: DNA-directed RNA polymerases II, IV and V subunit 12

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 12 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Molecular weightTheoretical: 5.983796 KDa
SequenceString:
MDQQSEPVTY VCGDCGQENT LKSGDVIQCR ECGYRILYKK RTRRVVQYEA R

UniProtKB: Uncharacterized protein

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.1 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 8 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7068 / Average exposure time: 2.9975 sec. / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1609875
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 63603
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8hil:
A cryo-EM structure of B. oleracea RNA polymerase V at 3.57 Angstrom

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  • 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

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