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- EMDB-38470: NTP-bound Pol IV transcription elongation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38470
TitleNTP-bound Pol IV transcription elongation complex
Map data
Sample
  • Complex: NTP-bound Pol IV transcription elongation complex
    • Protein or peptide: x 13 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsTranscription / elongation / Pol IV / RNA polymerase / TRANSCRIPTION/DNA/RNA / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing ...RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / plastid / RNA polymerase complex / regulation of immune response / defense response to fungus / heterochromatin / RNA polymerase II, core complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase IV/V subunit 1, C-terminal / DNA-directed RNA polymerase IV/V subunit 1, N-terminal / Protein of unknown function (DUF3223) / RDR2 PH-like domain / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon ...DNA-directed RNA polymerase IV/V subunit 1, C-terminal / DNA-directed RNA polymerase IV/V subunit 1, N-terminal / Protein of unknown function (DUF3223) / RDR2 PH-like domain / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / 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 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. / 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. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3
Similarity search - Domain/homology
DNA-directed RNA polymerases II and IV subunit 5A / RNA-dependent RNA polymerase 2 / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases II, IV and V subunit 3 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A / DNA-directed RNA polymerase IV subunit 7 / DNA-directed RNA polymerases II, IV and V subunit 10 / DNA-directed RNA polymerases II, IV and V subunit 6A / DNA-directed RNA polymerases II, IV and V subunit 12 ...DNA-directed RNA polymerases II and IV subunit 5A / RNA-dependent RNA polymerase 2 / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases II, IV and V subunit 3 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A / DNA-directed RNA polymerase IV subunit 7 / DNA-directed RNA polymerases II, IV and V subunit 10 / DNA-directed RNA polymerases II, IV and V subunit 6A / DNA-directed RNA polymerases II, IV and V subunit 12 / DNA-directed RNA polymerases IV and V subunit 2 / DNA-directed RNA polymerase IV subunit 1 / DNA-directed RNA polymerases II, IV and V subunit 8B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHuang K / Fang CL / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2024
Title: Transcription elongation of the plant RNA polymerase IV is prone to backtracking.
Authors: Chengli Fang / Kun Huang / Xiaoxian Wu / Hongwei Zhang / Zhanxi Gu / Jiawei Wang / Yu Zhang /
Abstract: RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2) to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In the "backtracking- ...RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2) to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In the "backtracking-triggered RNA channeling" model, Pol IV backtracks and delivers its transcript's 3' terminus to RDR2, which synthesizes dsRNA. However, the mechanisms underlying Pol IV backtracking and RNA protection from cleavage are unclear. Here, we determined cryo-electron microscopy structures of Pol IV elongation complexes at four states of its nucleotide addition cycle (NAC): posttranslocation, guanosine triphosphate-bound, pretranslocation, and backtracked states. The structures reveal that Pol IV maintains an open DNA cleft and kinked bridge helix in all NAC states, loosely interacts with the nucleoside triphosphate substrate, and barely contacts proximal backtracked nucleotides. Biochemical data indicate that Pol IV is inefficient in forward translocation and RNA cleavage. These findings suggest that Pol IV transcription elongation is prone to backtracking and incapable of RNA hydrolysis, ensuring efficient dsRNA production by Pol IV-RDR2.
History
DepositionDec 27, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38470.png

Downloads & links

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Map

FileDownload / File: emd_38470.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.02940854 - 0.06439925
Average (Standard dev.)0.000023547564 (±0.0028690996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38470_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_38470_half_map_2.map
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Sample components

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Entire : NTP-bound Pol IV transcription elongation complex

EntireName: NTP-bound Pol IV transcription elongation complex
Components
  • Complex: NTP-bound Pol IV transcription elongation complex
    • Protein or peptide: DNA-directed RNA polymerase IV subunit 1
    • Protein or peptide: DNA-directed RNA polymerases IV and V subunit 2
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 3
    • Protein or peptide: DNA-directed RNA polymerases IV and V subunit 4
    • Protein or peptide: DNA-directed RNA polymerases II and IV subunit 5A
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 6A
    • Protein or peptide: DNA-directed RNA polymerase IV subunit 7
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 8B
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 9A
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 10
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 11
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 12
    • Protein or peptide: RNA-dependent RNA polymerase 2
    • DNA: Nontemplate_DNA
    • RNA: RNA
    • DNA: Template_DNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: NTP-bound Pol IV transcription elongation complex

SupramoleculeName: NTP-bound Pol IV transcription elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 0.65 kDa/nm

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Macromolecule #1: DNA-directed RNA polymerase IV subunit 1

MacromoleculeName: DNA-directed RNA polymerase IV subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 168.101781 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MEDDCEELQV PVGTLTSIGF SISNNNDRDK MSVLEVEAPN QVTDSRLGLP NPDSVCRTCG SKDRKVCEGH FGVINFAYSI INPYFLKEV AALLNKICPG CKYIRKKQFQ ITEDQPERCR YCTLNTGYPL MKFRVTTKEV FRRSGIVVEV NEESLMKLKK R GVLTLPPD ...String:
MEDDCEELQV PVGTLTSIGF SISNNNDRDK MSVLEVEAPN QVTDSRLGLP NPDSVCRTCG SKDRKVCEGH FGVINFAYSI INPYFLKEV AALLNKICPG CKYIRKKQFQ ITEDQPERCR YCTLNTGYPL MKFRVTTKEV FRRSGIVVEV NEESLMKLKK R GVLTLPPD YWSFLPQDSN IDESCLKPTR RIITHAQVYA LLLGIDQRLI KKDIPMFNSL GLTSFPVTPN GYRVTEIVHQ FN GARLIFD ERTRIYKKLV GFEGNTLELS SRVMECMQYS RLFSETVSSS KDSANPYQKK SDTPKLCGLR FMKDVLLGKR SDH TFRTVV VGDPSLKLNE IGIPESIAKR LQVSEHLNQC NKERLVTSFV PTLLDNKEMH VRRGDRLVAI QVNDLQTGDK IFRS LMDGD TVLMNRPPSI HQHSLIAMTV RILPTTSVVS LNPICCLPFR GDFDGDCLHG YVPQSIQAKV ELDELVALDK QLINR QNGR NLLSLGQDSL TAAYLVNVEK NCYLNRAQMQ QLQMYCPFQL PPPAIIKASP SSTEPQWTGM QLFGMLFPPG FDYTYP LNN VVVSNGELLS FSEGSAWLRD GEGNFIERLL KHDKGKVLDI IYSAQEMLSQ WLLMRGLSVS LADLYLSSDL QSRKNLT EE ISYGLREAEQ VCNKQQLMVE SWRDFLAVNG EDKEEDSVSD LARFCYERQK SATLSELAVS AFKDAYRDVQ ALAYRYGD Q SNSFLIMSKA GSKGNIGKLV QHSMCIGLQN SAVSLSFGFP RELTCAAWND PNSPLRGAKG KDSTTTESYV PYGVIENSF LTGLNPLESF VHSVTSRDSS FSGNADLPGT LSRRLMFFMR DIYAAYDGTV RNSFGNQLVQ FTYETDGPVE DITGEALGSL SACALSEAA YSALDQPISL LETSPLLNLK NVLECGSKKG QREQTMSLYL SEYLSKKKHG FEYGSLEIKN HLEKLSFSEI V STSMIIFS PSSNTKVPLS PWVCHFHISE KVLKRKQLSA ESVVSSLNEQ YKSRNRELKL DIVDLDIQNT NHCSSDDQAM KD DNVCITV TVVEASKHSV LELDAIRLVL IPFLLDSPVK GDQGIKKVNI LWTDRPKAPK RNGNHLAGEL YLKVTMYGDR GKR NCWTAL LETCLPIMDM IDWGRSHPDN IRQCCSVYGI DAGRSIFVAN LESAVSDTGK EILREHLLLV ADSLSVTGEF VALN AKGWS KQRQVESTPA PFTQACFSSP SQCFLKAAKE GVRDDLQGSI DALAWGKVPG FGTGDQFEII ISPKVHGFTT PVDVY DLLS STKTMRRTNS APKSDKATVQ PFGLLHSAFL KDIKVLDGKG IPMSLLRTIF TWKNIELLSQ SLKRILHSYE INELLN ERD EGLVKMVLQL HPNSVEKIGP GVKGIRVAKS KHGDSCCFEV VRIDGTFEDF SYHKCVLGAT KIIAPKKMNF YKSKYLK NG TLESGGFSEN PGSGSGSDYK DHDGDYKDHD IDYKDDDDKE NLYFQGHHHH HHHHHH

UniProtKB: DNA-directed RNA polymerase IV subunit 1

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

MacromoleculeName: DNA-directed RNA polymerases IV and V subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 132.848047 KDa
SequenceString: MPDMDIDVKD LEEFEATTGE INLSELGEGF LQSFCKKAAT SFFDKYGLIS HQLNSYNYFI EHGLQNVFQS FGEMLVEPSF DVVKKKDND WRYATVKFGE VTVEKPTFFS DDKELEFLPW HARLQNMTYS ARIKVNVQVE VFKNTVVKSD KFKTGQDNYV E KKILDVKK ...String:
MPDMDIDVKD LEEFEATTGE INLSELGEGF LQSFCKKAAT SFFDKYGLIS HQLNSYNYFI EHGLQNVFQS FGEMLVEPSF DVVKKKDND WRYATVKFGE VTVEKPTFFS DDKELEFLPW HARLQNMTYS ARIKVNVQVE VFKNTVVKSD KFKTGQDNYV E KKILDVKK QDILIGSIPV MVKSILCKTS EKGKENCKKG DCAFDQGGYF VIKGAEKVFI AQEQMCTKRL WISNSPWTVS FR SENKRNR FIVRLSENEK AEDYKRREKV LTVYFLSTEI PVWLLFFALG VSSDKEAMDL IAFDGDDASI TNSLIASIHV ADA VCEAFR CGNNALTYVE QQIKSTKFPP AESVDECLHL YLFPGLQSLK KKARFLGYMV KCLLNSYAGK RKCENRDSFR NKRI ELAGE LLEREIRVHL AHARRKMTRA MQKHLSGDGD LKPIEHYLDA SVITNGLSRA FSTGAWSHPF RKMERVSGVV ANLGR ANPL QTLIDLRRTR QQVLYTGKVG DARYPHPSHW GRVCFLSTPD GENCGLVKNM SLLGLVSTQS LESVVEKLFA CGMEEL MDD TCTPLFGKHK VLLNGDWVGL CADSESFVAE LKSRRRQSEL PREMEIKRDK DDNEVRIFTD AGRLLRPLLV VENLQKL KQ EKPSQYPFDH LLDHGILELI GIEEEEDCNT AWGIKQLLKE PKIYTHCELD LSFLLGVSCA VVPFANHDHG RRVLYQSQ K HCQQAIGFSS TNPNIRCDTL SQQLFYPQKP LFKTLASECL KKEVLFNGQN AIVAVNVHLG YNQEDSIVMN KASLERGMF RSEQIRSYKA EVDAKDSEKR KKMDELVQFG KTHSKIGKVD SLEDDGFPFI GANMSTGDIV IGRCTESGAD HSIKLKHTER GIVQKVVLS SNDEGKNFAA VSLRQVRSPC LGDKFSSMHG QKGVLGYLEE QQNFPFTIQG IVPDIVINPH AFPSRQTPGQ L LEAALSKG IACPIQKEGS SAAYTKLTRH ATPFSTPGVT EITEQLHRAG FSRWGNERVY NGRSGEMMRS MIFMGPTFYQ RL VHMSEDK VKFRNTGPVH PLTRQPVADR KRFGGIKFGE MERDCLIAHG ASANLHERLF TLSDSSQMHI CRKCKTYANV IER TPSSGR KIRGPYCRVC VSSDHVVRVY VPYGAKLLCQ ELFSMGITLN FDTKLC

UniProtKB: DNA-directed RNA polymerases IV and V subunit 2

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Macromolecule #3: DNA-directed RNA polymerases II, IV and V subunit 3

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 35.503219 KDa
SequenceString: MDGATYQRFP KIKIRELKDD YAKFELRETD VSMANALRRV MISEVPTVAI DLVEIEVNSS VLNDEFIAHR LGLIPLTSER AMSMRFSRD CDACDGDGQC EFCSVEFRLS SKCVTDQTLD VTSRDLYSAD PTVTPVDFTI DSSVSDSSEH KGIIIVKLRR G QELKLRAI ...String:
MDGATYQRFP KIKIRELKDD YAKFELRETD VSMANALRRV MISEVPTVAI DLVEIEVNSS VLNDEFIAHR LGLIPLTSER AMSMRFSRD CDACDGDGQC EFCSVEFRLS SKCVTDQTLD VTSRDLYSAD PTVTPVDFTI DSSVSDSSEH KGIIIVKLRR G QELKLRAI ARKGIGKDHA KWSPAATVTF MYEPDIIINE DMMDTLSDEE KIDLIESSPT KVFGMDPVTR QVVVVDPEAY TY DEEVIKK AEAMGKPGLI EISPKDDSFI FTVESTGAVK ASQLVLNAID LLKQKLDAVR LSDDTVEADD QFGELGAHMR GG

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 3

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Macromolecule #4: DNA-directed RNA polymerases IV and V subunit 4

MacromoleculeName: DNA-directed RNA polymerases IV and V subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.447604 KDa
SequenceString: MSEKGGKGLK SSLKSKDGGK DGSSTKLKKG RKIHFDQRTP PANYKILNVS SDQQPFQSSA AKCGKSDKPT KSSKNSLHSF ELKDLPENA ECMMDCEAFQ ILDGIKGQLV GLSEDPSIKI PVSYDRALAY VESCVHYTNP QSVRKVLEPL KTYGISDGEM C VIANASSE ...String:
MSEKGGKGLK SSLKSKDGGK DGSSTKLKKG RKIHFDQRTP PANYKILNVS SDQQPFQSSA AKCGKSDKPT KSSKNSLHSF ELKDLPENA ECMMDCEAFQ ILDGIKGQLV GLSEDPSIKI PVSYDRALAY VESCVHYTNP QSVRKVLEPL KTYGISDGEM C VIANASSE SVDEVLAFIP SLKTKKEVIN QPLQDALEEL SKLKKSE

UniProtKB: DNA-directed RNA polymerases IV and V subunit 4

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Macromolecule #5: DNA-directed RNA polymerases II and IV subunit 5A

MacromoleculeName: DNA-directed RNA polymerases II and IV subunit 5A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.340389 KDa
SequenceString: MLTEEELKRL YRIQKTLMQM LRDRGYFIAD SELTMTKQQF IRKHGDNMKR EDLVTLKAKR NDNSDQLYIF FPDEAKVGVK TMKMYTNRM KSENVFRAIL VVQQNLTPFA RTCISEISSK FHLEVFQEAE MLVNIKEHVL VPEHQVLTTE EKKTLLERYT V KETQLPRI ...String:
MLTEEELKRL YRIQKTLMQM LRDRGYFIAD SELTMTKQQF IRKHGDNMKR EDLVTLKAKR NDNSDQLYIF FPDEAKVGVK TMKMYTNRM KSENVFRAIL VVQQNLTPFA RTCISEISSK FHLEVFQEAE MLVNIKEHVL VPEHQVLTTE EKKTLLERYT V KETQLPRI QVTDPIARYF GLKRGQVVKI IRPSETAGRY VTYRYVV

UniProtKB: DNA-directed RNA polymerases II and IV subunit 5A

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Macromolecule #6: DNA-directed RNA polymerases II, IV and V subunit 6A

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.670346 KDa
SequenceString:
MADEDYNDVD DLGYEDEPAE PEIEEGVEED VEMKENDDVN GEPIEAEDKV ETEPVQRPRK TSKFMTKYER ARILGTRALQ ISMNAPVMV ELEGETDPLE IAMKELRQRK IPFTIRRYLP DGSFEEWGVD ELIVEDSWKR QVGGD

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 6A

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Macromolecule #7: DNA-directed RNA polymerase IV subunit 7

MacromoleculeName: DNA-directed RNA polymerase IV subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.873297 KDa
SequenceString:
MFIKVKLPWD VTIPAEDMDT GLMLQRAIVI RLLEAFSKEK ATKDLGYLIT PTILENIGEG KIKEQTGEIQ FPVVFNGICF KMFKGEIVH GVVHKVHKTG VFLKSGPYEI IYLSHMKMPG YEFIPGENPF FMNQYMSRIQ IGARVRFVVL DTEWREAEKD F MALASIDG DNLGPF

UniProtKB: DNA-directed RNA polymerase IV subunit 7

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Macromolecule #8: DNA-directed RNA polymerases II, IV and V subunit 8B

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 8B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.626299 KDa
SequenceString:
MASNIIMFED IFVVDKLDPD GKKFDKVTRV EARSHNLEMF MHLDVNTEVY PLAVGDKFTL AMAPTLNLDG TPDTGYFTPG AKKTLADKY EYIMHGKLYK ISERDGKTPK AELYVSFGGL LMLLQGDPAH ISHFELDQRL FLLMRKL

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 8B

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Macromolecule #9: DNA-directed RNA polymerases II, IV and V subunit 9A

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 9A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.297145 KDa
SequenceString:
MSTMKFCREC NNILYPKEDK EQKILLYACR NCDHQEVADN SCVYRNEVHH SVSERTQILT DVASDPTLPR TKAVRCSKCQ HREAVFFQA TARGEEGMTL FFVCCNPNCG HRWRE

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 9A

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

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 8.32369 KDa
SequenceString:
MIIPVRCFTC GKVIGNKWDQ YLDLLQLDYT EGDALDALQL VRYCCRRMLM THVDLIEKLL NYNTLEKSDN S

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 10

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Macromolecule #11: DNA-directed RNA polymerases II, IV and V subunit 11

MacromoleculeName: DNA-directed RNA polymerases II, IV and V subunit 11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.582286 KDa
SequenceString:
MNAPERYERF VVPEGTKKVS YDRDTKIINA ASFTVEREDH TIGNIVRMQL HRDENVLFAG YQLPHPLKYK IIVRIHTTSQ SSPMQAYNQ AINDLDKELD YLKNQFEAEV AKFSNQF

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 11

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Macromolecule #12: 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: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 5.905768 KDa
SequenceString:
MDPAPEPVTY VCGDCGQENT LKSGDVIQCR ECGYRILYKK RTRRVVQYEA R

UniProtKB: DNA-directed RNA polymerases II, IV and V subunit 12

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Macromolecule #13: RNA-dependent RNA polymerase 2

MacromoleculeName: RNA-dependent RNA polymerase 2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 129.494531 KDa
SequenceString: MVSETTTNRS TVKISNVPQT IVADELLRFL ELHLGEDTVF ALEIPTTRDN WKPRDFARVQ FTTLEVKSRA QLLSSQSKLL FKTHNLRLS EAYDDIIPRP VDPRKRLDDI VLTVGFPESD EKRFCALEKW DGVRCWILTE KRRVEFWVWE SGDCYKIEVR F EDIIETLS ...String:
MVSETTTNRS TVKISNVPQT IVADELLRFL ELHLGEDTVF ALEIPTTRDN WKPRDFARVQ FTTLEVKSRA QLLSSQSKLL FKTHNLRLS EAYDDIIPRP VDPRKRLDDI VLTVGFPESD EKRFCALEKW DGVRCWILTE KRRVEFWVWE SGDCYKIEVR F EDIIETLS CCVNGDASEI DAFLLKLKYG PKVFKRVTVH IATKFKSDRY RFCKEDFDFM WIRTTDFSGS KSIGTSTCFC LE VHNGSTM LDIFSGLPYY REDTLSLTYV DGKTFASAAQ IVPLLNAAIL GLEFPYEILF QLNALVHAQK ISLFAASDME LIK ILRGMS LETALVILKK LHQQSSICYD PVFFVKTQMQ SVVKKMKHSP ASAYKRLTEQ NIMSCQRAYV TPSKIYLLGP ELET ANYVV KNFAEHVSDF MRVTFVEEDW SKLPANALSV NSKEGYFVKP SRTNIYNRVL SILGEGITVG PKRFEFLAFS ASQLR GNSV WMFASNEKVK AEDIREWMGC FRKIRSISKC AARMGQLFSA SRQTLIVRAQ DVEQIPDIEV TTDGADYCFS DGIGKI SLA FAKQVAQKCG LSHVPSAFQI RYGGYKGVIA VDRSSFRKLS LRDSMLKFDS NNRMLNVTRW TESMPCFLNR EIICLLS TL GIEDAMFEAM QAVHLSMLGN MLEDRDAALN VLQKLSGENS KNLLVKMLLQ GYAPSSEPYL SMMLRVHHES QLSELKSR C RILVPKGRIL IGCMDEMGIL EYGQVYVRVT LTKAELKSRD QSYFRKIDEE TSVVIGKVVV TKNPCLHPGD IRVLDAIYE VHFEEKGYLD CIIFPQKGER PHPNECSGGD LDGDQFFVSW DEKIIPSEMD PPMDYAGSRP RLMDHDVTLE EIHKFFVDYM ISDTLGVIS TAHLVHADRD PEKARSQKCL ELANLHSRAV DFAKTGAPAE MPYALKPREF PDFLERFEKP TYISESVFGK L YRAVKSSL AQRKPEAESE DTVAYDVTLE EAGFESFIET AKAHRDMYGE KLTSLMIYYG AANEEEILTG ILKTKEMYLA RD NRRYGDM KDRITLSVKD LHKEAMGWFE KSCEDEQQKK KLASAWYYVT YNPNHRDEKL TFLSFPWIVG DVLLDIKAEN AQR QSVEEK TSGLVSI

UniProtKB: RNA-dependent RNA polymerase 2

+
Macromolecule #14: Nontemplate_DNA

MacromoleculeName: Nontemplate_DNA / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.211011 KDa
SequenceString:
(DT)(DT)(DG)(DT)(DG)(DC)(DT)(DT)(DA)(DT) (DC)(DG)(DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)

+
Macromolecule #16: Template_DNA

MacromoleculeName: Template_DNA / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.938428 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DC)(DA)(DA) (DC)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC) (DC)(DT)(DA)(DT)

+
Macromolecule #15: RNA

MacromoleculeName: RNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.794866 KDa
SequenceString:
UUUUAUCGAG AGGUA

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, 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

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7eu1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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