[English] 日本語
Yorodumi
- EMDB-35086: A cryo-EM structure of KTF1-bound polymerase V transcription elon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35086
TitleA cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
Map data
Sample
  • Complex: KTF1-bound polymerase V transcription elongation complex
    • Protein or peptide: x 13 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsPol V / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase IV complex / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / DNA-templated transcription elongation / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / plastid / RNA polymerase complex ...RNA polymerase IV complex / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / DNA-templated transcription elongation / 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 / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / heterochromatin formation / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / nuclear body / nucleotide binding / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / nucleolus / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
RDM3 beta-solenoid / 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) / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 ...RDM3 beta-solenoid / 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) / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal domain superfamily / 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 / 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 / HRDC-like superfamily / 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 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 5 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site
Similarity search - Domain/homology
DNA-directed RNA polymerase V subunit 7 / Protein RNA-directed DNA methylation 3 / DNA-directed RNA polymerases II and V subunit 8A / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases IV and V subunit 3B / DNA-directed RNA polymerase V subunit 1 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A / DNA-directed RNA polymerases II, IV and V subunit 10 / DNA-directed RNA polymerases II, IV and V subunit 6A ...DNA-directed RNA polymerase V subunit 7 / Protein RNA-directed DNA methylation 3 / DNA-directed RNA polymerases II and V subunit 8A / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases IV and V subunit 3B / DNA-directed RNA polymerase V subunit 1 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A / 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 V subunit 5A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZhang H / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2020YFA0907902 China
National Natural Science Foundation of China (NSFC)JCYJ-SHFY-2022-012 China
CitationJournal: Nat Commun / Year: 2023
Title: A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex.
Authors: Hong-Wei Zhang / Kun Huang / Zhan-Xi Gu / Xiao-Xian Wu / Jia-Wei Wang / Yu Zhang /
Abstract: De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. ...De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
History
DepositionJan 6, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35086.png

Downloads & links

-
Map

FileDownload / File: emd_35086.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.006967795 - 0.02915679
Average (Standard dev.)0.00014692632 (±0.0017930665)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: #3

Fileemd_35086_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_35086_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_35086_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35086_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35086_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : KTF1-bound polymerase V transcription elongation complex

EntireName: KTF1-bound polymerase V transcription elongation complex
Components
  • Complex: KTF1-bound polymerase V transcription elongation complex
    • Protein or peptide: DNA-directed RNA polymerase V subunit 1
    • Protein or peptide: DNA-directed RNA polymerases IV and V subunit 2
    • Protein or peptide: DNA-directed RNA polymerases IV and V subunit 3B
    • Protein or peptide: DNA-directed RNA polymerases IV and V subunit 4
    • Protein or peptide: DNA-directed RNA polymerase V subunit 5A
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 6A
    • Protein or peptide: DNA-directed RNA polymerase V subunit 7
    • Protein or peptide: DNA-directed RNA polymerases II and V subunit 8A
    • 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
    • DNA: DNA (48-MER)
    • RNA: RNA (30-MER)
    • DNA: DNA (48-MER)
    • Protein or peptide: Protein RNA-directed DNA methylation 3
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: KTF1-bound polymerase V transcription elongation complex

SupramoleculeName: KTF1-bound polymerase V transcription elongation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 608.5 kDa/nm

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

MacromoleculeName: DNA-directed RNA polymerase V 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: 218.495594 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MEEESTSEIL DGEIVGITFA LASHHEICIQ SISESAINHP SQLTNAFLGL PLEFGKCESC GATEPDKCEG HFGYIQLPVP IYHPAHVNE LKQMLSLLCL KCLKIKKAKG TSGGLADRLL GVCCEEASQI SIKDRASDGA SYLELKLPSR SRLQPGCWNF L ERYGYRYG ...String:
MEEESTSEIL DGEIVGITFA LASHHEICIQ SISESAINHP SQLTNAFLGL PLEFGKCESC GATEPDKCEG HFGYIQLPVP IYHPAHVNE LKQMLSLLCL KCLKIKKAKG TSGGLADRLL GVCCEEASQI SIKDRASDGA SYLELKLPSR SRLQPGCWNF L ERYGYRYG SDYTRPLLAR EVKEILRRIP EESRKKLTAK GHIPQEGYIL EYLPVPPNCL SVPEASDGFS TMSVDPSRIE LK DVLKKVI AIKSSRSGET NFESHKAEAS EMFRVVDTYL QVRGTAKAAR NIDMRYGVSK ISDSSSSKAW TEKMRTLFIR KGS GFSSRS VITGDAYRHV NEVGIPIEIA QRITFEERVS VHNRGYLQKL VDDKLCLSYT QGSTTYSLRD GSKGHTELKP GQVV HRRVM DGDVVFINRP PTTHKHSLQA LRVYVHEDNT VKINPLMCSP LSADFDGDCV HLFYPQSLSA KAEVMELFSV EKQLL SSHT GQLILQMGSD SLLSLRVMLE RVFLDKATAQ QLAMYGSLSL PPPALRKSSK SGPAWTVFQI LQLAFPERLS CKGDRF LVD GSDLLKFDFG VDAMGSIINE IVTSIFLEKG PKETLGFFDS LQPLLMESLF AEGFSLSLED LSMSRADMDV IHNLIIR EI SPMVSRLRLS YRDELQLENS IHKVKEVAAN FMLKSYSIRN LIDIKSNSAI TKLVQQTGFL GLQLSDKKKF YTKTLVED M AIFCKRKYGR ISSSGDFGIV KGCFFHGLDP YEEMAHSIAA REVIVRSSRG LAEPGTLFKN LMAVLRDIVI TNDGTVRNT CSNSVIQFKY GVDSERGHQG LFEAGEPVGV LAATAMSNPA YKAVLDSSPN SNSSWELMKE VLLCKVNFQN TTNDRRVILY LNECHCGKR FCQENAACTV RNKLNKVSLK DTAVEFLVEY RKQPTISEIF GIDSCLHGHI HLNKTLLQDW NISMQDIHQK C EDVINSLG QKKKKKATDD FKRTSLSVSE CCSFRDPCGS KGSDMPCLTF SYNATDPDLE RTLDVLCNTV YPVLLEIVIK GD SRICSAN IIWNSSDMTT WIRNRHASRR GEWVLDVTVE KSAVKQSGDA WRVVIDSCLS VLHLIDTKRS IPYSVKQVQE LLG LSCAFE QAVQRLSASV RMVSKGVLKE HIILLANNMT CSGTMLGFNS GGYKALTRSL NIKAPFTEAT LIAPRKCFEK AAEK CHTDS LSTVVGSCSW GKRVDVGTGS QFELLWNQKE TGLDDKEETD VYSFLQMVIS TTNADAFVSS PGFDVTEEEM AEWAE SPER DSALGEPKFE DSADFQNLHD EGKPSGANWE KSSSWDNGCS GGSEWGVSKS TGGEANPESN WEKTTNVEKE DAWSSW NTR KDAQESSKSD SGGAWGIKTK DADADTTPNW ETSPAPKDSI VPENNEPTSD VWGHKSVSDK SWDKKNWGTE SAPAAWG ST DAAVWGSSDK KNSETESDAA AWGSRDKNNS DVGSGAGVLG PWNKKSSETE SNGATWGSSD KTKSGAAAWN SWDKKNIE T DSEPAAWGSQ GKKNSETESG PAAWGAWDKK KSETEPGPAG WGMGDKKNSE TELGPAAMGN WDKKKSDTKS GPAAWGSTD AAAWGSSDKN NSETESDAAA WGSRNKKTSE IESGAGAWGS WGQPSPTAED KDTNEDDRNP WVSLKETKSR EKDDKERSQW GNPAKKFPS SGGWSNGGGA DWKGNRNHTP RPPRSEDNLA PMFTATRQRL DSFTSEEQEL LSDVEPVMRT LRKIMHPSAY P DGDPISDD DKTFVLEKIL NFHPQKETKL GSGVDFITVD KHTIFSDSRC FFVVSTDGAK QDFSYRKSLN NYLMKKYPDR AE EFIDKYF TKPRPSGNRD RNNQDATPPG EEQSQPPNQS IGNGGDDFQT QTQSQSPSQT RAQSPSQAQA QSPSQTQSQS QSQ SQSQSQ SQSQSQSQSQ SQSQSQSQSQ SPSQTQTQSP SQTQAQAQSP SSQSPSQTQT

UniProtKB: DNA-directed RNA polymerase V subunit 1

+
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

+
Macromolecule #3: DNA-directed RNA polymerases IV and V subunit 3B

MacromoleculeName: DNA-directed RNA polymerases IV and V subunit 3B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 35.617375 KDa
SequenceString: MDGVTYQRFP TVKIRELKDD YAKFELRETD VSMANALRRV MISEVPTMAI HLVKIEVNSS VLNDEFIAQR LSLIPLTSER AMSMRFCQD CEDCNGDEHC EFCSVEFPLS AKCVTDQTLD VTSRDLYSAD PTVTPVDFTS NSSTSDSSEH KGIIIAKLRR G QELKLKAL ...String:
MDGVTYQRFP TVKIRELKDD YAKFELRETD VSMANALRRV MISEVPTMAI HLVKIEVNSS VLNDEFIAQR LSLIPLTSER AMSMRFCQD CEDCNGDEHC EFCSVEFPLS AKCVTDQTLD VTSRDLYSAD PTVTPVDFTS NSSTSDSSEH KGIIIAKLRR G QELKLKAL ARKGIGKDHA KWSPAATVTY MYEPDIIINE EMMNTLTDEE KIDLIESSPT KVFGIDPVTG QVVVVDPEAY TY DEEVIKK AEAMGKPGLI EIHPKHDSFV FTVESTGALK ASQLVLNAID ILKQKLDAIR LSDNTVEADD QFGELGAHMR EG

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

+
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

+
Macromolecule #5: DNA-directed RNA polymerase V subunit 5A

MacromoleculeName: DNA-directed RNA polymerase V subunit 5A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.626555 KDa
SequenceString: MEVKGKETAS VLCLSKYVDL SSEESHRYYL ARRNGLQMLR DRGYEVSDED INLSLHDFRT VYGERPDVDR LRISALHRSD STKKVKIVF FGTSMVKVNA IRSVVADILS QETITGLILV LQNHVTNQAL KAIELFSFKV EIFQITDLLV NITKHSLKPQ H QVLNDEEK ...String:
MEVKGKETAS VLCLSKYVDL SSEESHRYYL ARRNGLQMLR DRGYEVSDED INLSLHDFRT VYGERPDVDR LRISALHRSD STKKVKIVF FGTSMVKVNA IRSVVADILS QETITGLILV LQNHVTNQAL KAIELFSFKV EIFQITDLLV NITKHSLKPQ H QVLNDEEK TTLLKKFSIE EKQLPRISKK DAIVRYYGLE KGQVVKVNYR GELTESHVAF RCVW

UniProtKB: DNA-directed RNA polymerase V subunit 5A

+
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

+
Macromolecule #7: DNA-directed RNA polymerase V subunit 7

MacromoleculeName: DNA-directed RNA polymerase V subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.287941 KDa
SequenceString:
MFLKVQLPWN VMIPAENMDA KGLMLKRAIL VELLEAFASK KATKELGYYV AVTTLDKIGE GKIREHTGEV LFPVMFSGMT FKIFKGEII HGVVHKVLKH GVFMRCGPIE NVYLSYTKMP DYKYIPGENP IFMNEKTSRI QVETTVRVVV IGIKWMEVER E FQALASLE GDYLGPLSEE

UniProtKB: DNA-directed RNA polymerase V subunit 7

+
Macromolecule #8: DNA-directed RNA polymerases II and V subunit 8A

MacromoleculeName: DNA-directed RNA polymerases II and V subunit 8A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.533148 KDa
SequenceString:
MASNIILFED IFVVDQLDPD GKKFDKVTRV QATSHNLEMF MHLDVNTEVY PLAVGDKFTL ALAPTLNLDG TPDTGYFTPG AKKTLADKY EYIMHGKLYK ISERDGKTPK AELYVSFGGL LMLLKGDPAH ISHFELDQRL FLLMRKL

UniProtKB: DNA-directed RNA polymerases II and V subunit 8A

+
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

+
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

+
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

+
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

+
Macromolecule #16: Protein RNA-directed DNA methylation 3

MacromoleculeName: Protein RNA-directed DNA methylation 3 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 158.254062 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDRKGKGKQV AGSDSYSGGQ KRKNSVEFRD EGLRIKKRKN PEVLQFFEES AEVGYYGGSS DEDDDGLGFL NDMEDEPEVE ESSKAGKGE KGKSSFVFPK EEDLNEEEFD RIMEERYKPG SGFLRYADDD IKDAIEMDAL APTSKDPPIW KVKCAIGRER R SVFCLMHK ...String:
MDRKGKGKQV AGSDSYSGGQ KRKNSVEFRD EGLRIKKRKN PEVLQFFEES AEVGYYGGSS DEDDDGLGFL NDMEDEPEVE ESSKAGKGE KGKSSFVFPK EEDLNEEEFD RIMEERYKPG SGFLRYADDD IKDAIEMDAL APTSKDPPIW KVKCAIGRER R SVFCLMHK FVELRKIGTK LEIISVFSVD HVKGFIFIEA DKEHDVLEAC KSLVGIYATR MVLLPKAETP NLLTVQKKTK KV SEGTWAR VKNGKYKGDL AQIVAVSDTR NKALIKLIPR IDIQALTQKY GGGVTVQKGQ TPAPRLISSS ELEEFRPLIQ VRR DRDTGI TFEHLDSLML KDGYLYKKVS LDSISSWGVI PTKDELLKFT PVDRKETGDV EWISEIYGEE RKKKILPTCR EGGK GEGSG GGKGEGSGGG KGEGSRGGKG EGSSDFKSES SYELYNLVCF SRKDFGLIVG VDDKGDGYKV LKEGIDGPVV VTVGK KEMQ NGPFDSKFTA LDLNKKQISV NDVVKISKGP SEGKQGVVRQ VYRGIIFLYD ESEEENGGYF CCKSQSCEKV KLFTEE SNE KTGGFDGTAF EDFVSSPKSP LSPEKEWQPR ERYNSSNQGD IGSTYSIGQK LRIRVGPLKG YLCRVIALRY SDVTVKL DS QHKIFTVKSE HLAEVRDRNT VLSTSGDAGT GSFQPFGMLG TESSTGDWAI GAGTSSEGGN WNIGGPSTDS HESLNIER N MVQLCREKNP WGGSKPTSDV SPTVADDNTS AWANAAAENK PASASDQPGG WNPWGKTPAS EAGTVSGWGD TSASNVEAS SWEKQGASTS NVADLGSWGT HGGSSGGNKQ DEDSVWGKLC EASESSQKKE ESSWGKKGGS DGESSWGNKD GNSSASKKDG VSWGQQDKG SDESKGGSAW SNQCGDFGSG KKKDGSSGWN KSAEDSNANS KGVPDWGQPN DGSSWGKKGD GAASWGKKDD G GSWGKKDD GNKDDGGSSW GKKDDGQKDD GGSSWEKKFD GGSSWGKKDD GGSSWGKKDD GGSLWGKKDD GGSSWGKEDD GG SLWGKKD DGESSWGKKD DGESSWGKKD DGGSSWGKKD EGGYSEQTFD RGGRGFGGRR GGGRRGGRDQ FGRGSSFGNS EDP APWSKP SGGSSWGKQD GDGGGSSWGK ENDAGGGSSW GKQDNGVGSS WGKQNDGSGG GSSWGKQNDA GGGSSWGKQD SGGD GSSWG KQDGGGDSGS AWGKQNNTSG GSSWGKQSDA GGGSSWGKQD GGGGGSSWGK QDGGGGSGSA WGKQNETSNG SSWGK QNDS GGGSSWGKQD GGGGGSSWGK QNDGGGGSSW GKQGDGGSKP WNEHSGGGRG FGERRGGGGF RGGRNQSGRG GRSFDG GRS SSWKTDNQEN TWKSDQSGGS DWKKGWGEDS NNSKPSGSSA GGCAGNWPSW DTNSKKETND KPGDDSKSAW GTSNDQV NT DNNNDSWNKK PNNDVGTSGE ADNAWGGKTN AVAPSPSGSA AWGTGDKKTG W

UniProtKB: Protein RNA-directed DNA methylation 3

+
Macromolecule #13: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.926555 KDa
SequenceString:
(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DT)(DG)(DG)(DT)(DT)(DA)(DG)(DT)(DG) (DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC) (DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)

+
Macromolecule #15: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.643407 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DA)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC) (DG)(DA)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DG)

+
Macromolecule #14: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.492561 KDa
SequenceString:
AUCUUGAAUC UAUUUCUUUU AUCGAGAGGU

+
Macromolecule #17: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xon

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30359
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more