[English] 日本語
Yorodumi
- EMDB-31306: The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31306
TitleThe cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme
Map data
Sample
  • Complex: A. thaliana Pol IV-RDR2 holoenzyme
    • Protein or peptide: x 11 types
  • Ligand: x 2 types
KeywordsDNA-directed RNA polymerase IV / RNA- dependent RNA polymerase 2 / RNA-directed DNA methylation pathway / TRANSPORT PROTEIN / TRANSCRIPTION
Function / homology
Function and homology information


stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / RNA polymerase V complex / transposable element silencing by siRNA-mediated heterochromatin formation / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing ...stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / RNA polymerase V complex / transposable element silencing by siRNA-mediated heterochromatin formation / 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 / RNA polymerase complex / RNA polymerase II activity / regulation of immune response / defense response to fungus / RNA polymerase II, core complex / heterochromatin / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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 subunit RPABC5/Rpb10 ...RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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 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 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, 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. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Nucleic acid-binding, OB-fold
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 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 polymerases II, IV and V subunit 8B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsFang CL / Wu XX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2021
Title: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.
Authors: Kun Huang / Xiao-Xian Wu / Cheng-Li Fang / Zhou-Geng Xu / Hong-Wei Zhang / Jian Gao / Chuan-Miao Zhou / Lin-Lin You / Zhan-Xi Gu / Wen-Hui Mu / Yu Feng / Jia-Wei Wang / Yu Zhang /
Abstract: DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded ...DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo–electron microscopy structures of the Pol IV–RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV–generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a ‘backtracking-triggered RNA channeling’ mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases.
History
DepositionMay 15, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7eu1
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31306.png

Downloads & links

-
Map

FileDownload / File: emd_31306.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.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0788664 - 0.1307563
Average (Standard dev.)0.0003247899 (±0.0038408216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0790.1310.000

-
Supplemental data

-
Additional map: #1

Fileemd_31306_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_31306_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_31306_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : A. thaliana Pol IV-RDR2 holoenzyme

EntireName: A. thaliana Pol IV-RDR2 holoenzyme
Components
  • Complex: A. thaliana Pol IV-RDR2 holoenzyme
    • 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 II and IV subunit 5A
    • Protein or peptide: DNA-directed RNA polymerases II, IV and V subunit 6A
    • 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
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: A. thaliana Pol IV-RDR2 holoenzyme

SupramoleculeName: A. thaliana Pol IV-RDR2 holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Arabidopsis thaliana (thale cress)

+
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
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 169.535281 KDa
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 HHHHHHSSNF PDRSNIWQ

+
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 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

+
Macromolecule #4: DNA-directed RNA polymerases II and IV subunit 5A

MacromoleculeName: DNA-directed RNA polymerases II and IV subunit 5A / type: protein_or_peptide / ID: 4 / 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

+
Macromolecule #5: 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: 5 / 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 #6: 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: 6 / 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

+
Macromolecule #7: 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: 7 / 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 #8: 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: 8 / 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 #9: 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: 9 / 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 #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: 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 #11: RNA-dependent RNA polymerase 2

MacromoleculeName: RNA-dependent RNA polymerase 2 / type: protein_or_peptide / ID: 11 / 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 #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #13: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mmol/LC2H18N2O4SHEPES
100.0 mmol/LNaClSodium chloride
5.0 mmol/LMgCl2Magnesium chloride
2.0 mmol/LC4H10O2S2DL-dithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 135 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 282.65 K / Instrument: FEI VITROBOT MARK III
DetailsThe complex contains 11 protein subunits (A, B, C, E, F, H , I, J, K, L, M)

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.366 sec. / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 132247
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7eu1:
The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme

+
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