[English] 日本語
Yorodumi
- EMDB-3729: RNA polymerase I pre-initiation complex (Pol-Rrn3 focused refinement) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3729
TitleRNA polymerase I pre-initiation complex (Pol-Rrn3 focused refinement)
Map data
Sample
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
    • Protein or peptide: x 15 types
    • DNA: x 2 types
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsSadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW
CitationJournal: EMBO J / Year: 2017
Title: Structural insights into transcription initiation by yeast RNA polymerase I.
Authors: Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller /
Abstract: In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of ...In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.
History
DepositionMay 17, 2017-
Header (metadata) releaseMay 31, 2017-
Map releaseJul 26, 2017-
UpdateSep 27, 2017-
Current statusSep 27, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5oa1
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3729.png

Downloads & links

-
Map

FileDownload / File: emd_3729.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.19132352 - 0.27216372
Average (Standard dev.)0.0001855439 (±0.0046788706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1910.2720.000

-
Supplemental data

-
Sample components

+
Entire : RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

EntireName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Components
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
    • Protein or peptide: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
    • Protein or peptide: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
    • Protein or peptide: RPA49_YEAST DNA-directed RNA polymerase I subunit RPA49
    • Protein or peptide: RPA43_YEAST DNA-directed RNA polymerase I subunit RPA43
    • Protein or peptide: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
    • Protein or peptide: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
    • Protein or peptide: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
    • Protein or peptide: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
    • Protein or peptide: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • Protein or peptide: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
    • DNA: non-template DNA strand
    • DNA: template DNA strand

+
Supramolecule #1: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

SupramoleculeName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190

MacromoleculeName: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDE KFCPGHQGHI ELPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA C KLRLLQYG LIDESYKLDE ITLGSLNSSM YTDDEAIEDN EDEMDGEGSK ...String:
MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDE KFCPGHQGHI ELPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA C KLRLLQYG LIDESYKLDE ITLGSLNSSM YTDDEAIEDN EDEMDGEGSK QSKDISSTLL NE LKSKRSE YVDMAIAKAL SDGRTTERGS FTATVNDERK KLVHEFHKKL LSRGKCDNCG MFS PKFRKD GFTKIFETAL NEKQITNNRV KGFIRQDMIK KQKQAKKLDG SNEASANDEE SFDV GRNPT TRPKTGSTYI LSTEVKNILD TVFRKEQCVL QYVFHSRPNL SRKLVKADSF FMDVL VVPP TRFRLPSKLG EEVHENSQNQ LLSKVLTTSL LIRDLNDDLS KLQKDKVSLE DRRVIF SRL MNAFVTIQND VNAFIDSTKA QGRTSGKVPI PGVKQALEKK EGLFRKHMMG KRVNYAA RS VISPDPNIET NEIGVPPVFA VKLTYPEPVT AYNIAELRQA VINGPDKWPG ATQIQNED G SLVSLIGMSV EQRKALANQL LTPSSNVSTH TLNKKVYRHI KNRDVVLMNR QPTLHKASM MGHKVRVLPN EKTLRLHYAN TGAYNADFDG DEMNMHFPQN ENARAEALNL ANTDSQYLTP TSGSPVRGL IQDHISAGVW LTSKDSFFTR EQYQQYIYGC IRPEDGHTTR SKIVTLPPTI F KPYPLWTG KQIITTVLLN VTPPDMPGIN LISKNKIKNE YWGKGSLENE VLFKDGALLC GI LDKSQYG ASKYGIVHSL HEVYGPEVAA KVLSVLGRLF TNYITATAFT CGMDDLRLTA EGN KWRTDI LKTSVDTGRE AAAEVTNLDK DTPADDPELL KRLQEILRDN NKSGILDAVT SSKV NAITS QVVSKCVPDG TMKKFPCNSM QAMALSGAKG SNVNVSQIMC LLGQQALEGR RVPVM VSGK TLPSFKPYET DAMAGGYVKG RFYSGIKPQE YYFHCMAGRE GLIDTAVKTS RSGYLQ RCL TKQLEGVHVS YDNSIRDADG TLVQFMYGGD AIDITKESHM TQFEFCLDNY YALLKKY NP SALIEHLDVE SALKYSKKTL KYRKKHSKEP HYKQSVKYDP VLAKYNPAKY LGSVSENF Q DKLESFLDKN SKLFKSSDGV NEKKFRALMQ LKYMRSLINP GEAVGIIASQ SVGEPSTQM TLNTFHFAGH GAANVTLGIP RLREIVMTAS AAIKTPQMTL PIWNDVSDEQ ADTFCKSISK VLLSEVIDK VIVTETTGTS NTAGGNAARS YVIHMRFFDN NEYSEEYDVS KEELQNVISN Q FIHLLEAA IVKEIKKQKR TTGPDIGVAV PRLQTDVANS SSNSKRLEED NDEEQSHKKT KQ AVSYDEP DEDEIETMRE AEKSSDEEGI DSDKESDSDS EDEDVDMNEQ INKSIVEANN NMN KVQRDR QSAIISHHRF ITKYNFDDES GKWCEFKLEL AADTEKLLMV NIVEEICRKS IIRQ IPHID RCVHPEPENG KRVLVTEGVN FQAMWDQEAF IDVDGITSND VAAVLKTYGV EAARN TIVN EINNVFSRYA ISVSFRHLDL IADMMTRQGT YLAFNRQGME TSTSSFMKMS YETTCQ FLT KAVLDNEREQ LDSPSARIVV GKLNNVGTGS FDVLAKVPNA A

+
Macromolecule #2: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135

MacromoleculeName: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIG EKVIFDGKPL NSEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER K VYPSESRQ RLTSYRGKLL LKLKWSVNNG EENLFEVRDC GGLPVMLQSN ...String:
MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIG EKVIFDGKPL NSEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER K VYPSESRQ RLTSYRGKLL LKLKWSVNNG EENLFEVRDC GGLPVMLQSN RCHLNKMSPY EL VQHKEES DEIGGYFIVN GIEKLIRMLI VQRRNHPMAI IRPSFANRGA SYSHYGIQIR SVR PDQTSQ TNVLHYLNDG QVTFRFSWRK NEYLVPVVMI LKALCHTSDR EIFDGIIGND VKDS FLTDR LELLLRGFKK RYPHLQNRTQ VLQYLGDKFR VVFQASPDQS DLEVGQEVLD RIVLV HLGK DGSQDKFRML LFMIRKLYSL VAGECSPDNP DATQHQEVLL GGFLYGMILK EKIDEY LQN IIAQVRMDIN RGMAINFKDK RYMSRVLMRV NENIGSKMQY FLSTGNLVSQ SGLDLQQ VS GYTVVAEKIN FYRFISHFRM VHRGSFFAQL KTTTVRKLLP ESWGFLCPVH TPDGSPCG L LNHFAHKCRI STQQSDVSRI PSILYSLGVA PASHTFAAGP SLCCVQIDGK IIGWVSHEQ GKIIADTLRY WKVEGKTPGL PIDLEIGYVP PSTRGQYPGL YLFGGHSRML RPVRYLPLDK EDIVGPFEQ VYMNIAVTPQ EIQNNVHTHV EFTPTNILSI LANLTPFSDF NQSPRNMYQC Q MGKQTMGT PGVALCHRSD NKLYRLQTGQ TPIVKANLYD DYGMDNFPNG FNAVVAVISY TG YDMDDAM IINKSADERG FGYGTMYKTE KVDLALNRNR GDPITQHFGF GNDEWPKEWL EKL DEDGLP YIGTYVEEGD PICAYFDDTL NKTKIKTYHS SEPAYIEEVN LIGDESNKFQ ELQT VSIKY RIRRTPQIGD KFSSRHGQKG VCSRKWPTID MPFSETGIQP DIIINPHAFP SRMTI GMFV ESLAGKAGAL HGIAQDSTPW IFNEDDTPAD YFGEQLAKAG YNYHGNEPMY SGATGE ELR ADIYVGVVYY QRLRHMVNDK FQVRSTGPVN SLTMQPVKGR KRHGGIRVGE MERDALI GH GTSFLLQDRL LNSSDYTQAS VCRECGSILT TQQSVPRIGS ISTVCCRRCS MRFEDAKK L LTKSEDGEKI FIDDSQIWED GQGNKFVGGN ETTTVAIPFV LKYLDSELSA MGIRLRYNV EPK

+
Macromolecule #3: RPA49_YEAST DNA-directed RNA polymerase I subunit RPA49

MacromoleculeName: RPA49_YEAST DNA-directed RNA polymerase I subunit RPA49
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSS SQASNQYVVG LFNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT R PSALRNAL GEAFGTKKAK KAIADLERNR IDSDKLTDSA IDIVDSVRTA ...String:
MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSS SQASNQYVVG LFNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT R PSALRNAL GEAFGTKKAK KAIADLERNR IDSDKLTDSA IDIVDSVRTA SKDLPTRAQL DE ITSNDRP TPLANIDATD VEQIYPIESI IPKKELQFIR VSSILKEADK EKKLELFPYQ NNS KYVAKK LDSLTQPSQM TKLQLLYYLS LLLGVYENRR VNNKTKLLER LNSPPEILVD GILS RFTVI KPGQFGRSKD RSYFIDPQNE DKILCYILAI IMHLDNFIVE ITPLAHELNL KPSKV VSLF RVLGAIVKGA TVAQAEAFGI PKSTAASYKI ATMKVPFKLP EMTRRGRGPR R

+
Macromolecule #4: RPA43_YEAST DNA-directed RNA polymerase I subunit RPA43

MacromoleculeName: RPA43_YEAST DNA-directed RNA polymerase I subunit RPA43
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString: MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPL VMKYNNKVGG VVLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH V NLYVWQPQ VGDVLEGYIF IQSASHIGLL IHDAFNASIK KNNIPVDWTF ...String:
MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPL VMKYNNKVGG VVLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH V NLYVWQPQ VGDVLEGYIF IQSASHIGLL IHDAFNASIK KNNIPVDWTF VHNDVEEDAD VI NTDENNG NNNNEDNKDS NGGSNSLGKF SFGNRSLGHW VDSNGEPIDG KLRFTVRNVH TTG RVVSVD GTLISDADEE GNGYNSSRSQ AESLPIVSNK KIVFDDEVSI ENKESHKELD LPEV KEDNG SEIVYEENTS ESNDGESSDS D

+
Macromolecule #5: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
SequenceString: MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRR IMISEVPSVA AEYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN L PDDEKFTD ENTIVLSLNV KCTRNPDAPK GSTDPKELYN NAHVYARDLK ...String:
MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRR IMISEVPSVA AEYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN L PDDEKFTD ENTIVLSLNV KCTRNPDAPK GSTDPKELYN NAHVYARDLK FEPQGRQSTT FA DCPVVPA DPDILLAKLR PGQEISLKAH CILGIGGDHA KFSPVSTASY RLLPQINILQ PIK GESARR FQKCFPPGVI GIDEGSDEAY VKDARKDTVS REVLRYEEFA DKVKLGRVRN HFIF NVESA GAMTPEEIFF KSVRILKNKA EYLKNCPITQ

+
Macromolecule #6: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34

MacromoleculeName: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
SequenceString: MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKS LPVDFESSTT MTIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL K IASTAKDN APLQFDKVFS VSETAKIPAI DYSKVRVPRK DVPKVEGLKL ...String:
MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKS LPVDFESSTT MTIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL K IASTAKDN APLQFDKVFS VSETAKIPAI DYSKVRVPRK DVPKVEGLKL EHFATGYDAE DF HVAEEVK ENKKEPKKRS HHDDEEESSE KKKKKKEKRE KREKKDKKDK KKKHRD

+
Macromolecule #7: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESI SKFPDMGSLW VEFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS A MKLVPSIP PATIETFNEA ALVVNITHHE LVPKHIRLSS DEKRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESI SKFPDMGSLW VEFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS A MKLVPSIP PATIETFNEA ALVVNITHHE LVPKHIRLSS DEKRELLKRY RLKESQLPRI QR ADPVALY LGLKRGEVVK IIRKSETSGR YASYRICM

+
Macromolecule #8: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTL KEKAIPKDQR ATTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR I AMKELAEK KIPLVIRRYL PDGSFEDWSV EELIVDL

+
Macromolecule #9: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEED HTLGNALRYV IMKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK G LKDLMDLC DVVESKFTEK IKSM

+
Macromolecule #10: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTP ANDSSATRSW RPPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG G LLMRLEGN YRNLNNLKQE NAYLLIRR

+
Macromolecule #11: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14

MacromoleculeName: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
SequenceString:
MMKGSRRTGN NTATTLNTPV VIHATQLPQH VSTDEVLQFL ESFIDEKENI IDSTTMNTIS GNAADADAA AVANTSLNID TNLSSSISQL KRIQRDFKGL PPAQDFSAAP IQVSTTEKKE T SIGVSATG GKKTTFADE

+
Macromolecule #12: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12

MacromoleculeName: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
SequenceString:
MSVVGSLIFC LDCGDLLENP NAVLGSNVEC SQCKAIYPKS QFSNLKVVTT TADDAFPSSL RAKKSVVKT SLKKNELKDG ATIKEKCPQC GNEEMNYHTL QLRSADEGAT VFYTCTSCGY K FRTNN

+
Macromolecule #13: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEA R

+
Macromolecule #14: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKR D

+
Macromolecule #15: RRN3_YEAST RNA polymerase I-specific transcription initiation fac...

MacromoleculeName: RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
SequenceString: MMAFENTSKR PPQDFVAPID QKKRKVQFSD STGLVTLQPE EIKDEVFSAA MYSRFVKSAL DDLDKNDST QIGIIANQVA LPSKNPERIN DKNLNILLDI LSSNINRIES SRGTFLIQSI I NFEKWWEL PPHTLSKYIY FIKILCSSIP KWWQDVSMIL VSCFILPIKQ ...String:
MMAFENTSKR PPQDFVAPID QKKRKVQFSD STGLVTLQPE EIKDEVFSAA MYSRFVKSAL DDLDKNDST QIGIIANQVA LPSKNPERIN DKNLNILLDI LSSNINRIES SRGTFLIQSI I NFEKWWEL PPHTLSKYIY FIKILCSSIP KWWQDVSMIL VSCFILPIKQ TVCHHDMLKY FL RMIPSSM GFIDTYLAKF FPNKNDTRRK LVNYTSNLLK LRGYCSELGF QIWSLLIEKI ISI DVELQN ELDELDDDVD DDDLEEVDLE DDDDLDDDSG DDDDENCGNS NEELRSGAAD GSQS DSEDM DIIEGMDGTE EYNVELTQGI KELSTKLDSI LTLVSTHVEE QVTPESLESG EGVGV FNTL TTLFKTHVLP TYYTRSIQYI MFHVSQQQLE LMDSFLVTLI DISFAVNEAA EKKIKS LQY LGSYIARAKK LSRTQIIFVA SYLTSWLNRY VIEREEEVDQ RGGMERFKHF YAAFQAL CY IFCFRHNIFR DTDGNWECEL DKFFQRMVIS KFNPLKFCNE NVMLMFARIA QQESVAYC F SIIENNNNER LRGIIGKADS DKKENSAQAN TTSSSWSLAT RQQFIDLQSY FPYDPLFLK NYKILMKEYY IEWSEASGEY ESDGSDD

+
Macromolecule #16: non-template DNA strand

MacromoleculeName: non-template DNA strand / type: dna / ID: 16 / Classification: DNA
SequenceString:
GGTTTAGTCA TGGAGTACAA GTGTGAGGAA AAGTAGTTGG CGTAGCAGGA GAAGTAAAGC AGTTGAAGAC

+
Macromolecule #17: template DNA strand

MacromoleculeName: template DNA strand / type: dna / ID: 17 / Classification: DNA
SequenceString:
CCAAATCAGT ACCTCATGTT CACACTCCTT TTCATCAACC CTCCATGAAG TACGCTTTCG TCAACTTCTG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4235 / Average exposure time: 20.0 sec. / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 38589

+
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