[English] 日本語
Yorodumi
- EMDB-14449: Structure of yeast RNA Polymerase III Delta C53-C37-C11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14449
TitleStructure of yeast RNA Polymerase III Delta C53-C37-C11
Map dataPol III Delta C53/C37/C11 Sharpened with LocalDeblur
Sample
  • Complex: Yeast RNA Polymerase III Delta C53-C37-C11
    • Protein or peptide: x 14 types
    • RNA: x 1 types
    • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


RNA polymerase III activity / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...RNA polymerase III activity / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / nucleotidyltransferase activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like ...DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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. / 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 Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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, 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 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC3 ...DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGirbig M / Mueller CW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Cell Rep / Year: 2022
Title: Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals.
Authors: Mathias Girbig / Juanjuan Xie / Helga Grötsch / Domenico Libri / Odil Porrua / Christoph W Müller /
Abstract: RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches ...RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches the termination signal, it pauses and forms the pre-termination complex (PTC). Here, we report cryoelectron microscopy (cryo-EM) structures of the yeast Pol III PTC and complementary functional states at resolutions of 2.7-3.9 Å. Pol III recognizes the poly(dT) termination signal with subunit C128 that forms a hydrogen-bond network with the NT strand and, thereby, induces pausing. Mutating key interacting residues interferes with transcription termination in vitro, impairs yeast growth, and causes global termination defects in vivo, confirming our structural results. Additional cryo-EM analysis reveals that C53-C37, a Pol III subcomplex and key termination factor, participates indirectly in Pol III termination. We propose a mechanistic model of Pol III transcription termination and rationalize why Pol III, unlike Pol I and Pol II, terminates on poly(dT) signals.
History
DepositionFeb 24, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14449.png

Downloads & links

-
Map

FileDownload / File: emd_14449.map.gz / Format: CCP4 / Size: 158 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPol III Delta C53/C37/C11 Sharpened with LocalDeblur
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 346 pix.
= 364.338 Å		1.05 Å/pix.
x 346 pix.
= 364.338 Å		1.05 Å/pix.
x 346 pix.
= 364.338 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.030160436 - 0.36180076
Average (Standard dev.)0.00041664642 (±0.0057330793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions346346346
Spacing346346346
CellA=B=C: 364.33798 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Pol III Delta C53/C37/C11 Unsharpened map

Fileemd_14449_additional_1.map
AnnotationPol III Delta C53/C37/C11 Unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Pol III Delta C53/C37/C11 Half map 2, not resampled

Fileemd_14449_half_map_1.map
AnnotationPol III Delta C53/C37/C11 Half map 2, not resampled
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Pol III Delta C53/C37/C11 Half map 1, not resampled

Fileemd_14449_half_map_2.map
AnnotationPol III Delta C53/C37/C11 Half map 1, not resampled
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Yeast RNA Polymerase III Delta C53-C37-C11

EntireName: Yeast RNA Polymerase III Delta C53-C37-C11
Components
  • Complex: Yeast RNA Polymerase III Delta C53-C37-C11
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC1Polymerase
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC2Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC9Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC8Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC3Polymerase
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC6Polymerase
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC7Polymerase
    • RNA: RNA
    • DNA: NT-DNA
    • DNA: T-DNATransfer DNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: CHAPSOCHAPS detergent

+
Supramolecule #1: Yeast RNA Polymerase III Delta C53-C37-C11

SupramoleculeName: Yeast RNA Polymerase III Delta C53-C37-C11 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 635 KDa

+
Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 162.517812 KDa
SequenceString: MKEVVVSETP KRIKGLEFSA LSAADIVAQS EVEVSTRDLF DLEKDRAPKA NGALDPKMGV SSSSLECATC HGNLASCHGH FGHLKLALP VFHIGYFKAT IQILQGICKN CSAILLSETD KRQFLHELRR PGVDNLRRMG ILKKILDQCK KQRRCLHCGA L NGVVKKAA ...String:
MKEVVVSETP KRIKGLEFSA LSAADIVAQS EVEVSTRDLF DLEKDRAPKA NGALDPKMGV SSSSLECATC HGNLASCHGH FGHLKLALP VFHIGYFKAT IQILQGICKN CSAILLSETD KRQFLHELRR PGVDNLRRMG ILKKILDQCK KQRRCLHCGA L NGVVKKAA AGAGSAALKI IHDTFRWVGK KSAPEKDIWV GEWKEVLAHN PELERYVKRC MDDLNPLKTL NLFKQIKSAD CE LLGIDAT VPSGRPETYI WRYLPAPPVC IRPSVMMQDS PASNEDDLTV KLTEIVWTSS LIKAGLDKGI SINNMMEHWD YLQ LTVAMY INSDSVNPAM LPGSSNGGGK VKPIRGFCQR LKGKQGRFRG NLSGKRVDFS GRTVISPDPN LSIDEVAVPD RVAK VLTYP EKVTRYNRHK LQELIVNGPN VHPGANYLLK RNEDARRNLR YGDRMKLAKN LQIGDVVERH LEDGDVVLFN RQPSL HRLS ILSHYAKIRP WRTFRLNECV CTPYNADFDG DEMNLHVPQT EEARAEAINL MGVKNNLLTP KSGEPIIAAT QDFITG SYL ISHKDSFYDR ATLTQLLSMM SDGIEHFDIP PPAIMKPYYL WTGKQVFSLL IKPNHNSPVV INLDAKNKVF VPPKSKS LP NEMSQNDGFV IIRGSQILSG VMDKSVLGDG KKHSVFYTIL RDYGPQEAAN AMNRMAKLCA RFLGNRGFSI GINDVTPA D DLKQKKEELV EIAYHKCDEL ITLFNKGELE TQPGCNEEQT LEAKIGGLLS KVREEVGDVC INELDNWNAP LIMATCGSK GSTLNVSQMV AVVGQQIISG NRVPDGFQDR SLPHFPKNSK TPQSKGFVRN SFFSGLSPPE FLFHAISGRE GLVDTAVKTA ETGYMSRRL MKSLEDLSCQ YDNTVRTSAN GIVQFTYGGD GLDPLEMEGN AQPVNFNRSW DHAYNITFNN QDKGLLPYAI M ETANEILG PLEERLVRYD NSGCLVKRED LNKAEYVDQY DAERDFYHSL REYINGKATA LANLRKSRGM LGLLEPPAKE LQ GIDPDET VPDNVKTSVS QLYRISEKSV RKFLEIALFK YRKARLEPGT AIGAIGAQSI GEPGTQMTLK TFHFAGVASM NVT LGVPRI KEIINASKVI STPIINAVLV NDNDERAARV VKGRVEKTLL SDVAFYVQDV YKDNLSFIQV RIDLGTIDKL QLEL TIEDI AVAITRASKL KIQASDVNII GKDRIAINVF PEGYKAKSIS TSAKEPSEND VFYRMQQLRR ALPDVVVKGL PDISR AVIN IRDDGKRELL VEGYGLRDVM CTDGVIGSRT TTNHVLEVFS VLGIEAARYS IIREINYTMS NHGMSVDPRH IQLLGD VMT YKGEVLGITR FGLSKMRDSV LQLASFEKTT DHLFDAAFYM KKDAVEGVSE CIILGQTMSI GTGSFKVVKG TNISEKD LV PKRCLFESLS NEAALKAN

+
Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 129.629383 KDa
SequenceString: MVAATKRRKT HIHKHVKDEA FDDLLKPVYK GKKLTDEINT AQDKWHLLPA FLKVKGLVKQ HLDSFNYFVD TDLKKIIKAN QLILSDVDP EFYLKYVDIR VGKKSSSSTK DYLTPPHECR LRDMTYSAPI YVDIEYTRGR NIIMHKDVEI GRMPIMLRSN K CILYDADE ...String:
MVAATKRRKT HIHKHVKDEA FDDLLKPVYK GKKLTDEINT AQDKWHLLPA FLKVKGLVKQ HLDSFNYFVD TDLKKIIKAN QLILSDVDP EFYLKYVDIR VGKKSSSSTK DYLTPPHECR LRDMTYSAPI YVDIEYTRGR NIIMHKDVEI GRMPIMLRSN K CILYDADE SKMAKLNECP LDPGGYFIVN GTEKVILVQE QLSKNRIIVE ADEKKGIVQA SVTSSTHERK SKTYVITKNG KI YLKHNSI AEEIPIAIVL KACGILSDLE IMQLVCGNDS SYQDIFAVNL EESSKLDIYT QQQALEYIGA KVKTMRRQKL TIL QEGIEA IATTVIAHLT VEALDFREKA LYIAMMTRRV VMAMYNPKMI DDRDYVGNKR LELAGQLISL LFEDLFKKFN NDFK LSIDK VLKKPNRAME YDALLSINVH SNNITSGLNR AISTGNWSLK RFKMERAGVT HVLSRLSYIS ALGMMTRISS QFEKS RKVS GPRALQPSQF GMLCTADTPE GEACGLVKNL ALMTHITTDD EEEPIKKLCY VLGVEDITLI DSASLHLNYG VYLNGT LIG SIRFPTKFVT QFRHLRRTGK VSEFISIYSN SHQMAVHIAT DGGRICRPLI IVSDGQSRVK DIHLRKLLDG ELDFDDF LK LGLVEYLDVN EENDSYIALY EKDIVPSMTH LEIEPFTILG AVAGLIPYPH HNQSPRNTYQ CAMGKQAIGA IAYNQFKR I DTLLYLMTYP QQPMVKTKTI ELIDYDKLPA GQNATVAVMS YSGYDIEDAL VLNKSSIDRG FGRCETRRKT TTVLKRYAN HTQDIIGGMR VDENGDPIWQ HQSLGPDGLG EVGMKVQSGQ IYINKSVPTN SADAPNPNNV NVQTQYREAP VIYRGPEPSH IDQVMMSVS DNDQALIKVL LRQNRRPELG DKFSSRHGQK GVCGIIVKQE DMPFNDQGIV PDIIMNPHGF PSRMTVGKMI E LISGKAGV LNGTLEYGTC FGGSKLEDMS KILVDQGFNY SGKDMLYSGI TGECLQAYIF FGPIYYQKLK HMVLDKMHAR AR GPRAVLT RQPTEGRSRD GGLRLGEMER DCVIAYGASQ LLLERLMISS DAFEVDVCDK CGLMGYSGWC TTCKSAENII KMT IPYAAK LLFQELLSMN IAPRLRLEDI FQQ

+
Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 37.732613 KDa
SequenceString: MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRRI MISEVPSVAA EYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN LPDDEKFTDE NTIVLSLNVK CTRNPDAPKG STDPKELYNN A HVYARDLK ...String:
MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRRI MISEVPSVAA EYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN LPDDEKFTDE NTIVLSLNVK CTRNPDAPKG STDPKELYNN A HVYARDLK FEPQGRQSTT FADCPVVPAD PDILLAKLRP GQEISLKAHC ILGIGGDHAK FSPVSTASYR LLPQINILQP IK GESARRF QKCFPPGVIG IDEGSDEAYV KDARKDTVSR EVLRYEEFAD KVKLGRVRNH FIFNVESAGA MTPEEIFFKS VRI LKNKAE YLKNCPITQ

+
Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.623123 KDa
SequenceString:
MKVLEERNAF LSDYEVLKFL TDLEKKHLWD QKSLAALKKS RSKGKQNRPY NHPELQGITR NVVNYLSINK NFINQEDEGE ERESSGAKD AEKSGISKMS DESFAELMTK LNSFKLFKAE KLQIVNQLPA NMVHLYSIVE ECDARFDEKT IEEMLEIISG Y A

+
Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

+
Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

+
Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 24.34977 KDa
SequenceString: MFILSKIADL VRIPPDQFHR DTISAITHQL NNKFANKIIP NVGLCITIYD LLTVEEGQLK PGDGSSYINV TFRAVVFKPF LGEIVTGWI SKCTAEGIKV SLLGIFDDIF IPQNMLFEGC YYTPEESAWI WPMDEETKLY FDVNEKIRFR IEREVFVDVK P KSPKEREL ...String:
MFILSKIADL VRIPPDQFHR DTISAITHQL NNKFANKIIP NVGLCITIYD LLTVEEGQLK PGDGSSYINV TFRAVVFKPF LGEIVTGWI SKCTAEGIKV SLLGIFDDIF IPQNMLFEGC YYTPEESAWI WPMDEETKLY FDVNEKIRFR IEREVFVDVK P KSPKEREL EERAQLENEI EGKNEETPQN EKPPAYALLG SCQTDGMGLV SWWE

+
Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

+
Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

+
Macromolecule #10: DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.16786 KDa
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEEDH TLGNALRYVI MKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK GLKDLMDLCD VVESKFTEKI KSM

+
Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

+
Macromolecule #12: DNA-directed RNA polymerase III subunit RPC3

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC3 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 74.11282 KDa
SequenceString: MDELLGEALS AENQTGESTV ESEKLVTPED VMTISSLEQR TLNPDLFLYK ELVKAHLGER AASVIGMLVA LGRLSVRELV EKIDGMDVD SVKTTLVSLT QLRCVKYLQE TAISGKKTTY YYYNEEGIHI LLYSGLIIDE IITQMRVNDE EEHKQLVAEI V QNVISLGS ...String:
MDELLGEALS AENQTGESTV ESEKLVTPED VMTISSLEQR TLNPDLFLYK ELVKAHLGER AASVIGMLVA LGRLSVRELV EKIDGMDVD SVKTTLVSLT QLRCVKYLQE TAISGKKTTY YYYNEEGIHI LLYSGLIIDE IITQMRVNDE EEHKQLVAEI V QNVISLGS LTVEDYLSSV TSDSMKYTIS SLFVQLCEMG YLIQISKLHY TPIEDLWQFL YEKHYKNIPR NSPLSDLKKR SQ AKMNAKT DFAKIINKPN ELSQILTVDP KTSLRIVKPT VSLTINLDRF MKGRRSKQLI NLAKTRVGSV TAQVYKIALR LTE QKSPKI RDPLTQTGLL QDLEEAKSFQ DEAELVEEKT PGLTFNAIDL ARHLPAELDL RGSLLSRKPS DNKKRSGSNA AASL PSKKL KTEDGFVIPA LPAAVSKSLQ ESGDTQEEDE EEEDLDADTE DPHSASLINS HLKILASSNF PFLNETKPGV YYVPY SKLM PVLKSSVYEY VIASTLGPSA MRLSRCIRDN KLVSEKIINS TALMKEKDIR STLASLIRYN SVEIQEVPRT ADRSAS RAV FLFRCKETHS YNFMRQNLEW NMANLLFKKE KLKQENSTLL KKANRDDVKG RENELLLPSE LNQLKMVNER ELNVFAR LS RLLSLWEVFQ MA

+
Macromolecule #13: DNA-directed RNA polymerase III subunit RPC6

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 36.17416 KDa
SequenceString: MSGMIENGLQ LSDNAKTLHS QMMSKGIGAL FTQQELQKQM GIGSLTDLMS IVQELLDKNL IKLVKQNDEL KFQGVLESEA QKKATMSAE EALVYSYIEA SGREGIWSKT IKARTNLHQH VVLKCLKSLE SQRYVKSVKS VKFPTRKIYM LYSLQPSVDI T GGPWFTDG ...String:
MSGMIENGLQ LSDNAKTLHS QMMSKGIGAL FTQQELQKQM GIGSLTDLMS IVQELLDKNL IKLVKQNDEL KFQGVLESEA QKKATMSAE EALVYSYIEA SGREGIWSKT IKARTNLHQH VVLKCLKSLE SQRYVKSVKS VKFPTRKIYM LYSLQPSVDI T GGPWFTDG ELDIEFINSL LTIVWRFISE NTFPNGFKNF ENGPKKNVFY APNVKNYSTT QEILEFITAA QVANVELTPS NI RSLCEVL VYDDKLEKVT HDCYRVTLES ILQMNQGEGE PEAGNKALED EEEFSIFNYF KMFPASKHDK EVVYFDEWTI

+
Macromolecule #14: DNA-directed RNA polymerase III subunit RPC7

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC7 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.752971 KDa
SequenceString: MSSYRGGSRG GGSNYMSNLP FGLGYGDVGK NHITEFPSIP LPINGPITNK ERSLAVKYIN FGKTVKDGPF YTGSMSLIID QQENSKSGK RKPNIILDED DTNDGIERYS DKYLKKRKIG ISIDDHPYNL NLFPNELYNV MGINKKKLLA ISKFNNADDV F TGTGLQDE ...String:
MSSYRGGSRG GGSNYMSNLP FGLGYGDVGK NHITEFPSIP LPINGPITNK ERSLAVKYIN FGKTVKDGPF YTGSMSLIID QQENSKSGK RKPNIILDED DTNDGIERYS DKYLKKRKIG ISIDDHPYNL NLFPNELYNV MGINKKKLLA ISKFNNADDV F TGTGLQDE NIGLSMLAKL KELAEDVDDA STGDGAAKGS KTGEGEDDDL ADDDFEEDED EEDDDDYNAE KYFNNGDDDD YG DEEDPNE EAAF

+
Macromolecule #15: RNA

MacromoleculeName: RNA / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.676638 KDa
SequenceString:
UAUGCUAUGC AUAACGCCAC AGAG

+
Macromolecule #16: NT-DNA

MacromoleculeName: NT-DNA / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.428645 KDa
SequenceString:
(DG)(DA)(DA)(DT)(DC)(DT)(DC)(DT)(DT)(DA) (DG)(DC)(DA)(DA)(DC)(DC)(DA)(DT)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DC) (DC)(DT)(DT)(DC)(DC)(DG)(DA)(DA)(DA)(DA) (DT) (DT)(DT)(DT)(DG)

+
Macromolecule #17: T-DNA

MacromoleculeName: T-DNA / type: dna / ID: 17 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.593733 KDa
SequenceString:
(DC)(DA)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DC) (DG)(DG)(DA)(DA)(DG)(DG)(DC)(DA)(DT)(DG) (DC)(DT)(DC)(DT)(DG)(DT)(DG)(DG)(DC) (DT)(DT)(DT)(DG)(DC)(DT)(DA)(DA)(DG)(DA) (DG) (DA)(DT)(DT)(DC)

+
Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #19: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #20: CHAPSO

MacromoleculeName: CHAPSO / type: ligand / ID: 20 / Number of copies: 2 / Formula: 1N7
Molecular weightTheoretical: 631.884 Da
Chemical component information

ChemComp-1N7:
CHAPSO / detergent*YM / CHAPS detergent

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
0.015 MHEPES
0.15 MAmmonium sulfate
0.005 MMagnesium chloride
0.01 MDTT
0.004 MCHAPSOCHAPS detergent
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS 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: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 359678
CTF correctionSoftware: (Name: Warp (ver. 1.0.7W), RELION (ver. 3.1))
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 18530
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7z1n:
Structure of yeast RNA Polymerase III Delta C53-C37-C11

+
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