[English] 日本語
Yorodumi
- EMDB-4181: RNA Polymerase III initially transcribing complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4181
TitleRNA Polymerase III initially transcribing complex
Map data
SampleRNA Polymerase III initially transcribing complex
  • RNA Polymerase III
  • Transcription factorsTranscription factor
  • Nucleic acidsNucleic acid
  • (DNA-directed RNA polymerase III subunit ...Polymerase) x 10
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • TATA-box-binding protein
  • (Transcription factor ...) x 2
  • (nucleic-acidNucleic acid) x 3
  • ligand
Function / homology
Function and homology information


positive regulation of transposon integration / RNA polymerase III core binding / termination of RNA polymerase III transcription / tRNA 3'-trailer cleavage / transcription initiation from RNA polymerase III promoter / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding ...positive regulation of transposon integration / RNA polymerase III core binding / termination of RNA polymerase III transcription / tRNA 3'-trailer cleavage / transcription initiation from RNA polymerase III promoter / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / transposon integration / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase III activity / general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / RNA polymerase II preinitiation complex assembly / DNA binding, bending / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II transcribes snRNA genes / mRNA Capping / Formation of the Early Elongation Complex / transcription factor TFIID complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / transcription preinitiation complex / RNA polymerase II, core complex / RNA polymerase II core promoter sequence-specific DNA binding / TBP-class protein binding / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / single-stranded DNA binding / DNA-binding transcription factor binding / ribosome biogenesis / disordered domain specific binding / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated / chromatin binding / nucleolus / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor TFIIIB component B'', fungi / Myb DNA-binding like / Transcription factor IIIB subunit Brf1 / Transcription factor TFIIIB component B'', Myb domain / Brf1-like TBP-binding domain / Brf1, TBP-binding domain / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC1, N-terminal ...Transcription factor TFIIIB component B'', fungi / Myb DNA-binding like / Transcription factor IIIB subunit Brf1 / Transcription factor TFIIIB component B'', Myb domain / Brf1-like TBP-binding domain / Brf1, TBP-binding domain / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC1, C-terminal / Pol III subunit C11, C-terminal zinc ribbon / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC9 / RPC5 protein / RNA polymerase III subunit Rpc25 / RNA polymerase III subunit RPC82 helix-turn-helix domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 / RNA polymerase Rpc34 subunit / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 / RNA polymerase Rpc34-like / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC40 / DNA-directed RNA polymerases I and III subunit AC19 / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / Rpb4/RPC9 superfamily / TBP domain superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Cyclin-like superfamily / SANT/Myb domain / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb8 / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb5, C-terminal domain / : / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / C2C2 Zinc finger
Similarity search - Domain/homology
DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / Transcription factor TFIIIB component B'' / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / Transcription factor IIIB 70 kDa subunit / TATA-box-binding protein ...DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / Transcription factor TFIIIB component B'' / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / Transcription factor IIIB 70 kDa subunit / TATA-box-binding protein / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsVorlaender MK / Khatter H / Wetzel R / Hagen WJH / Mueller CW
Funding support1 items
OrganizationGrant numberCountry
European Research CouncilERC-2013-AdG340964-POL1PIC
CitationJournal: Nature / Year: 2018
Title: Molecular mechanism of promoter opening by RNA polymerase III.
Authors: Matthias K Vorländer / Heena Khatter / Rene Wetzel / Wim J H Hagen / Christoph W Müller /
Abstract: RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures ...RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site. Our structures reveal an extremely tight, multivalent interaction between TFIIIB and promoter DNA, and explain how TFIIIB recruits Pol III. Together, TFIIIB and Pol III subunit C37 activate the intrinsic transcription factor-like activity of the Pol III-specific heterotrimer to initiate the melting of double-stranded DNA, in a mechanism similar to that of the Pol II system.
History
DepositionNov 29, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6f41
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4181.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.35 Å/pix.
x 240 pix.
= 324. Å
1.35 Å/pix.
x 240 pix.
= 324. Å
1.35 Å/pix.
x 240 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.11963552 - 0.20997699
Average (Standard dev.)0.001266515 (±0.008234556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1200.2100.001

-
Supplemental data

-
Segmentation: #1

Fileemd_4181_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: ITC map sharpened with Loc Scale

Fileemd_4181_additional.map
AnnotationITC map sharpened with LocScale
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire RNA Polymerase III initially transcribing complex

EntireName: RNA Polymerase III initially transcribing complex / Number of Components: 28

+
Component #1: protein, RNA Polymerase III initially transcribing complex

ProteinName: RNA Polymerase III initially transcribing complex / Recombinant expression: No
MassTheoretical: 893 kDa

+
Component #2: protein, RNA Polymerase III

ProteinName: RNA Polymerase III / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #3: protein, Transcription factors

ProteinName: Transcription factorsTranscription factor / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, Nucleic acids

ProteinName: Nucleic acidsNucleic acid / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Synthetic construct (others)

+
Component #5: protein, DNA-directed RNA polymerase III subunit RPC1

ProteinName: DNA-directed RNA polymerase III subunit RPC1Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 162.517812 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #6: protein, DNA-directed RNA polymerase III subunit RPC2

ProteinName: DNA-directed RNA polymerase III subunit RPC2Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 129.629383 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #7: protein, DNA-directed RNA polymerases I and III subunit RPAC1

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.732613 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #8: protein, DNA-directed RNA polymerase III subunit RPC9

ProteinName: DNA-directed RNA polymerase III subunit RPC9Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.623123 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #10: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #11: protein, DNA-directed RNA polymerase III subunit RPC8

ProteinName: DNA-directed RNA polymerase III subunit RPC8Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.34977 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #12: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #13: protein, DNA-directed RNA polymerase III subunit RPC10

ProteinName: DNA-directed RNA polymerase III subunit RPC10Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.525109 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #15: protein, DNA-directed RNA polymerases I and III subunit RPAC2

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.16786 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #16: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #17: protein, DNA-directed RNA polymerase III subunit RPC5

ProteinName: DNA-directed RNA polymerase III subunit RPC5Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.178115 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #18: protein, DNA-directed RNA polymerase III subunit RPC4

ProteinName: DNA-directed RNA polymerase III subunit RPC4Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.751469 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #19: protein, DNA-directed RNA polymerase III subunit RPC3

ProteinName: DNA-directed RNA polymerase III subunit RPC3Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.11282 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #20: protein, DNA-directed RNA polymerase III subunit RPC6

ProteinName: DNA-directed RNA polymerase III subunit RPC6Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.17416 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #21: protein, DNA-directed RNA polymerase III subunit RPC7

ProteinName: DNA-directed RNA polymerase III subunit RPC7Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.752971 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #22: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.042275 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #23: protein, Transcription factor IIIB 70 kDa subunit

ProteinName: Transcription factor IIIB 70 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.011477 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #24: protein, Transcription factor TFIIIB component B''

ProteinName: Transcription factor TFIIIB component B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.801906 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #25: nucleic-acid, RNA

nucleic acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUGCC
MassTheoretical: 1.86815 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

+
Component #26: nucleic-acid, Non-Template DNA

nucleic acidName: Non-Template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DG)(DT)(DC)(DC)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DT)(DC)(DG)(DG)(DC)(DT)(DA)(DC) (DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DA) (DT)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DG)(DC)(DA)(DG)(DT)(DC) ...Sequence:
(DC)(DG)(DT)(DC)(DC)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DT)(DC)(DG)(DG)(DC)(DT)(DA)(DC) (DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DA) (DT)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DG)(DC)(DA)(DG)(DT)(DC)(DT)(DA)(DT)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA)(DC)(DA)(DG) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DT)(DC)(DG) (DT)(DG)(DG)(DA)(DC)(DA)(DT)(DT)(DT)(DG) (DG)
MassTheoretical: 24.885926 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

+
Component #27: nucleic-acid, Template-DNA

nucleic acidName: Template-DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DC)(DC) (DA)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DC)(DT)(DT)(DC)(DG)(DG)(DC)(DA)(DA) (DC)(DC)(DC)(DA)(DT)(DA)(DG)(DT)(DT)(DG) (DC)(DG)(DA)(DA)(DA)(DA) ...Sequence:
(DC)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DC)(DC) (DA)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DC)(DT)(DT)(DC)(DG)(DG)(DC)(DA)(DA) (DC)(DC)(DC)(DA)(DT)(DA)(DG)(DT)(DT)(DG) (DC)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DC) (DA)(DT)(DT)(DT)(DA)(DT)(DT)(DT)(DA)(DT) (DA)(DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DA) (DA)(DA)(DT)(DA)(DG)(DT)(DG)(DG)(DA)(DC) (DG)
MassTheoretical: 25.041104 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

+
Component #28: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 61.3 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 29951
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Target Criteria: Cross-correlation coefficient / Refinement space: REAL / Overall BValue: 142
Output model

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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