[English] 日本語
Yorodumi
- EMDB-0092: Structure of a yeast closed complex with distorted DNA (CCdist) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0092
TitleStructure of a yeast closed complex with distorted DNA (CCdist)
Map dataLocally filtered map
Samplecomplex
  • (transcription ...) x 3
  • Polymerase
  • Nucleic acid
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription and DNA repair factor IIH subunit ...) x 5
  • RNA polymerase II transcription factor B subunit 3
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • TATA-box-binding protein
  • (Transcription initiation factor IIF subunit ...) x 2
  • (Transcription initiation factor IIA ...) x 2
  • (Transcription initiation factor IIE subunit ...) x 2
  • Unknown protein
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 3
Function / homologyPH-like domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / TFIIH p62 subunit, N-terminal / Transcription initiation factor TFIIE, beta subunit ...PH-like domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / TFIIH p62 subunit, N-terminal / Transcription initiation factor TFIIE, beta subunit / Cyclin-like / Transcription factor TFIIB, cyclin-like domain / Zinc finger, TFIIB-type / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / ATP-dependent helicase Rad3/Chl1-like / Nucleic acid-binding, OB-fold / Cdk-activating kinase assembly factor MAT1, centre / Zinc finger, RING-type, conserved site / RNA polymerase subunit, RPB6/omega / TFIIEalpha/SarR/Rpc3 HTH domain / ERCC3/RAD25/XPB helicase, C-terminal domain / TATA-box binding protein, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / P-loop containing nucleoside triphosphate hydrolase / TFIIH subunit Tfb1/GTF2H1 / RNA polymerase subunit RPB10 / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor TFIIB, conserved site / RNA-binding domain, S1 / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / TBP domain superfamily / TFIIH subunit Ssl1/p44 / TATA-box binding protein, eukaryotic / RNA polymerase Rpb1, domain 7 / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 7 / Helicase/UvrB, N-terminal / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / Ssl1-like / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase subunit/transcription factor S / TFIIH subunit TTDA/Tfb5 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / Transcription Factor IIF, Rap30/Rap74, interaction / HRDC-like superfamily / Helical and beta-bridge domain / DEAD2 / Transcription factor IIA, beta-barrel / RNA polymerase, beta subunit, protrusion / Transcription factor IIA, helical / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription initiation factor IIF, alpha subunit / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / Helicase XPB/Ssl2, N-terminal domain / Pol II subunit B9, C-terminal zinc ribbon / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb2, domain 7 / Type III restriction enzyme, res subunit / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / Ssl1-like / RNA polymerase Rpb1, domain 7 / BSD domain / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb4 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / Transcription factor Tfb4 / Transcription factor Tfb2 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 6 / Transcription factor IIA, alpha/beta subunit / TFIIH C1-like domain / ERCC3/RAD25/XPB C-terminal helicase / RNA polymerase Rpb3/Rpb11 dimerisation domain / Helicase conserved C-terminal domain
Function and homology information
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 6.7 Å resolution
AuthorsDienemann C / Schwalb B / Schilbach S / Cramer P
CitationJournal: Mol. Cell / Year: 2018
Title: Promoter Distortion and Opening in the RNA Polymerase II Cleft.
Authors: Christian Dienemann / Björn Schwalb / Sandra Schilbach / Patrick Cramer
Abstract: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron ...Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.
Validation ReportPDB-ID: 6gym

SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0057
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0057
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6gym
  • Surface level: 0.0057
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0092.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
1.37 Å/pix.
= 479.5 Å
350 pix
1.37 Å/pix.
= 479.5 Å
350 pix
1.37 Å/pix.
= 479.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour Level:0.0057 (by author), 0.0057 (movie #1):
Minimum - Maximum-0.016232325 - 0.033904575
Average (Standard dev.)0.00015959734 (0.0011921575)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions350350350
Origin0.00.00.0
Limit349.0349.0349.0
Spacing350350350
CellA=B=C: 479.5 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z479.500479.500479.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0160.0340.000

-
Supplemental data

-
Sample components

+
Entire complex

EntireName: complex / Number of components: 39

+
Component #1: protein, complex

ProteinName: complex / Recombinant expression: No

+
Component #2: protein, transcription factors

ProteinName: transcription factorsTranscription factor / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #3: protein, Polymerase

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

+
Component #4: protein, Nucleic acid

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

+
Component #5: 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 #6: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPD,General transcription and DNA repair factor IIH helicase subunit XPD,DNA repair helicase RAD3,DNA repair helicase RAD3,General transcription and DNA repair factor IIH helicase subunit XPD
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 89.111453 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #7: protein, General transcription and DNA repair factor IIH subunit ...

ProteinName: General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.440922 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #8: protein, General transcription and DNA repair factor IIH subunit ...

ProteinName: General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.406277 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #9: protein, RNA polymerase II transcription factor B subunit 3

ProteinName: RNA polymerase II transcription factor B subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.188438 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #10: protein, General transcription and DNA repair factor IIH subunit ...

ProteinName: General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4,RNA polymerase II transcription factor B subunit 4,General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.878043 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #11: protein, General transcription and DNA repair factor IIH subunit TFB5

ProteinName: General transcription and DNA repair factor IIH subunit TFB5
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.24349 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #12: protein, General transcription and DNA repair factor IIH subunit ...

ProteinName: General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.122695 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #13: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.049695 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #14: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 191.821578 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #15: protein, DNA-directed RNA polymerase II subunit RPB2

ProteinName: DNA-directed RNA polymerase II subunit RPB2Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 138.937297 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #16: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.330457 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #17: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.451191 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #18: 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)

+
Component #19: 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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #20: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.081053 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #21: 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)

+
Component #22: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.308161 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #23: 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)

+
Component #24: protein, DNA-directed RNA polymerase II subunit RPB11

ProteinName: DNA-directed RNA polymerase II subunit RPB11Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.633493 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #25: 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)

+
Component #26: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.25734 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #27: 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)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #28: protein, Transcription initiation factor IIF subunit alpha

ProteinName: Transcription initiation factor IIF subunit alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.32057 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #29: protein, Transcription initiation factor IIF subunit beta

ProteinName: Transcription initiation factor IIF subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.684492 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #30: protein, Transcription initiation factor IIA large subunit,Transc...

ProteinName: Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.432029 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #31: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.47307 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #32: protein, Transcription initiation factor IIE subunit alpha,Transc...

ProteinName: Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.921543 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #33: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.050434 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #34: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.677524 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #35: nucleic-acid, non-template DNA (HIS4)

Nucleic-acidName: non-template DNA (HIS4) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DC)(DA)(DG)(DT)(DA)(DG)(DC)(DA) (DC)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DA)(DT)(DA)(DG)(DC)(DT)(DA) (DT)(DG)(DG)(DA)(DA)(DC)(DG)(DT)(DT)(DC) (DG)(DA)(DT)(DT)(DC)(DA)(DC)(DC)(DT)(DC) (DC)(DG)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT) (DT)(DG)(DT)(DA)(DC)(DA)(DT)(DA)(DC)(DA) (DT)(DA)(DA)(DA)(DA)
MassTheoretical: 23.150875 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #36: nucleic-acid, Template DNA (HIS4)

Nucleic-acidName: Template DNA (HIS4) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT)(DA)(DT) (DG)(DT)(DA)(DC)(DA)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DC)(DA)(DA)(DA)(DG)(DG)(DT) (DG)(DA)(DA)(DT)(DC)(DG)(DA)(DA)(DC)(DG) (DT)(DT)(DC)(DC)(DA)(DT)(DA)(DG)(DC)(DT) (DA)(DT)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DC)(DA)(DG)(DC)(DG)(DT)(DG)(DC)(DT)(DA) (DC)(DT)(DG)(DT)(DT)
MassTheoretical: 23.060822 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #37: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

+
Component #38: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #39: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

-
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: 42 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 60000
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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