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- EMDB-12615: TFIIH in a pre-translocated state (without ADP-BeF3) -

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Basic information

Entry
Database: EMDB / ID: EMD-12615
TitleTFIIH in a pre-translocated state (without ADP-BeF3)Transcription factor II H
Map data
SampleTFIIH (without ADP-BeF3)
  • TFIIH basal transcription factor complex helicase XPD subunit
  • (General transcription ...) x 7
  • CDK-activating kinase assembly factor MAT1
  • (nucleic-acidNucleic acid) x 2
  • (Unassigned Peptide, likely ...) x 2
  • (ligand) x 2
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination ...cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination / transcription factor TFIIK complex / adult heart development / hair cell differentiation / nucleotide-excision repair factor 3 complex / embryonic cleavage / transcription factor TFIIE complex / negative regulation of DNA helicase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / UV protection / transcription open complex formation at RNA polymerase II promoter / G protein-coupled receptor internalization / transcription elongation from RNA polymerase I promoter / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / 5'-3' DNA helicase activity / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / transcription initiation from RNA polymerase I promoter / thyroid hormone receptor binding / bone mineralization / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation And Promoter Clearance / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Promoter Escape / termination of RNA polymerase I transcription / ATPase activator activity / snRNA transcription by RNA polymerase II / RNA polymerase II general transcription initiation factor activity / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / transcription factor TFIID complex / RNA Polymerase I Transcription Initiation / spinal cord development / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II transcribes snRNA genes / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / hematopoietic stem cell differentiation / erythrocyte maturation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / DNA topological change / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / embryonic organ development / 7-methylguanosine mRNA capping / response to UV / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation from RNA polymerase II promoter / Cyclin A:Cdk2-associated events at S phase entry / post-embryonic development / hormone-mediated signaling pathway / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / NoRC negatively regulates rRNA expression / nucleotide-excision repair, DNA duplex unwinding / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / nucleotide-excision repair, DNA incision, 5'-to lesion / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Dual Incision in GG-NER / positive regulation of DNA binding / nucleotide-excision repair, DNA incision / chromosome segregation / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of smooth muscle cell proliferation / cellular response to gamma radiation / protein-macromolecule adaptor activity / G1/S transition of mitotic cell cycle / transcription by RNA polymerase II / multicellular organism growth / spindle
Similarity search - Function
CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH subunit Tfb4/GTF2H3 / TFIIH p62 subunit, N-terminal / C-terminal general transcription factor TFIIE alpha / Transcription factor Tfb4 ...CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH subunit Tfb4/GTF2H3 / TFIIH p62 subunit, N-terminal / C-terminal general transcription factor TFIIE alpha / Transcription factor Tfb4 / TFIIH p62 subunit, N-terminal domain / RAD3/XPD family / TFIIH C1-like domain / Ssl1-like / BSD domain profile. / BSD domain / TFIIH C1-like domain / TFIIH C1-like domain / BSD domain / Ssl1-like / domain in transcription factors and synapse-associated proteins / TFIIH subunit Ssl1/p44 / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2, N-terminal domain / Helicase XPB/Ssl2 / Helicase conserved C-terminal domain / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / TFIIH subunit TTDA/Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEXDc2 / HELICc2 / DEAD2 / Helicase C-terminal domain / DEAD_2 / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor E / Transcription initiation factor IIE / Zinc finger, TFIIB-type / TFIIB zinc-binding / Type III restriction enzyme, res subunit / Helicase/UvrB, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger RING-type signature. / Zinc finger, RING-type, conserved site / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIE subunit 1 / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Human mastadenovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAibara S / Schilbach S / Cramer P
Funding support Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 16, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nvw
  • Surface level: 11
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12615.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 Å
1.05 Å/pix.
x 450 pix.
= 472.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 11.0 / Movie #1: 11
Minimum - Maximum-56.218018 - 86.632416
Average (Standard dev.)-0.0046110596 (±0.93484133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 472.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z472.500472.500472.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-56.21886.632-0.005

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Supplemental data

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Segmentation: #1

Fileemd_12615_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Locally filtered map without sharpening

Fileemd_12615_additional_1.map
AnnotationLocally filtered map without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 1

Fileemd_12615_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 2

Fileemd_12615_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire TFIIH (without ADP-BeF3)

EntireName: TFIIH (without ADP-BeF3) / Number of components: 16

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Component #1: protein, TFIIH (without ADP-BeF3)

ProteinName: TFIIH (without ADP-BeF3) / Recombinant expression: No
MassTheoretical: 490 kDa

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Component #2: protein, TFIIH basal transcription factor complex helicase XPD subunit

ProteinName: TFIIH basal transcription factor complex helicase XPD subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, General transcription factor IIH subunit 1

ProteinName: General transcription factor IIH subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.116492 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, General transcription factor IIH subunit 4

ProteinName: General transcription factor IIH subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.245156 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, CDK-activating kinase assembly factor MAT1

ProteinName: CDK-activating kinase assembly factor MAT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.873965 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, General transcription factor IIH subunit 3

ProteinName: General transcription factor IIH subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, General transcription factor IIH subunit 5

ProteinName: General transcription factor IIH subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, General transcription factor IIH subunit 2

ProteinName: General transcription factor IIH subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.481996 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPB
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 89.404734 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #10: nucleic-acid, Non-template DNA

nucleic acidName: Non-template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC) ...Sequence:
(DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT)(DC)(DC) (DT)(DC)(DA)(DC)(DT)(DC)(DT)(DC)(DT)(DT) (DC)(DC)(DG)(DC)(DA)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DG) (DG)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DT)(DT) (DG)(DG)(DG)(DG)(DT)(DG)(DA)(DG)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)
MassTheoretical: 32.911859 kDa
SourceSpecies: Human mastadenovirus C

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Component #11: nucleic-acid, Template DNA

nucleic acidName: Template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG) ...Sequence:
(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DC) (DG)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DC) (DC)(DC)(DA)(DC)(DC)(DC)(DC)(DC)(DT)(DT) (DT)(DT)(DA)(DT)(DA)(DG)(DC)(DC)(DC)(DC) (DC)(DC)(DT)(DT)(DC)(DA)(DG)(DG)(DA)(DA) (DC)(DA)(DC)(DC)(DC)(DG)
MassTheoretical: 32.508752 kDa
SourceSpecies: Human mastadenovirus C

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Component #12: protein, General transcription factor IIE subunit 1

ProteinName: General transcription factor IIE subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.516094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, Unassigned Peptide, likely XPB

ProteinName: Unassigned Peptide, likely XPB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #14: protein, Unassigned Peptide, likely TFIIE-Beta

ProteinName: Unassigned Peptide, likely TFIIE-Beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.635006 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: ligand, IRON/SULFUR CLUSTER

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

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Component #16: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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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: 41.1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 129156
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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