[English] 日本語
Yorodumi
- EMDB-2784: Architecture of the RNA polymerase II-Mediator core transcription... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2784
TitleArchitecture of the RNA polymerase II-Mediator core transcription initiation complex
Map data
SamplePol II-DNA/RNA
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • (nucleic-acidNucleic acid) x 3
Keywordstranscription / transcription initiation / RNA polymerase II / General Transcription Factors
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / positive regulation of translational initiation / 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-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7 ...RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7 / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / Zinc finger TFIIS-type signature. / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit 9 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / RNA polymerase Rpb8 / 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 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / : / : / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / Zinc finger, TFIIS-type / C2C2 Zinc finger / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / RNA-binding domain, S1 / S1 domain / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / : / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, N-terminal / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsPlaschka C / Lariviere L / Wenzeck L / Hemann M / Tegunov D / Petrotchenko EV / Borchers CH / Baumeister W / Herzog F / Villa E / Cramer P
CitationJournal: Nature / Year: 2015
Title: Architecture of the RNA polymerase II-Mediator core initiation complex.
Authors: C Plaschka / L Larivière / L Wenzeck / M Seizl / M Hemann / D Tegunov / E V Petrotchenko / C H Borchers / W Baumeister / F Herzog / E Villa / P Cramer /
Abstract: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all ...The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.
History
DepositionSep 21, 2014-
Header (metadata) releaseOct 29, 2014-
Map releaseFeb 4, 2015-
UpdateMar 4, 2015-
Current statusMar 4, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4v1m
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2784.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 280 pix.
= 378. Å
1.35 Å/pix.
x 280 pix.
= 378. Å
1.35 Å/pix.
x 280 pix.
= 378. 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: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.04966678 - 0.10112445
Average (Standard dev.)0.00006485 (±0.00348376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0500.1010.000

-
Supplemental data

-
Sample components

+
Entire Pol II-DNA/RNA

EntireName: Pol II-DNA/RNA / Number of Components: 15
MassTheoretical: 570 kDa

+
Component #1: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1Polymerase / a.k.a: RPO21 RPB1 RPB220 SUA8 YDL140C D2150 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 192 kDa / Experimental: 192 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB1

+
Component #2: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2Polymerase / a.k.a: RPB2 RPB150 RPO22 YOR151C / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 139 kDa / Experimental: 139 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB2

+
Component #3: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3Polymerase / a.k.a: RPB3 YIL021W / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35 kDa / Experimental: 35 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB3

+
Component #4: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4Polymerase / a.k.a: RPB4 YJL140W J0654 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 25 kDa / Experimental: 25 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB4

+
Component #5: protein, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1

ProteinName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1RNA polymerase
a.k.a: RPB5 RPA7 RPC9 YBR154C YBR1204 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 25 kDa / Experimental: 25 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerases I, II, and III subunit RPABC1

+
Component #6: protein, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

ProteinName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2RNA polymerase
a.k.a: RPO26 RPB6 YPR187W P9677.8 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 18 kDa / Experimental: 18 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerases I, II, and III subunit RPABC2

+
Component #7: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7Polymerase / a.k.a: RPB7 YDR404C D9509.22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19 kDa / Experimental: 19 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB7

+
Component #8: protein, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

ProteinName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3RNA polymerase
a.k.a: RPB8 YOR224C YOR50-14 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 17 kDa / Experimental: 17 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
Component #9: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9Polymerase / a.k.a: RPB9 YGL070C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14 kDa / Experimental: 14 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB9

+
Component #10: protein, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

ProteinName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5RNA polymerase
a.k.a: RPB10 YOR210W / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8 kDa / Experimental: 8 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
Component #11: protein, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

ProteinName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11Polymerase
a.k.a: RPB11 YOL005C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13 kDa / Experimental: 13 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerase II subunit RPB11

+
Component #12: protein, DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

ProteinName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4RNA polymerase
a.k.a: RPC10 RPB12 YHR143W-A YHR143BW / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 8 kDa / Experimental: 8 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio
Source (natural)Organelle: Nucleus
External referencesUniProt: DNA-directed RNA polymerases I, II, and III subunit RPABC4

+
Component #13: nucleic-acid, template DNA

nucleic acidName: template DNA / Class: DNA / Structure: SINGLE STRANDED / Synthetic: Yes
Sequence:
CGAGAACAGT AGCACGCTGT GTATATAATA GTGTGTTGTA CATAGCGGAG GTCGGTGGGG CACAACTGCG CT
SourceSpecies: synthetic construct (others)

+
Component #14: nucleic-acid, nontemplate DNA

nucleic acidName: nontemplate DNA / Class: DNA / Structure: SINGLE STRANDED / Synthetic: Yes
Sequence:
AGCGCAGTTG TGCTATGATA TTTTTATGTA TGTACAACAC ACTATTATAT ACACAGCGTG CTACTGTTCT CG
SourceSpecies: synthetic construct (others)

+
Component #15: nucleic-acid, RNA

nucleic acidName: RNA / Class: RNA / Structure: SINGLE STRANDED / Synthetic: Yes
Sequence:
AUAUCA
SourceSpecies: synthetic construct (others)

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/mL
Buffer solution: 25 mM HEPES-KOH pH 7.5, 180 mM Potassium acetate, 5 % Glycerol, 5 mM DTT
pH: 7.5
Support filmLacey carbon copper grids (Quantifoil)
VitrificationInstrument: OTHER / Cryogen Name: ETHANE
Method: Grids were glow-discharged for 20 s before deposition of 4 microliters sample and incubated for 30 s. Grids were washed twice with 4 microliters distilled water, blotted, and then vitrified.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 31, 2013
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 25 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 37000 X (nominal), 37169 X (calibrated) / Cs: 2 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 2972

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 14777
Details: Particles were picked using EMAN2 and were processed using RELION 1.2.
3D reconstructionAlgorithm: RELION 1.2 / Software: RELION, 1.2 / CTF correction: Each particle
Details: The density was filtered according to local resolution and further a temperature factor of minus 240 A2 was applied.
Resolution: 6.6 Å / Resolution Method: FSC 0.143, gold-standard

-
Atomic model buiding

Modeling #1Software: SITUS / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 4A3D
Chain ID: A, B, C, E, F, H, I, J, K, L
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