[English] 日本語
Yorodumi
- PDB-9mu8: Structure of a native Drosophila melanogaster Pol II Elongation C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mu8
TitleStructure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk
Components
  • (DNA-directed RNA polymerase II subunit ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • Non-template DNA
  • RNA
  • RPB5 homolog
  • Template DNA
KeywordsTRANSCRIPTION / polymerase / Pol II / mRNA
Function / homology
Function and homology information


Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation ...Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Processing of Capped Intron-Containing Pre-mRNA / Dual incision in TC-NER / polytene chromosome puff / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / polytene chromosome / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / mitotic cell cycle / cellular response to heat / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / mitochondrion / DNA binding / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. ...RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsVenette-Smith, N.L. / Vishwakarma, R.K. / Dollinger, R. / Schultz, J. / Venkatakrishnan, V. / Babitzke, P. / Anand, G. / Gilmour, D.S. / Armache, J.-P. / Murakami, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047477 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098399 United States
CitationJournal: To Be Published
Title: Structural Characterization of Native RNA Polymerase II Transcription Complexes in Drosophila melanogaster
Authors: Venette-Smith, N.L. / Vishwakarma, R.K. / Dollinger, R. / Schultz, J. / Venkatakrishnan, V. / Babitzke, P. / Anand, G. / Gilmour, D.S. / Armache, J.-P. / Murakami, K.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerase II subunit RPB12
R: RNA
T: Template DNA
N: Non-template DNA
E: RPB5 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,40621
Polymers451,88313
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ABCIKL

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit A


Mass: 166420.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P04052, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / DNA-directed RNA polymerase II 140 kDa ...RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / DNA-directed RNA polymerase II 140 kDa polypeptide / RNA polymerase II subunit B


Mass: 132640.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P08266, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II p33 subunit / RNA polymerase II subunit C


Mass: 30676.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O97183, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II 15.1 kDa polypeptide / RNA polymerase ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II 15.1 kDa polypeptide / RNA polymerase II subunit I


Mass: 13786.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P36958
#8: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.3 kDa polypeptide / DNA-directed ...RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.3 kDa polypeptide / DNA-directed RNA polymerase II subunit J


Mass: 13288.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJE4
#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB12 / HDC06513 / IP17848p / Rpb12


Mass: 5647.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q6IGE3

-
DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / RNA polymerase II / I and III subunit F / RPB6 homolog


Mass: 9736.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24320
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16946.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VNZ3
#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / RNA polymerase II / I and III subunit L / RPB10 homolog


Mass: 7671.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VC49

-
DNA chain , 2 types, 2 molecules TN

#11: DNA chain Template DNA


Mass: 15134.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
#12: DNA chain Non-template DNA


Mass: 12170.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)

-
RNA chain / Protein / Non-polymers , 3 types, 10 molecules RE

#10: RNA chain RNA


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
#13: Protein RPB5 homolog


Mass: 24518.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JZF5
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Native purified Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk
Type: COMPLEX
Details: This entry represents a native Pol II elongation complex from Drosophila melanogaster without the Rpb4/Rpb7 stalk, obtained through stringent 3D classification and refinement.
Entity ID: #4-#5, #8, #10-#13 / Source: NATURAL
Molecular weightValue: 0.930 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.5
Details: 10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
210 mMHEPESHEPES-HCl1
35 percentGlycerolGlycerol1
41 mMEDTAEDTA1
5350 ug/mLFLAG peptideFLAG1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

-
Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.65 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 31103
Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was ...Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360
Image scansSampling size: 0.944 µm / Width: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2EPU3.4image acquisition
4cryoSPARC4.3.1CTF correction
7UCSF ChimeraX1.8model fitting
9Coot0.9.8.7model refinement
10PHENIX1.21.5207model refinement
11cryoSPARC4.3.1initial Euler assignment
12cryoSPARC4.3.1final Euler assignment
14cryoSPARC4.3.13D reconstruction
CTF correctionDetails: 'Patch CTF Estimation' in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2349308
Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (2,349,308) is the starting number of particles after initial cleanup and 3D ...Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (2,349,308) is the starting number of particles after initial cleanup and 3D classification of the data.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96409 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: AB INITIO MODEL
Details: The model was based on PDB: 6GML. First, 6GML was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila ...Details: The model was based on PDB: 6GML. First, 6GML was rigid-body fit in the cryo-EM Coulomb potential density map using UCSF ChimeraX. Next, AlphaFold2 models for individual Drosophila melanogaster Pol II subunits were aligned to their 6GML counterparts, and further optimized in the density using rigid-body fit. For the final model optimization, phenix.real_space_refine was used
Atomic model building
ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameType
11P04052A1AlphaFoldin silico model
21P08266B2AlphaFoldin silico model
31O97183C3AlphaFoldin silico model
41Q9VEA5D4AlphaFoldin silico model
51Q7JZF5E5AlphaFoldin silico model
61Q24320F6AlphaFoldin silico model
71Q9VFB5G7AlphaFoldin silico model
81Q9VNZ3H8AlphaFoldin silico model
91P36958I9AlphaFoldin silico model
101Q9VC49J10AlphaFoldin silico model
111Q9VJE4K11AlphaFoldin silico model
121Q6IGE3L12AlphaFoldin silico model
RefinementHighest resolution: 3.37 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00434750
ELECTRON MICROSCOPYf_angle_d0.71947334
ELECTRON MICROSCOPYf_dihedral_angle_d14.6855505
ELECTRON MICROSCOPYf_chiral_restr0.0495242
ELECTRON MICROSCOPYf_plane_restr0.0065805

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more