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- PDB-7ok0: Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase... -

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Entry
Database: PDB / ID: 7ok0
TitleCryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase at 2.88 A
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 10
  • (DNA-directed RNA polymerase, subunit ...Polymerase) x 2
  • Conserved proteinConservation
KeywordsTRANSCRIPTION / RNA polymerase / Archaea / Crenarchaea
Function / homology
Function and homology information


RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / transcription, DNA-templated / protein dimerization activity / nucleotide binding / DNA binding ...RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / transcription, DNA-templated / protein dimerization activity / nucleotide binding / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit P (Rpo12) / DNA-directed RNA polymerase subunit A'' / DNA-directed RNA polymerase subunit A' (Rpo1N) / DNA-directed RNA polymerase subunit B (Rpo2) / DNA-directed RNA polymerase subunit F (Rpo4) / DNA-directed RNA polymerase subunit D (Rpo3) ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit P (Rpo12) / DNA-directed RNA polymerase subunit A'' / DNA-directed RNA polymerase subunit A' (Rpo1N) / DNA-directed RNA polymerase subunit B (Rpo2) / DNA-directed RNA polymerase subunit F (Rpo4) / DNA-directed RNA polymerase subunit D (Rpo3) / DNA-directed RNA polymerase subunit L (Rpo11) / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / S1 RNA binding domain / RNA-binding domain, S1 / Ribosomal protein S1-like RNA-binding domain / S1 domain / RNA polymerase subunit, RPB6/omega / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase, alpha subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, subunit 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 6 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit D / DNA-directed RNA polymerase, subunit G / Conserved protein / DNA-directed RNA polymerase subunit P / DNA-directed RNA polymerase subunit L / DNA-directed RNA polymerase subunit N / FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit E / DNA-directed RNA polymerase subunit K / DNA-directed RNA polymerase subunit H ...DNA-directed RNA polymerase subunit D / DNA-directed RNA polymerase, subunit G / Conserved protein / DNA-directed RNA polymerase subunit P / DNA-directed RNA polymerase subunit L / DNA-directed RNA polymerase subunit N / FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit E / DNA-directed RNA polymerase subunit K / DNA-directed RNA polymerase subunit H / DNA-directed RNA polymerase subunit A'' / DNA-directed RNA polymerase subunit B / DNA-directed RNA polymerase subunit A' / DNA-directed RNA polymerase, subunit F
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPilotto, S. / Fouqueau, T. / Lukoyanova, N. / Sheppard, C. / Lucas-Staat, S. / Diaz-Santin, L.M. / Matelska, D. / Prangishvili, D. / Cheung, A.C.M. / Werner, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of RNA polymerase inhibition by viral and host factors.
Authors: Simona Pilotto / Thomas Fouqueau / Natalya Lukoyanova / Carol Sheppard / Soizick Lucas-Staat / Luis Miguel Díaz-Santín / Dorota Matelska / David Prangishvili / Alan C M Cheung / Finn Werner /
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution ...RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit A'
B: DNA-directed RNA polymerase subunit B
C: DNA-directed RNA polymerase subunit A''
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase subunit E
F: DNA-directed RNA polymerase, subunit F
G: DNA-directed RNA polymerase, subunit G
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
Q: Conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,97421
Polymers405,26113
Non-polymers7138
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, monomeric in solution (by size exclusion chromatography) and on micrographs (by both negative staining and cryo-EM)
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area62240 Å2
ΔGint-425 kcal/mol
Surface area123220 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase subunit ... , 10 types, 10 molecules ABCDEHKLNP

#1: Protein DNA-directed RNA polymerase subunit A' / Polymerase / DNA-directed RNA polymerase subunit RPO1


Mass: 99929.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO1
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P11512, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit B / Polymerase / DNA-directed RNA polymerase subunit RPO2


Mass: 126647.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO2
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P11513, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit A'' / Polymerase / DNA-directed RNA polymerase subunit RPO1


Mass: 44507.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO1
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P11514, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D / Polymerase / DNA-directed RNA polymerase subunit RPO3


Mass: 29858.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO3
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P39471, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit E / Polymerase / DNA-directed RNA polymerase subunit RPO7


Mass: 20496.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO7
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P39466, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit H / Polymerase / DNA-directed RNA polymerase subunit RPO5


Mass: 9477.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO5
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P11521, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit K / Polymerase / DNA-directed RNA polymerase subunit RPO6


Mass: 10251.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO6
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P39463, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit L / Polymerase / DNA-directed RNA polymerase subunit RPO11


Mass: 10061.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO11
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P46217, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase subunit N / Polymerase / DNA-directed RNA polymerase subunit RPO10


Mass: 7673.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO10
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: P39472, DNA-directed RNA polymerase
#12: Protein/peptide DNA-directed RNA polymerase subunit P / Polymerase / DNA-directed RNA polymerase subunit RPO12


Mass: 5662.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO12
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: Q4JAE8, DNA-directed RNA polymerase

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DNA-directed RNA polymerase, subunit ... , 2 types, 2 molecules FG

#6: Protein DNA-directed RNA polymerase, subunit F / Polymerase / DNA-directed RNA polymerase subunit RPO4


Mass: 13070.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit RPO4
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: Q4JB12, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase, subunit G / Polymerase / DNA-directed RNA polymerase subunit RPO8


Mass: 15292.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-directed RNA polymerase subunit RPO8
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: rpoG, Saci_0661
Production host: Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain (production host): ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: Q4JAY4, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules Q

#13: Protein Conserved protein / Conservation / DNA-directed RNA polymerase subunit 13


Mass: 12331.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-directed RNA polymerase subunit 13
Source: (natural) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
References: UniProt: Q4JAJ6

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Non-polymers , 3 types, 8 molecules

#14: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#15: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: apo-RNA polymerase / Type: COMPLEX / Details: 13 subunits / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.404 MDa / Experimental value: YES
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaClSodium chloride1
35 mMmagnesium chlorideMgCl21
4100 microMzinc sulfateZnSO41
SpecimenConc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was crosslinked with bis(sulfosuccinimidyl)suberate (BS3)
Specimen supportDetails: The grid was coated with graphene oxide prior to use
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 44.46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1676
Details: Images were collected in movie-mode for a total of 40 frames in super-resolution mode and with a tilt of 30 degrees
Image scansWidth: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
4GctfCTF correction
7PHENIX1.15model fittingDock in map
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.19model refinementReal-space refinement
Image processingDetails: Movie stacks were aligned and summed using MotionCor2
CTF correctionDetails: CTF aplitude was further corrected on selected particles after 3D recostruction to correct the 30 degrees tilt used during data collection
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1286432
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 423157 / Symmetry type: POINT
Atomic model buildingB value: 57.7772 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: CC
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00326075
ELECTRON MICROSCOPYf_angle_d0.52235207
ELECTRON MICROSCOPYf_dihedral_angle_d3.9783565
ELECTRON MICROSCOPYf_chiral_restr0.0453997
ELECTRON MICROSCOPYf_plane_restr0.0044519

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