[English] 日本語
Yorodumi
- PDB-8u9r: STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u9r
TitleSTRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER
Components
  • (DNA-directed RNA polymerase II subunit ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • (DNA-directed RNA polymerases II subunit ...) x 2
  • DNA (5'-D(P*CP*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')
  • DNA-directed RNA polymerase subunit beta
  • RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*G)-3')
KeywordsTRANSCRIPTION / Multiprotein complex / Free-electron laser / Molecular machine
Function / homology
Function and homology information


: / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes ...: / : / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription-coupled nucleotide-excision repair / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / translesion synthesis / RNA polymerase II, core complex / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / Rpb4/RPC9 superfamily / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase, subunit RPB6 / HRDC-like superfamily / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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, 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 Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RPB4 isoform 1 / RPC10 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta ...ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RPB4 isoform 1 / RPC10 isoform 1 / RPB3 isoform 1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta / RPB11 isoform 1 / RPB10 isoform 1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsArjunan, P. / Calero, G. / Kaplan, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112686, R01GM097260, R35GM144116 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Authors: Lin, G. / Barnes, C.O. / Weiss, S. / Dutagaci, B. / Qiu, C. / Feig, M. / Song, J. / Lyubimov, A. / Cohen, A.E. / Kaplan, C.D. / Calero, G.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: 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 subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases II subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases II subunit RPABC4
R: RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*G)-3')
T: DNA (5'-D(P*CP*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,81027
Polymers521,61514
Non-polymers1,19513
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.195, 387.440, 276.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z3
#4: Protein DNA-directed RNA polymerase II subunit RPB4


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTI6
#7: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q270
#9: Protein DNA-directed RNA polymerase II subunit RPB9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9EWC2
#11: Protein DNA-directed RNA polymerase II subunit RPB11


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7A1

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

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q456
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8C2

-
DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules JL

#10: Protein DNA-directed RNA polymerases II subunit RPABC5


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Q6
#12: Protein DNA-directed RNA polymerases II subunit RPABC4


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY05

-
Protein / RNA chain / DNA chain , 3 types, 3 molecules BRT

#13: RNA chain RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*G)-3')


Mass: 3280.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain DNA (5'-D(P*CP*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3')


Mass: 4176.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase

-
Non-polymers , 5 types, 30 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.59 Å3/Da / Density % sol: 77.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 10-15 % tacsimate 100mM Hepes pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30505 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30505 Å / Relative weight: 1
ReflectionResolution: 3.3→24.68 Å / Num. obs: 166660 / % possible obs: 95.85 % / Redundancy: 10.25 % / CC1/2: 0.9144 / Rmerge(I) obs: 0.6 / Net I/σ(I): 3.93
Reflection shellResolution: 3.3→3.36 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 5833 / CC1/2: 0.59
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
cctbx.xfeldata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→19.97 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 8170 4.95 %
Rwork0.2551 --
obs0.2554 165059 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30116 496 48 17 30677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231300
X-RAY DIFFRACTIONf_angle_d0.59342358
X-RAY DIFFRACTIONf_dihedral_angle_d19.36911906
X-RAY DIFFRACTIONf_chiral_restr0.044779
X-RAY DIFFRACTIONf_plane_restr0.0055382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.380.39122560.38794540X-RAY DIFFRACTION86
3.38-3.420.3662590.37254817X-RAY DIFFRACTION91
3.42-3.460.35752740.36244773X-RAY DIFFRACTION92
3.46-3.50.38112570.36225085X-RAY DIFFRACTION96
3.5-3.550.37312610.35665194X-RAY DIFFRACTION99
3.55-3.60.3742510.34935216X-RAY DIFFRACTION99
3.6-3.650.34412630.34735263X-RAY DIFFRACTION99
3.65-3.70.3472380.33675279X-RAY DIFFRACTION100
3.7-3.760.3752880.33185226X-RAY DIFFRACTION100
3.76-3.820.3352680.32415268X-RAY DIFFRACTION100
3.82-3.890.3222770.31855227X-RAY DIFFRACTION100
3.89-3.960.30482790.30565300X-RAY DIFFRACTION100
3.96-4.030.30582460.29945301X-RAY DIFFRACTION100
4.03-4.110.30212280.28355294X-RAY DIFFRACTION100
4.11-4.20.27512860.27045245X-RAY DIFFRACTION100
4.2-4.30.27413170.26075237X-RAY DIFFRACTION100
4.3-4.410.2882910.24935270X-RAY DIFFRACTION100
4.41-4.520.24072860.24135272X-RAY DIFFRACTION100
4.52-4.660.26282870.2325264X-RAY DIFFRACTION100
4.66-4.80.25623040.23395291X-RAY DIFFRACTION100
4.8-4.970.24653030.23485244X-RAY DIFFRACTION100
4.97-5.170.24623010.23185294X-RAY DIFFRACTION100
5.17-5.40.23322570.23675304X-RAY DIFFRACTION100
5.4-5.680.2362570.23355338X-RAY DIFFRACTION100
5.68-6.020.25152580.23525364X-RAY DIFFRACTION100
6.02-6.470.25142870.23715290X-RAY DIFFRACTION100
6.47-7.10.20952320.21675409X-RAY DIFFRACTION100
7.1-8.070.19333030.19185358X-RAY DIFFRACTION100
8.07-9.950.16822480.17545427X-RAY DIFFRACTION100
9.95-19.970.18713080.20275499X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 106.2787 Å / Origin y: 50.6464 Å / Origin z: -1.3135 Å
111213212223313233
T0.4404 Å20.0153 Å20.0414 Å2-0.4322 Å20.0276 Å2--0.4509 Å2
L0.346 °20.0033 °2-0.0209 °2-0.3503 °20.012 °2--0.2289 °2
S0.0143 Å °-0.0126 Å °0.1657 Å °0.1339 Å °-0.0429 Å °0.0833 Å °-0.0572 Å °-0.0179 Å °0.0243 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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