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- PDB-5x51: RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) -

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Basic information

Entry
Database: PDB / ID: 5x51
TitleRNA Polymerase II from Komagataella Pastoris (Type-3 crystal)
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
KeywordsTRANSFERASE / transcription / RNA polymerase
Function / homology
Function and homology information


telomeric repeat-containing RNA transcription by RNA polymerase II / regulation of septum digestion after cytokinesis / heterochromatin assembly by small RNA / RNA polymerase III activity / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II activity / RNA polymerase I activity ...telomeric repeat-containing RNA transcription by RNA polymerase II / regulation of septum digestion after cytokinesis / heterochromatin assembly by small RNA / RNA polymerase III activity / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II activity / RNA polymerase I activity / positive regulation of translational initiation / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / pericentric heterochromatin / 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 / single-stranded DNA binding / single-stranded RNA binding / nucleic acid binding / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / protein dimerization activity / chromatin / nucleotide binding / nucleolus / RNA binding / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Rpb4/RPC9 superfamily / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. ...Rpb4/RPC9 superfamily / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / 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 / 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 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / 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 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / : / RNA polymerase Rpb5, C-terminal domain / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / C2C2 Zinc finger / Zinc finger, TFIIS-type / S1 RNA binding domain / S1 domain / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / : / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, alpha subunit / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerases D / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / RNA polymerase II subunit B12.5 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / DNA-directed RNA polymerase subunit beta ...DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit / RNA polymerase II subunit B12.5 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / DNA-directed RNA polymerase subunit beta / RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.996 Å
AuthorsEhara, H. / Umehara, T. / Sekine, S. / Yokoyama, S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of RNA polymerase II from Komagataella pastoris
Authors: Ehara, H. / Umehara, T. / Sekine, S.I. / Yokoyama, S.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
M: DNA-directed RNA polymerase subunit
N: DNA-directed RNA polymerase subunit beta
O: RNA polymerase II third largest subunit B44, part of central core
P: RNA polymerase II subunit B32
Q: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
R: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
S: RNA polymerase II subunit
T: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
U: DNA-directed RNA polymerase subunit
V: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
W: RNA polymerase II subunit B12.5
X: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,022,01140
Polymers1,020,96524
Non-polymers1,04716
Water0
1
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,00620
Polymers510,48212
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58510 Å2
ΔGint-401 kcal/mol
Surface area156860 Å2
MethodPISA
2
M: DNA-directed RNA polymerase subunit
N: DNA-directed RNA polymerase subunit beta
O: RNA polymerase II third largest subunit B44, part of central core
P: RNA polymerase II subunit B32
Q: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
R: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
S: RNA polymerase II subunit
T: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
U: DNA-directed RNA polymerase subunit
V: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
W: RNA polymerase II subunit B12.5
X: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,00620
Polymers510,48212
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58150 Å2
ΔGint-397 kcal/mol
Surface area157610 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)148.770, 158.050, 254.960
Angle α, β, γ (deg.)90.000, 92.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA-directed RNA polymerase ... , 3 types, 6 molecules AMBNIU

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


Mass: 194107.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 139746.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 13612.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
References: UniProt: F2QPE6

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RNA polymerase II ... , 4 types, 8 molecules CODPGSKW

#3: Protein RNA polymerase II third largest subunit B44, part of central core


Mass: 34216.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32 /


Mass: 20622.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein RNA polymerase II subunit /


Mass: 18802.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein RNA polymerase II subunit B12.5 /


Mass: 13832.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 4 types, 8 molecules EQFRHTJV

#5: Protein RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III /


Mass: 24962.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III /


Mass: 17803.588 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#8: Protein RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III /


Mass: 16249.220 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#10: Protein RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III /


Mass: 8554.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009

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Protein / Non-polymers , 2 types, 18 molecules LX

#12: Protein RNA polymerase subunit, found in RNA polymerase complexes I, II, and III /


Mass: 7972.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7→33.267 Å / Num. obs: 18745 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.782 % / Biso Wilson estimate: 220.99 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.265 / Rrim(I) all: 0.309 / Χ2: 0.893 / Net I/σ(I): 6.3 / Num. measured all: 70891
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
7-7.413.7771.1461.5411047298029250.5391.33598.2
7.41-7.913.8440.712.410739279727940.7660.82699.9
7.91-8.533.840.4813.69958259725930.860.55999.8
8.53-9.313.8210.3025.529307243824360.9290.35299.9
9.31-10.373.8080.2137.368358220021950.9610.24899.8
10.37-11.883.7980.1549.637349194019350.9780.1899.7
11.88-14.353.740.12611.396332170016930.9820.14899.6
14.35-19.493.6910.11212.354927133813350.9840.13199.8
19.49-33.2673.4260.06916.2228749228390.9940.08191

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.996→33.267 Å / SU ML: 1.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3351 1869 10.04 %
Rwork0.3375 16750 -
obs0.3372 18619 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 351.45 Å2 / Biso mean: 261.8857 Å2 / Biso min: 189.03 Å2
Refinement stepCycle: final / Resolution: 6.996→33.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56599 0 16 0 56615
Biso mean--252.36 --
Num. residues----7636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01457470
X-RAY DIFFRACTIONf_angle_d1.81977514
X-RAY DIFFRACTIONf_chiral_restr0.528929
X-RAY DIFFRACTIONf_plane_restr0.0089944
X-RAY DIFFRACTIONf_dihedral_angle_d19.21820952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.9965-7.18380.39641430.4231230137396
7.1838-7.39290.39781370.403812911428100
7.3929-7.62880.39481410.384912621403100
7.6288-7.89790.39211360.367913141450100
7.8979-8.20960.39931400.354812751415100
8.2096-8.57720.29961570.333912601417100
8.5772-9.02080.31761440.33313011445100
9.0208-9.57330.28471350.315312871422100
9.5733-10.29220.31241510.313041455100
10.2922-11.2910.27761450.283212951440100
11.291-12.84180.28951450.28291282142799
12.8418-15.88080.311460.316913231469100
15.8808-33.26750.41561490.408513261475100

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