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- PDB-5xog: RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1 -

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Entry
Database: PDB / ID: 5xog
TitleRNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 5
  • DNA (30-MER)
  • DNA (39-MER)
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')
  • Spt4/5 complex component
  • Transcription elongation factor 1 homolog
KeywordsTRANSCRIPTION / transcription / complex
Function / homologyDNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / RPB6/omega subunit-like superfamily / RPB5-like RNA polymerase subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / Spt5 transcription elongation factor, N-terminal / RNA polymerases, subunit N, zinc binding site ...DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / RPB6/omega subunit-like superfamily / RPB5-like RNA polymerase subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / Spt5 transcription elongation factor, N-terminal / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Transcription elongation factor Spt5 / DNA-directed RNA polymerase, subunit 2 / Ribosomal protein L2, domain 2 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 6 / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / HRDC-like superfamily / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Translation protein SH3-like domain superfamily / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / Transcription elongation factor 1 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb4 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / Early transcription elongation factor of RNA pol II, NGN section / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb6 / NusG, N-terminal domain superfamily / Transcription elongation factor 1 superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb5, C-terminal domain / KOW motif / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / Transcription elongation factor Elf1 like / Spt5 transcription elongation factor, acidic N-terminal / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / S1 domain profile. / Zinc finger TFIIS-type profile. / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 3 / Zinc finger, TFIIS-type / RNA polymerase subunit RPB4/RPC9 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6
Function and homology information
Specimen sourceKomagataella pastoris (fungus)
Komagataella phaffii (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3 Å resolution
AuthorsEhara, H. / Shirouzu, M. / Sekine, S.
CitationJournal: Science / Year: 2017
Title: Structure of the complete elongation complex of RNA polymerase II with basal factors.
Authors: Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine
Abstract: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we ...In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 28, 2017 / Release: Aug 16, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 16, 2017Structure modelrepositoryInitial release
1.1Aug 23, 2017Structure modelDatabase referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation_author.name
1.2Sep 13, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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 ABC10-alpha
P: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')
T: DNA (39-MER)
N: DNA (30-MER)
M: Transcription elongation factor 1 homolog
W: Spt4/5 complex component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,71728
Polyers555,59817
Non-polymers1,11811
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)78600
ΔGint (kcal/M)-399
Surface area (Å2)168130
Unit cell
γ
α
β
Length a, b, c (Å)155.250, 159.910, 268.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase / RNA polymerase II subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase subunit beta / Polymerase / RNA polymerase II subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase / RNA polymerase II subunit Rpb9


Mass: 13612.320 Da / Num. of mol.: 1
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, 4 molecules CDGK

#3: Protein/peptide RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein/peptide RNA polymerase II subunit B32 / / RNA polymerase II subunit Rpb4


Mass: 20622.980 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein/peptide RNA polymerase II subunit / / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein/peptide RNA polymerase II subunit B12.5 / / RNA polymerase II subunit Rpb11


Mass: 13832.896 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 5 types, 5 molecules EFHJL

#5: Protein/peptide RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb5


Mass: 24962.680 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein/peptide RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb6


Mass: 17803.588 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#8: Protein/peptide RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb8


Mass: 16249.220 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#10: Protein/peptide RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb10


Mass: 8554.064 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009
#12: Protein/peptide RNA polymerase subunit ABC10-alpha / / RNA polymerase II subunit Rpb12


Mass: 7862.048 Da / Num. of mol.: 1
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: F2QMI1

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RNA chain , 1 types, 1 molecules P

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


Mass: 5384.158 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules TN

#14: DNA chain DNA (39-MER)


Mass: 11909.657 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (30-MER)


Mass: 9315.981 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Protein/peptide , 2 types, 2 molecules MW

#16: Protein/peptide Transcription elongation factor 1 homolog / Transcription elongation factor Elf1


Mass: 9414.886 Da / Num. of mol.: 1 / Fragment: UNP residues 1-82 / Mutation: N53G, L54Q, S55R / Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: ELF1, ATY40_BA7504229 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2JER8
#17: Protein/peptide Spt4/5 complex component / Transcription elongation factor Spt5


Mass: 9201.514 Da / Num. of mol.: 1 / Fragment: UNP residues 736-815 / Source: (gene. exp.) Komagataella phaffii (fungus)
Strain: ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1
Gene: SPT5, PP7435_Chr3-0027 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QUC3

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Non-polymers , 3 types, 11 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Formula: Zn / Zinc
#19: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#20: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Formula: C11H18N5O12P3

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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: 3 / Density percent sol: 59.06 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL41XU / Synchrotron site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Collection date: Oct 8, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 84.07 Å2 / D resolution high: 3 Å / D resolution low: 49.552 Å / Number obs: 134084 / Observed criterion sigma I: -3 / CC half: 0.998 / Rmerge I obs: 0.11 / Rrim I all: 0.119 / Chi squared: 1.026 / NetI over sigmaI: 15.48 / Redundancy: 6.733 % / Percent possible obs: 99.9
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRrim I allRedundancyPercent possible all
1.2893.0003.0801.52098410.5151.4056.40099.900
1.0143.0803.1602.05095620.6741.0996.78499.900
0.7533.1603.2502.90093100.8100.8127.120100.000
0.5793.2503.3503.78090570.8790.6257.086100.000
0.4243.3503.4605.14087880.9290.4587.001100.000
0.3093.4603.5906.90084970.9620.3356.868100.000
0.2413.5903.7208.68082380.9740.2616.67499.900
0.1763.7203.87010.99078760.9830.1926.29599.900
0.1413.8704.05014.52076110.9910.1537.045100.000
0.1064.0504.24018.63072700.9950.1156.943100.000
0.0824.2404.47022.69069340.9960.0896.838100.000
0.0714.4704.74025.42065660.9970.0776.68199.900
0.0644.7405.07025.75061750.9970.0706.07199.900
0.0665.0705.48027.25057610.9970.0716.97699.900
0.0645.4806.00027.71053200.9970.0696.90899.900
0.0596.0006.71029.16048450.9980.0646.725100.000
0.0446.7107.75034.04042810.9980.0486.02099.700
0.0327.7509.49046.05036510.9990.0356.63499.800
0.0279.49013.42050.76028770.9990.0306.24299.800
0.02613.42049.55250.89016240.9990.0285.98297.200

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Details: the entry contains Friedel pairs in F_Plus/Minus columns
Overall SU ML: 0.4 / Cross valid method: FREE R-VALUE / Sigma F: 0.98 / Overall phase error: 21.98
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 348.62 Å2 / B iso mean: 92.111 Å2 / B iso min: 23.73 Å2
Least-squares processR factor R free: 0.2253 / R factor R work: 0.1953 / R factor obs: 0.1956 / Highest resolution: 3 Å / Lowest resolution: 49.552 Å / Number reflection R free: 2987 / Number reflection obs: 134077 / Percent reflection R free: 1.15 / Percent reflection obs: 99.89
Refine hist #finalHighest resolution: 3 Å / Lowest resolution: 49.552 Å / B iso mean ligand: 85.56 / Number residues total: 4131
Number of atoms included #finalProtein: 32352 / Nucleic acid: 1319 / Ligand: 41 / Solvent: 0 / Total: 33712
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534460
X-RAY DIFFRACTIONf_angle_d0.88946814
X-RAY DIFFRACTIONf_chiral_restr0.0555229
X-RAY DIFFRACTIONf_plane_restr0.0065846
X-RAY DIFFRACTIONf_dihedral_angle_d13.66020878
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 21 / Percent reflection obs: 1

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection all
3.00000.36880.33443.04911251221312338
3.04910.33180.32073.10171461212812274
3.10170.31970.29813.15811471222012367
3.15810.28320.27063.21881351210112236
3.21880.27820.26283.28451411222812369
3.28450.29480.26463.35591411218912330
3.35590.29870.26353.43401451213712282
3.43400.26810.24463.51981511218212333
3.51980.20490.23003.61501401220212342
3.61500.28820.21773.72131421219512337
3.72130.25800.21133.84141411220912350
3.84140.23880.20193.97861531216712320
3.97860.22390.18404.13781411213612277
4.13780.18040.16394.32601421220112343
4.32600.22160.15734.55401441215212296
4.55400.15300.15344.83911431219712340
4.83910.21560.16655.21231361214012276
5.21230.20010.17835.73621501220912359
5.73620.23370.18876.56461321215912291
6.56460.21500.17138.26441481216212310
8.26440.18360.166749.55871441214612290

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