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- PDB-5u9g: 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I) -

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Entry
Database: PDB / ID: 5u9g
Title3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure I)
DescriptorRibosome
KeywordsRIBOSOME / ARFA RF2 ribosome rescue complex
Specimen sourceEscherichia coli k-12 / bacteria / image: Escherichia coli
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsDemo, G. / Svidritskiy, E. / Madireddy, R. / Diaz-Avalos, R. / Grant, T. / Grigorieff, N. / Sousa, D. / Korostelev, A.A.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Mechanism of ribosome rescue by ArfA and RF2.
Gabriel Demo / Egor Svidritskiy / Rohini Madireddy / Ruben Diaz-Avalos / Timothy Grant / Nikolaus Grigorieff / Duncan Sousa / Andrei A Korostelev

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 16, 2016 / Release: Mar 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelDatabase references
1.2Sep 27, 2017Structure modelAuthor supporting evidence / Data collection / Experimental preparationem_sample_support / em_software / pdbx_audit_support_em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: 16S ribosomal RNA
01: 23S ribosomal RNA
02: 5S ribosomal RNA
Y: Alternative ribosome-rescue factor A
X: fMet-tRNA (P- and E-site)
03: 50S ribosomal protein L1
04: 50S ribosomal protein L2
05: 50S ribosomal protein L3
06: 50S ribosomal protein L4
07: 50S ribosomal protein L5
08: 50S ribosomal protein L6
09: 50S ribosomal protein L9
10: 50S ribosomal protein L10
11: 50S ribosomal protein L11
12: 50S ribosomal protein L13
13: 50S ribosomal protein L14
14: 50S ribosomal protein L15
15: 50S ribosomal protein L16
16: 50S ribosomal protein L17
17: 50S ribosomal protein L18
18: 50S ribosomal protein L19
19: 50S ribosomal protein L20
20: 50S ribosomal protein L21
21: 50S ribosomal protein L22
22: 50S ribosomal protein L23
23: 50S ribosomal protein L24
24: 50S ribosomal protein L25
25: 50S ribosomal protein L27
26: 50S ribosomal protein L28
27: 50S ribosomal protein L29
28: 50S ribosomal protein L30
29: 50S ribosomal protein L31
30: 50S ribosomal protein L32
31: 50S ribosomal protein L33
32: 50S ribosomal protein L34
33: 50S ribosomal protein L35
34: 50S ribosomal protein L36
V: truncated mRNA
W: fMet-tRNA (P- and E-site)
Z: Peptide chain release factor RF2
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,305,207409
Polyers2,296,68460
Non-polymers8,524349
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 6 molecules A0102XWV

#1: RNA chain16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 944404559
#2: RNA chain23S ribosomal RNA


Mass: 941322.188 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 42756
#3: RNA chain5S ribosomal RNA


Mass: 38483.926 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1072784372
#5: RNA chainfMet-tRNA (P- and E-site)


Mass: 24802.785 Da / Num. of mol.: 2 / Source: (natural) Escherichia coli / References: GenBank: 1114191980
#38: RNA chaintruncated mRNA


Mass: 4597.844 Da / Num. of mol.: 1 / Source: (synth.) Escherichia coli

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Polypeptide(L) , 2 types, 2 molecules YZ

#4: Polypeptide(L)Alternative ribosome-rescue factor A


Mass: 8190.438 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli K-12 / References: UniProt: P36675

Molecular function

Biological process

#39: Polypeptide(L)Peptide chain release factor RF2 / RF-2


Mass: 41300.660 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P07012

Cellular component

Molecular function

  • translation release factor activity, codon specific (GO: 0016149)

Biological process

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50S ribosomal protein ... , 32 types, 32 molecules 03040506070809101112...

#6: Polypeptide(L)50S ribosomal protein L1


Mass: 24765.660 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MIX0

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9F8

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9F5

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9F6

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G7

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9H0

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZI15

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)50S ribosomal protein L10


Mass: 17736.596 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZA73

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)50S ribosomal protein L11


Mass: 14894.362 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZA71

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZET0

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G5

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D8BU19

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G2

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)50S ribosomal protein L17


Mass: 14423.683 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7N179

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9H1

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZKU3

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MAS6

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZEN7

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G0

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7X2Z9

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G6

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7XH79

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZEN6

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: S0YB49

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G3

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9H3

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZFP6

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZGG2

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9P0

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MGC4

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein L35


Mass: 7313.032 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z814

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: A0A0E2L017

Cellular component

Molecular function

Biological process

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJK...

#40: Polypeptide(L)30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZK99

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS9

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9H7

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9H2

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)30S ribosomal protein S6


Mass: 15211.058 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZI17

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)30S ribosomal protein S7


Mass: 17637.445 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZAN1

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G9

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZES9

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#48: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9F4

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCR3

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#50: Polypeptide(L)30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZAN0

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: H4UQ02

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G8

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZEL4

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MIU7

Cellular component

Molecular function

Biological process

#55: Polypeptide(L)30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9G4

Cellular component

Molecular function

Biological process

#56: Polypeptide(L)30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: A0A0E2KXL3

Cellular component

Molecular function

Biological process

#57: Polypeptide(L)30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7Z9F9

Cellular component

Molecular function

Biological process

#58: Polypeptide(L)30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: D7ZAS2

Cellular component

Molecular function

Biological process

#59: Polypeptide(L)30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: A0A0E2L2J1

Cellular component

Molecular function

Biological process

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Non-polymers , 2 types, 349 molecules

#60: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 348 / Formula: Mg
#61: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: ArfA-RF2 ribosome rescue complex (Structure I) / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59
Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Escherichia coli / Strain: MRE600
Source (recombinant)Organism: Escherichia coli / Strain: K-12
Buffer solutionpH: 7
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mMTris bufferTris-HCl1
2100mMamonium chlorideNH4Cl1
320mMmagnesium chlorideMgCl21
40.5mMEthylenediaminetetraacetic acidEDTA1
56mMbetamercaptoethanolBME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Using a Solarus 950 plasma cleaning system. The forward RF target was set to 7w.
Grid material: COPPER / Grid mesh size: 200 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number of grids imaged: 1 / Number of real images: 3760
Image scansMovie frames/image: 54 / Used frames/image: 2-27

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4ctffind4CTF CORRECTION1
7ChimeraMODEL FITTING1
9RSRefMODEL REFINEMENT1
10PHENIXMODEL REFINEMENT1
11FREALIGN9.11INITIAL EULER ASSIGNMENT1
12FREALIGN9.11FINAL EULER ASSIGNMENT1
13FREALIGN9.11CLASSIFICATION1
14FREALIGN9.11RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 539311
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 139861 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 100 / Ref protocol: OTHER / Ref space: REAL / Target criteria: Correlation coefficient

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