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- PDB-4ypi: Structure of Ebola virus nucleoprotein N-terminal fragment bound ... -

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Basic information

Entry
Database: PDB / ID: 4ypi
TitleStructure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35
Components
  • Nucleoprotein
  • Polymerase cofactor VP35
KeywordsRNA BINDING PROTEIN / protein complex. / Ebola virus / nucleoprotein / VP35 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / viral RNA genome packaging ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / viral RNA genome packaging / positive regulation of protein sumoylation / : / helical viral capsid / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / negative regulation of gene expression / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile.
Similarity search - Domain/homology
Nucleoprotein / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.71 Å
AuthorsLeung, D.W. / Borek, D.M. / Binning, J.M. / Otwinowski, Z. / Amarasinghe, G.K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 16items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081914 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109945 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109664 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109664 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM1003297 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI059536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077519 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107056 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM053163 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103399 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Defense Threat Reduction Agency (DTRA)DTRA 1_21_1_0002 United States
Defense Threat Reduction Agency (DTRA)HDTRA1_12_1_0051 United States
Defense Threat Reduction Agency (DTRA)HDTRA1_14_1_0013 United States
CitationJournal: Cell Rep / Year: 2015
Title: An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.
Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / ...Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / Robert A Davey / Zbyszek Otwinowski / Christopher F Basler / Gaya K Amarasinghe /
Abstract: During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In ...During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Aug 24, 2016Group: Other
Revision 1.4Aug 31, 2016Group: Other / Structure summary
Revision 1.5Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Nov 22, 2017Group: Refinement description / Category: software
Revision 1.7Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Nucleoprotein
G: Polymerase cofactor VP35
A: Nucleoprotein
E: Polymerase cofactor VP35
B: Nucleoprotein
F: Polymerase cofactor VP35
D: Nucleoprotein
H: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)168,1618
Polymers168,1618
Non-polymers00
Water0
1
C: Nucleoprotein
G: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)42,0402
Polymers42,0402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-18 kcal/mol
Surface area19380 Å2
MethodPISA
2
A: Nucleoprotein
E: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)42,0402
Polymers42,0402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area19190 Å2
MethodPISA
3
B: Nucleoprotein
F: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)42,0402
Polymers42,0402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-18 kcal/mol
Surface area19190 Å2
MethodPISA
4
D: Nucleoprotein
H: Polymerase cofactor VP35


Theoretical massNumber of molelcules
Total (without water)42,0402
Polymers42,0402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.752, 194.818, 347.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14G
24E
15G
25F
16G
26H
17A
27B
18A
28D
19E
29F
110E
210H
111B
211D
112F
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010C39 - 383
2010A39 - 383
1020C39 - 384
2020B39 - 384
1030C39 - 384
2030D39 - 384
1040G20 - 47
2040E20 - 47
1050G20 - 47
2050F20 - 47
1060G20 - 47
2060H20 - 47
1070A39 - 383
2070B39 - 383
1080A39 - 383
2080D39 - 383
1090E20 - 47
2090F20 - 47
10100E20 - 47
20100H20 - 47
10110B39 - 385
20110D39 - 385
10120F20 - 47
20120H20 - 47

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 38946.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: NP / Plasmid: pET15b
Details (production host): modified to add TEV protease site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18272
#2: Protein/peptide
Polymerase cofactor VP35


Mass: 3093.574 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Zaire ebolavirus (strain Mayinga-76) / References: UniProt: Q05127

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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

Crystal
IDDensity Matthews3/Da)Density % sol (%)
33.7767.4
1
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400
PH range: 7-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2014 / Details: Three data sets were used
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.7→25 Å / Num. all: 27102 / Num. obs: 23161 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 6.8
Reflection shellResolution: 3.7→3.72 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2 / % possible all: 10.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000phasing
SHELXDEphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.71→25 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.868 / SU B: 113.728 / SU ML: 0.723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.832
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1163 5 %RANDOM
Rwork0.2529 ---
obs0.2546 21925 84.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 567.16 Å2 / Biso mean: 153.465 Å2 / Biso min: 29.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-0 Å2
2--1.92 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 3.71→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11780 0 0 0 11780
Num. residues----1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911997
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211774
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.95816182
X-RAY DIFFRACTIONr_angle_other_deg0.934327019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.23751492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07324.681564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.443152168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1961564
X-RAY DIFFRACTIONr_chiral_restr0.0560.21816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022802
X-RAY DIFFRACTIONr_mcbond_it3.086.1135988
X-RAY DIFFRACTIONr_mcbond_other3.086.1125987
X-RAY DIFFRACTIONr_mcangle_it5.5949.1667470
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C205170.08
12A205170.08
21C207300.08
22B207300.08
31C207910.07
32D207910.07
41G12280.12
42E12280.12
51G12890.1
52F12890.1
61G12800.1
62H12800.1
71A206870.08
72B206870.08
81A208670.07
82D208670.07
91E11910.14
92F11910.14
101E12940.1
102H12940.1
111B211150.07
112D211150.07
121F12190.13
122H12190.13
LS refinement shellResolution: 3.705→3.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 12 -
Rwork0.346 389 -
all-401 -
obs--20.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
111.2781-1.2916-0.97831.8665-0.59225.423-0.08150.70830.1668-0.468-0.07940.5406-0.009-0.740.16090.37660.0261-0.03370.6816-0.04690.3415130.251342.9992-180.365
29.2269-2.3594-1.11077.41980.96047.5276-0.1622-0.3685-0.8503-0.06290.20320.49320.6984-0.4626-0.0410.2755-0.10340.1430.2555-0.04690.2162136.532734.2441-164.3896
36.1344-0.80421.04064.0833-0.818513.78780.07630.36350.30650.270.3288-0.4834-0.55220.1205-0.40510.125-0.02380.08590.088-0.08360.1877127.783145.9064-139.6028
43.2932.2361-4.617712.442-8.102114.4051-0.1587-0.3396-0.1751.43870.0414-0.2867-0.48210.3270.11740.30930.1558-0.03840.2502-0.11540.3069129.575336.5758-116.8979
59.5991-5.40126.375918.2524-6.484114.8497-0.2810.5914-1.1286-0.39420.4289-0.5229-0.3873-0.6515-0.14790.0383-0.00980.0680.2445-0.110.265120.752139.4235-139.1129
68.2772-1.7728-2.30625.37012.09214.9216-0.35151.2414-0.4737-1.537-0.03270.27110.5231-0.34480.38411.4350.3989-0.20271.1701-0.56240.9344138.9756-18.9315-148.0035
78.9306-2.73630.252412.3601-3.2498.41990.81550.1627-1.31080.2681-1.17120.00090.8674-0.12890.35570.74230.3032-0.20540.4897-0.18030.4443141.6554-14.1557-129.3553
85.30640.8282.207113.53914.49776.80910.24490.9589-0.28930.0593-0.24490.29050.0307-0.1564-0.00010.23860.11660.07360.2493-0.05280.0999129.129210.4118-121.4989
92.0984-0.5382-3.28161.3624-0.2798.63090.1907-0.3623-0.15270.7458-0.0324-0.1721-0.60250.2907-0.15830.9011-0.0157-0.08790.41320.01110.5478129.475318.0537-99.3012
106.60862.91950.86478.6563-10.382216.6256-0.21120.1048-1.4265-0.06420.4795-0.10020.1209-0.7343-0.26830.37510.14040.14210.134-0.13270.9759121.41716.7621-117.6524
110.32961.1535-0.28034.6729-1.06410.25180.0521-0.1636-0.1114-0.4683-0.01160.2467-0.00470.1074-0.04062.25-0.39180.1522.4596-0.39551.781994.0471-10.0502-159.7874
1211.264-0.1227-0.74358.3861-3.58941.7618-0.5342.37070.4541-1.26390.98940.49561.0484-0.6775-0.45541.9839-0.8335-0.02042.8869-0.49620.956389.36317.5929-153.1388
137.61520.4782-0.633512.75933.03278.4516-0.46041.4951-0.9864-0.28370.5163-0.06340.6508-0.7488-0.05590.2042-0.25530.11810.7936-0.0560.272998.41613.7621-126.7843
143.54084.10951.118411.4655-0.45722.1622-0.03640.12360.25620.7215-0.09710.7353-0.1463-0.4350.13350.44520.15880.06390.62790.06180.533795.398135.2542-118.093
156.8299-5.9797-1.618119.7972-9.44638.7189-0.38281.106-0.0139-0.32350.2424-0.12080.6183-0.7280.14040.0589-0.08340.02231.0616-0.02430.2941106.004918.2141-129.465
161.1821-0.04281.2520.0045-0.06271.4327-0.3522-0.28190.3871-0.04870.05170.0143-0.0152-0.59970.30062.3725-0.0748-0.02651.9134-0.20092.337391.0419-43.7878-98.5662
170.10650.01230.04580.0424-0.16870.8460.14520.2844-0.3343-0.11540.2392-0.00150.9434-0.7986-0.38442.2566-0.1679-0.14281.982-0.2312.341287.2429-26.3875-106.091
187.2610.1673-3.541713.5489-1.802110.26930.3302-0.0546-1.5259-0.15310.23381.17550.8434-1.025-0.5641.0664-0.0547-0.14860.33920.11850.819497.1762-4.1769-91.1515
198.28065.567-2.293510.3073-8.446611.16680.2182-0.2516-0.00880.82970.12691.0835-0.8229-1.1631-0.34521.00660.20410.12620.61020.06980.570495.549217.53-100.0441
204.5409-4.1331-2.26936.70961.27417.97390.1630.6846-1.0801-0.2097-0.16840.68560.5050.3260.00540.87820.0721-0.0020.4118-0.01390.8554104.8914-3.6807-96.7554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C39 - 146
2X-RAY DIFFRACTION2C147 - 239
3X-RAY DIFFRACTION3C240 - 332
4X-RAY DIFFRACTION4C333 - 385
5X-RAY DIFFRACTION5G20 - 45
6X-RAY DIFFRACTION6A39 - 146
7X-RAY DIFFRACTION7A147 - 239
8X-RAY DIFFRACTION8A240 - 328
9X-RAY DIFFRACTION9A329 - 385
10X-RAY DIFFRACTION10E20 - 47
11X-RAY DIFFRACTION11B39 - 146
12X-RAY DIFFRACTION12B147 - 239
13X-RAY DIFFRACTION13B240 - 328
14X-RAY DIFFRACTION14B329 - 384
15X-RAY DIFFRACTION15F20 - 47
16X-RAY DIFFRACTION16D39 - 146
17X-RAY DIFFRACTION17D147 - 239
18X-RAY DIFFRACTION18D240 - 328
19X-RAY DIFFRACTION19D329 - 385
20X-RAY DIFFRACTION20H20 - 46

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