[English] 日本語
Yorodumi
- PDB-5yl1: T=1 subviral particle of Penaeus vannamei nodavirus capsid protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yl1
TitleT=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Viral capsid protein
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPenaeus vannamei nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsChen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-B-213-001-MY3 Taiwan
CitationJournal: Commun Biol / Year: 2019
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen /
Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of  = 3 and  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls  = 3 and  = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
History
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6893
Polymers20,6091
Non-polymers802
Water00
1
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,241,360180
Polymers1,236,55060
Non-polymers4,809120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 103 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)103,44715
Polymers103,0465
Non-polymers40110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 124 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)124,13618
Polymers123,6556
Non-polymers48112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 1.24 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,241,360180
Polymers1,236,55060
Non-polymers4,809120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)196.981, 200.319, 419.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.313223, -0.816078, -0.485704), (0.755963, 0.523816, -0.392604), (0.574815, -0.244202, 0.780995)10.78738, -58.44395, -40.4454
3generate(-0.798005, -0.564479, -0.211071), (0.407096, -0.246667, -0.879448), (0.444365, -0.78773, 0.426638)81.50555, -65.02394, -51.5602
4generate(-0.798005, 0.407096, 0.444365), (-0.564479, -0.246667, -0.78773), (-0.211071, -0.879448, 0.426638)114.42439, -10.64664, -17.98413
5generate(0.313223, 0.755963, 0.574815), (-0.816078, 0.523816, -0.244202), (-0.485704, -0.392604, 0.780995)64.05119, 29.54037, 13.88183
6generate(-0.986957, -0.006135, 0.160866), (-0.006135, -0.997115, -0.075663), (0.160866, -0.075663, 0.984072)109.83443, -1.74874, -8.97192
7generate(-0.221307, 0.762937, 0.607413), (-0.799195, -0.498821, 0.335358), (0.558847, -0.411225, 0.720128)93.03999, 59.52064, -42.6157
8generate(0.856583, 0.431911, 0.282345), (-0.434648, 0.30902, 0.845924), (0.278113, -0.847325, 0.452431)21.49657, 66.48878, -41.67945
9generate(0.757106, -0.541746, -0.365106), (0.583716, 0.31, 0.75045), (-0.293371, -0.781288, 0.550928)-5.92527, 9.52596, -7.45705
10generate(-0.382265, -0.812473, -0.440184), (0.848551, -0.497236, 0.180878), (-0.365834, -0.304375, 0.879501)48.67054, -32.64716, 12.75732
11generate(-0.999371, -0.035442, -0.001403), (-0.035442, 0.996244, 0.079001), (-0.001403, 0.079001, -0.996874)102.12416, 5.8902, -103.02187
12generate(-0.340625, 0.797342, 0.498218), (0.787433, 0.531479, -0.312216), (-0.513735, 0.285965, -0.808888)93.47163, -55.91181, -67.33521
13generate(0.782452, 0.573971, 0.241509), (0.468955, -0.287966, -0.834959), (-0.409696, 0.766572, -0.494486)23.04677, -65.85152, -56.87416
14generate(0.817805, -0.396864, -0.416766), (-0.550751, -0.329646, -0.766816), (0.166936, 0.85664, -0.488159)-11.82567, -10.19259, -86.09556
15generate(-0.283422, -0.773501, -0.566893), (-0.862485, 0.46404, -0.201957), (0.419275, 0.431698, -0.798652)37.04685, 34.14624, -114.61641
16generate(0.986328, 0.041576, -0.159463), (0.041576, -0.99913, -0.003338), (-0.159463, -0.003338, -0.987198)-7.56659, -0.45346, -94.37021
17generate(0.248709, -0.744201, -0.619927), (-0.744201, -0.556474, 0.369462), (-0.619927, 0.369462, -0.692235)7.09299, 58.52313, -55.9677
18generate(-0.84103, -0.441403, -0.312783), (-0.441403, 0.225613, 0.868483), (-0.312783, 0.868483, -0.384583)78.34312, 68.07468, -56.25018
19generate(-0.776906, 0.531514, 0.337506), (0.531514, 0.266313, 0.804096), (0.337506, 0.804096, -0.489407)107.71855, 15.00127, -94.82727
20generate(0.352463, 0.830011, 0.432263), (0.830011, -0.490619, 0.265281), (0.432263, 0.265281, -0.861844)54.62342, -27.35145, -118.38673
21generate(-0.096723, -0.043196, -0.994374), (0.993282, 0.05958, -0.099205), (0.06353, -0.997288, 0.037143)4.77945, -55.00573, -52.0015
22generate(-0.634531, 0.299134, -0.712663), (0.299134, -0.75516, -0.583311), (-0.712663, -0.583311, 0.389691)46.47844, -43.76051, 5.46704
23generate(-0.382265, 0.848551, -0.365834), (-0.812473, -0.497236, -0.304375), (-0.440184, 0.180878, 0.879501)50.97487, 27.19316, 16.10906
24generate(0.311453, 0.845779, -0.433191), (-0.805336, 0.47691, 0.352123), (0.504411, 0.239195, 0.829672)12.05482, 59.79972, -34.78234
25generate(0.487927, 0.294649, -0.82165), (0.310681, 0.821041, 0.478925), (0.815723, -0.488952, 0.309066)-16.49552, 8.99802, -76.87698
26generate(-0.064234, 0.118903, -0.990826), (-0.996651, -0.057995, 0.057652), (-0.050608, 0.991211, 0.12223)3.15292, 54.87668, -43.61297
27generate(-0.499775, 0.356665, -0.789313), (-0.322877, 0.768887, 0.551873), (0.803726, 0.530663, -0.269112)35.58521, 45.18312, -107.03281
28generate(-0.340625, 0.787433, -0.513735), (0.797342, 0.531479, 0.285965), (0.498218, -0.312216, -0.808888)41.27313, -25.55738, -118.49243
29generate(0.193276, 0.815901, -0.544931), (0.815901, -0.442129, -0.372596), (-0.544931, -0.372596, -0.751148)12.35617, -59.58385, -62.15504
30generate(0.364095, 0.402726, -0.83979), (-0.292847, -0.806444, -0.513701), (-0.884124, 0.432966, -0.175685)-11.20342, -9.87287, -15.87699
31generate(0.099588, -0.118163, 0.987988), (-0.994629, 0.016315, 0.102209), (-0.028197, -0.99286, -0.115903)97.08949, 57.00356, -55.21435
32generate(0.509777, -0.384435, 0.769635), (-0.240456, 0.795281, 0.556515), (-0.82602, -0.468761, 0.312976)65.11012, 41.18671, 7.19591
33generate(0.311453, -0.805336, 0.504411), (0.845779, 0.47691, 0.239195), (-0.433191, 0.352123, 0.829672)61.94899, -30.39502, 13.02314
34generate(-0.221307, -0.799195, 0.558847), (0.762937, -0.498821, -0.411225), (0.607413, 0.335358, 0.720128)91.97469, -58.81812, -45.78569
35generate(-0.352247, -0.374499, 0.857714), (-0.374499, -0.783484, -0.495887), (0.857714, -0.495887, 0.135731)113.69271, -4.80282, -87.95878
36generate(0.06137, 0.042456, 0.997212), (0.997998, -0.0179, -0.060656), (0.015275, 0.998938, -0.04347)99.37014, -53.18651, -55.53518
37generate(0.624529, -0.271364, 0.732342), (0.264198, -0.809008, -0.525076), (0.734957, 0.521409, -0.433555)57.21824, -38.92132, -111.99414
38generate(0.411437, -0.830648, 0.375157), (-0.830648, -0.511153, -0.220785), (0.375157, -0.220785, -0.900284)50.19501, 32.44724, -117.00377
39generate(-0.283422, -0.862485, 0.419275), (-0.773501, 0.46404, 0.431698), (-0.566893, -0.201957, -0.798652)88.00632, 62.29025, -63.64093
40generate(-0.499775, -0.322877, 0.803726), (0.356665, 0.768887, 0.530663), (-0.789313, 0.551873, -0.269112)118.39822, 9.36568, -25.65125
41generate(-0.096723, 0.993282, 0.06353), (-0.043196, 0.05958, -0.997288), (-0.994374, -0.099205, 0.037143)58.40211, -48.37681, 1.22722
42generate(0.757106, 0.583716, -0.293371), (-0.541746, 0.31, -0.781288), (-0.365106, 0.75045, 0.550928)-3.26208, -11.98914, -5.20381
43generate(0.509777, -0.240456, -0.82602), (-0.384435, 0.795281, -0.468761), (0.769635, 0.556515, 0.312976)-17.34405, -4.35125, -75.28415
44generate(-0.49691, -0.340256, -0.798314), (0.211338, 0.844782, -0.491609), (0.841675, -0.413, -0.347872)35.617, -36.01846, -112.16516
45generate(-0.871748, 0.422235, -0.248542), (0.422235, 0.390093, -0.818257), (-0.248542, -0.818257, -0.518346)82.43071, -63.22775, -64.87853
46generate(0.099588, -0.994629, -0.028197), (-0.118163, 0.016315, -0.99286), (0.987988, 0.102209, -0.115903)45.47162, -44.27782, -108.14899
47generate(-0.736917, -0.595388, 0.320104), (-0.595388, 0.347434, -0.724433), (0.320104, -0.724433, -0.610517)105.8164, -6.3494, -98.77692
48generate(-0.49691, 0.211338, 0.841675), (-0.340256, 0.844782, -0.413), (-0.798314, -0.491609, -0.347872)119.71711, -3.77755, -28.29252
49generate(0.487927, 0.310681, 0.815723), (0.294649, 0.821041, -0.488952), (-0.82165, 0.478925, 0.309066)67.96344, -40.11648, 5.89715
50generate(0.856583, -0.434648, 0.278113), (0.431911, 0.30902, -0.847325), (0.282345, 0.845924, 0.452431)22.07721, -65.14703, -43.45687
51generate(0.06137, 0.997998, 0.015275), (0.042456, -0.0179, 0.998938), (0.997212, -0.060656, -0.04347)47.83003, 50.30529, -104.73324
52generate(0.782452, 0.468955, -0.409696), (0.573971, -0.287966, 0.766572), (0.241509, -0.834959, -0.494486)-10.45272, 11.40699, -88.67282
53generate(0.364095, -0.292847, -0.884124), (0.402726, -0.806444, 0.432966), (-0.83979, -0.513701, -0.175685)-12.84936, 3.42419, -17.26956
54generate(-0.615546, -0.234623, -0.752366), (-0.234623, -0.856815, 0.459152), (-0.752366, 0.459152, 0.472361)43.95218, 37.38885, 10.79965
55generate(-0.802641, 0.563163, -0.196507), (-0.457282, -0.369468, 0.808941), (0.382963, 0.739149, 0.554075)81.4541, 66.36297, -43.25588
56generate(-0.064234, -0.996651, -0.050608), (0.118903, -0.057995, 0.991211), (-0.990826, 0.057652, 0.12223)52.68824, 46.03734, 5.29102
57generate(-0.802641, -0.457282, 0.382963), (0.563163, -0.369468, 0.739149), (-0.196507, 0.808941, 0.554075)112.2904, 10.61955, -13.71046
58generate(-0.376961, 0.321965, 0.868469), (0.321965, -0.833619, 0.448795), (0.868469, 0.448795, 0.210581)114.8683, 8.39262, -85.51776
59generate(0.624529, 0.264198, 0.734957), (-0.271364, -0.809008, 0.521409), (0.732342, -0.525076, -0.433555)56.85938, 42.43409, -110.89564
60generate(0.817805, -0.550751, 0.166936), (-0.396864, -0.329646, 0.85664), (-0.416766, -0.766816, -0.488159)18.42998, 65.69981, -54.77272

-
Components

#1: Protein Capsid protein


Mass: 20609.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A5H7Q8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris 8.0, 20%(w/v) Poly(acrylic acid sodium salt) 5100

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.12→37.62 Å / Num. obs: 292229 / % possible obs: 99.7 % / Redundancy: 5 % / Rpim(I) all: 0.108 / Rrim(I) all: 0.244 / Net I/σ(I): 7.1
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 5 % / CC1/2: 0.646 / Rpim(I) all: 0.428 / Rrim(I) all: 0.963 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→37.62 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.916 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22071 14413 5 %RANDOM
Rwork0.21953 ---
obs0.21959 274292 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 3.12→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 2 0 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021486
X-RAY DIFFRACTIONr_bond_other_d0.0040.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9482031
X-RAY DIFFRACTIONr_angle_other_deg1.15933205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9085184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11924.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.57515235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.099158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211699
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02349
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8946.452739
X-RAY DIFFRACTIONr_mcbond_other2.8556.451738
X-RAY DIFFRACTIONr_mcangle_it4.1599.69922
X-RAY DIFFRACTIONr_mcangle_other4.1579.693923
X-RAY DIFFRACTIONr_scbond_it3.7396.694747
X-RAY DIFFRACTIONr_scbond_other3.7386.697748
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3189.9611110
X-RAY DIFFRACTIONr_long_range_B_refined7.22164.0186350
X-RAY DIFFRACTIONr_long_range_B_other7.2364.0186351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.119→3.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 931 -
Rwork0.345 17122 -
obs--84.42 %

+
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://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