[English] 日本語
Yorodumi
- PDB-1f2n: RICE YELLOW MOTTLE VIRUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f2n
TitleRICE YELLOW MOTTLE VIRUS
ComponentsCAPSID PROTEIN
KeywordsVIRUS / PLANT VIRUS / CAPSID PROTEIN / COAT PROTEIN / BETA-ANNULUS / DOMAIN SWAPPING / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / 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 speciesRice yellow mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsQu, C. / Liljas, L. / Opalka, N. / Brugidou, C. / Yeager, M. / Beachy, R.N. / Fauquet, C.M. / Johnson, J.E. / Lin, T.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: 3D domain swapping modulates the stability of members of an icosahedral virus group.
Authors: Qu, C. / Liljas, L. / Opalka, N. / Brugidou, C. / Yeager, M. / Beachy, R.N. / Fauquet, C.M. / Johnson, J.E. / Lin, T.
#1: Journal: J.GEN.VIROL. / Year: 1994
Title: NUCLEOTIDE SEQUENCE AND GENOME CHARACTERIZATION OF RICE YELLOW MOTTLE VIRUS RNA
Authors: YASSI, M.N. / RITZENTHALER, C. / BRUGIDOU, C. / FAUQUET, C. / BEACHY, R.N.
History
DepositionMay 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAPSID PROTEIN
B: CAPSID PROTEIN
C: CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1496
Polymers78,0293
Non-polymers1203
Water3,585199
1
A: CAPSID PROTEIN
B: CAPSID PROTEIN
C: CAPSID PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,688,947360
Polymers4,681,733180
Non-polymers7,214180
Water3,243180
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
B: CAPSID PROTEIN
C: CAPSID PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 391 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)390,74630
Polymers390,14415
Non-polymers60115
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAPSID PROTEIN
B: CAPSID PROTEIN
C: CAPSID PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 469 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)468,89536
Polymers468,17318
Non-polymers72118
Water32418
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
B: CAPSID PROTEIN
C: CAPSID PROTEIN
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.69 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,688,947360
Polymers4,681,733180
Non-polymers7,214180
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)283.500, 401.800, 284.000
Angle α, β, γ (deg.)90.00, 89.40, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.54724468, -0.80458246, 0.23058694), (0.7232674, 0.31595588, -0.61404898), (0.42119774, 0.50281105, 0.75483343)15.93512, -7.66651, -12.60505
3generate(-0.18532883, -0.57857436, 0.79429524), (0.36568878, -0.79085076, -0.49074107), (0.9120992, 0.19951639, 0.35814559)27.91731, 9.17669, -19.26273
4generate(-0.18532883, 0.36568878, 0.9120992), (-0.57857436, -0.79085076, 0.19951639), (0.79429524, -0.49074107, 0.35814559)19.38759, 27.25286, -10.77235
5generate(0.54724468, 0.7232674, 0.42119774), (-0.80458246, 0.31595588, 0.50281105), (0.23058694, -0.61404898, 0.75483343)2.13374, 21.58136, 1.13267
6generate(-0.98859032, -0.01176587, 0.15016908), (-0.01176587, -0.98786682, -0.15485709), (0.15016908, -0.15485709, 0.97645713)132.69091, 12.04486, -9.13799
7generate(-0.48625979, 0.8671916, -0.10737855), (-0.78615613, -0.38051957, 0.48699425), (0.38145768, 0.32122203, 0.86677935)115.13491, 21.38284, -17.8661
8generate(0.31588073, 0.61123925, -0.7256762), (-0.50031628, 0.75716612, 0.41997986), (0.80616561, 0.23040407, 0.54498713)102.09148, 5.63401, -25.17597
9generate(0.3093003, -0.42590547, -0.85025752), (0.45073272, 0.8529473, -0.26328865), (0.83736094, -0.30180363, 0.45578639)111.5862, -13.43727, -20.96561
10generate(-0.49690714, -0.81094381, -0.30895538), (0.75267348, -0.22554237, -0.61855742), (0.43193278, -0.53990812, 0.72244951)130.49768, -9.47515, -11.05359
11generate(0.97865435, -0.12847852, -0.16040242), (-0.12847852, -0.9916576, 0.01041529), (-0.16040242, 0.01041529, -0.98699675)13.1823, 8.4749, 155.82288
12generate(0.37507792, -0.90865377, 0.18347991), (-0.7831559, -0.20471156, 0.58716268), (-0.49596713, -0.36392513, -0.78840035)31.78414, 13.89884, 165.62814
13generate(-0.37465893, -0.49661989, 0.78294276), (-0.3293275, 0.86066556, 0.38832743), (-0.86670299, -0.11235425, -0.48600663)42.41448, -4.41264, 170.4527
14generate(-0.23444536, 0.5382063, 0.80954886), (0.60583125, 0.7321588, -0.31130691), (-0.76026565, 0.41746554, -0.49771343)30.38255, -21.1537, 163.62918
15generate(0.60194824, 0.76573018, 0.22652947), (0.72996275, -0.41263987, -0.54486945), (-0.32374789, 0.49334128, -0.80734236)12.31607, -13.18876, 154.58746
16generate(-0.99006403, 0.14024439, 0.01023334), (0.14024439, 0.97952441, 0.14444179), (0.01023334, 0.14444179, -0.98946038)142.95908, -20.61259, 143.68355
17generate(-0.43606281, 0.84604463, -0.30668829), (0.84604463, 0.26927525, -0.46010795), (-0.30668829, -0.46010795, -0.83321244)125.97811, -27.708, 155.21145
18generate(0.24410703, 0.463955, -0.85156181), (0.463955, -0.82698093, -0.31756621), (-0.85156181, -0.31756621, -0.4171261)116.40901, -10.49089, 164.35444
19generate(0.11047389, -0.47798961, -0.87139053), (-0.47798961, -0.79425534, 0.37507916), (-0.87139053, 0.37507916, -0.31621855)127.47595, 7.24528, 158.47722
20generate(-0.65228577, -0.67805377, -0.33877183), (-0.67805377, 0.32222636, 0.66061582), (-0.33877183, 0.66061582, -0.66994059)143.88479, 0.98973, 145.7019
21generate(-0.0003042, -0.98893291, -0.14836309), (-0.14806215, 0.14677239, -0.97802631), (0.98897801, 0.02166944, -0.14646819)82.97708, 81.66847, 11.81285
22generate(-0.7779196, -0.38681301, 0.49519368), (-0.38681301, -0.32626063, -0.86251359), (0.49519368, -0.86251359, 0.10418023)92.42401, 90.51192, 29.25245
23generate(-0.49690714, 0.75267348, 0.43193278), (-0.81094381, -0.22554237, -0.53990812), (-0.30895538, -0.61855742, 0.72244951)76.75133, 97.72132, 42.44269
24generate(0.45438351, 0.85479496, -0.25072137), (-0.8343202, 0.30973796, -0.45603969), (-0.3121625, 0.41639882, 0.85391252)57.61815, 93.33352, 33.15511
25generate(0.76130101, -0.22157698, -0.60936394), (-0.42463681, 0.53984113, -0.72681162), (0.49000445, 0.81208078, 0.31689185)61.46587, 83.41232, 14.22483
26generate(-0.01034316, 0.99991266, 0.00822739), (-0.0022234, 0.00820481, -0.99996387), (-0.99994404, -0.01036108, 0.00213834)72.38089, 72.72702, 144.64067
27generate(0.72100935, 0.32838703, -0.61017004), (-0.41646499, -0.49841162, -0.760357), (-0.55380721, 0.80233897, -0.22259773)64.44653, 85.23328, 128.75892
28generate(0.37507792, -0.7831559, -0.49596713), (-0.90865377, -0.20471156, -0.36392513), (0.18347991, 0.58716268, -0.78840035)81.10954, 92.00227, 116.58865
29generate(-0.57007196, -0.79860158, 0.19301158), (-0.79860158, 0.48342148, -0.35852362), (0.19301158, -0.35852362, -0.91334952)99.34222, 83.67948, 124.94876
30generate(-0.80827529, 0.30339539, 0.50462093), (-0.2383968, 0.61501104, -0.75161718), (-0.53838464, -0.72781361, -0.42476974)93.94761, 71.76672, 142.28587
31generate(0.15055672, 0.97917667, 0.13618265), (-0.00688098, -0.13671158, 0.990587), (0.98857742, -0.1500766, -0.01384515)51.4736, -71.43832, 2.21041
32generate(0.84795776, 0.25671547, -0.4637508), (0.31458839, 0.46041958, 0.83008912), (0.42661667, -0.84977113, 0.30965665)44.64928, -82.98626, 19.28859
33generate(0.45438351, -0.8343202, -0.3121625), (0.85479496, 0.30973796, 0.41639882), (-0.25072137, -0.45603969, 0.85391252)62.03909, -91.96638, 28.69832
34generate(-0.48625979, -0.78615613, 0.38145768), (0.8671916, -0.38051957, 0.32122203), (-0.10737855, 0.48699425, 0.86677935)79.61089, -85.96846, 17.43567
35generate(-0.67403507, 0.33464658, 0.65855022), (0.33464658, -0.65644055, 0.67608984), (0.65855022, 0.67608984, 0.33047562)73.08106, -73.28141, 1.06524
36generate(-0.13990937, -0.99015642, 0.00395304), (0.15716654, -0.01826562, 0.98740318), (-0.9776114, 0.13876824, 0.15817499)82.00072, -83.05001, 131.70451
37generate(-0.7910475, -0.19828949, 0.57872716), (0.48868961, 0.36425266, 0.79278147), (-0.36800314, 0.90994575, -0.19123915)87.31246, -92.85177, 113.06848
38generate(-0.33255429, 0.86480262, 0.37619684), (0.86480262, 0.12051597, 0.48743443), (0.37619684, 0.48743443, -0.78796168)68.93232, -97.85003, 102.63878
39generate(0.60194824, 0.72996275, -0.32374789), (0.76573018, -0.41263987, 0.49334128), (0.22652947, -0.54486945, -0.80734236)52.26103, -91.13737, 114.82889
40generate(0.72100935, -0.41646499, -0.55380721), (0.32838703, -0.49841162, 0.80233897), (-0.61017004, -0.760357, -0.22259773)60.33775, -81.99045, 132.7925
41generate(-0.0003042, -0.14806215, 0.98897801), (-0.98893291, 0.14677239, 0.02166944), (-0.14836309, -0.97802631, -0.14646819)0.4346, 69.81611, 93.91486
42generate(0.3093003, 0.45073272, 0.83736094), (-0.42590547, 0.8529473, -0.30180363), (-0.85025752, -0.26328865, 0.45578639)-10.90124, 52.65896, 100.89496
43generate(0.84795776, 0.31458839, 0.42661667), (0.25671547, 0.46041958, -0.84977113), (-0.4637508, 0.83008912, 0.30965665)-19.98303, 43.13723, 83.6193
44generate(0.87126187, -0.3683483, 0.32437983), (0.11557097, -0.48835081, -0.8649606), (0.47701792, 0.79109609, -0.38291107)-14.26003, 54.40962, 65.96225
45generate(0.34700715, -0.65428207, 0.67193825), (-0.65428207, -0.68219543, -0.32638071), (0.67193825, -0.32638071, -0.66481172)-1.64125, 70.89807, 72.32526
46generate(0.15055672, -0.00688098, 0.98857742), (0.97917667, -0.13671158, -0.1500766), (0.13618265, 0.990587, -0.01384515)-10.42642, -59.83646, 63.78666
47generate(0.49380115, 0.37375827, 0.78515297), (0.37375827, -0.90648337, 0.19645012), (0.78515297, 0.19645012, -0.58731777)-20.43559, -41.29334, 58.53693
48generate(0.87126187, 0.11557097, 0.47701792), (-0.3683483, -0.48835081, 0.79109609), (0.32437983, -0.8649606, -0.38291107)-25.32912, -30.86416, 76.94552
49generate(0.76130101, -0.42463681, 0.49000445), (-0.22157698, 0.53984113, 0.81208078), (-0.60936394, -0.72681162, 0.31689185)-18.34432, -42.96169, 93.57239
50generate(0.31588073, -0.50031628, 0.80616561), (0.61123925, 0.75716613, 0.23040407), (-0.7256762, 0.41997986, 0.54498714)-9.13394, -60.86756, 85.43977
51generate(-0.13990937, 0.15716654, -0.9776114), (-0.99015642, -0.01826562, 0.13876824), (0.00395304, 0.98740318, 0.15817499)153.28118, 61.40017, 60.84733
52generate(-0.37465893, -0.3293275, -0.86670299), (-0.49661989, 0.86066556, -0.11235425), (0.78294276, 0.38832743, -0.48600663)162.16963, 44.01276, 51.34658
53generate(-0.80827529, -0.2383968, -0.53838464), (0.30339539, 0.61501104, -0.72781361), (0.50462093, -0.75161718, -0.42476974)169.64901, 30.917, 66.97189
54generate(-0.84151538, 0.3042955, -0.44638114), (0.3042955, -0.41574298, -0.85706594), (-0.44638114, -0.85706594, 0.25725836)165.38308, 40.21078, 86.12961
55generate(-0.42844252, 0.54876709, -0.7178382), (-0.49516349, -0.80712949, -0.3214889), (-0.75581091, 0.21770776, 0.61753802)155.2672, 59.05042, 82.34442
56generate(-0.01034316, -0.0022234, -0.99994404), (0.99991266, 0.00820481, -0.01036108), (0.00822739, -0.99996387, 0.00213834)145.54293, -71.47265, 71.81959
57generate(-0.42844252, -0.49516349, -0.75581091), (0.54876709, -0.80712949, 0.21770776), (-0.7178382, -0.3214889, 0.61753802)157.9995, -55.47122, 79.58997
58generate(-0.91094434, -0.19176256, -0.36524996), (-0.19176256, -0.58707982, 0.78648866), (-0.36524996, 0.78648866, 0.49802416)164.49542, -43.2829, 62.83173
59generate(-0.7910475, 0.48868961, -0.36800314), (-0.19828949, 0.36425266, 0.90994575), (0.57872716, 0.79278147, -0.19123915)156.05355, -51.75154, 44.70419
60generate(-0.23444536, 0.60583125, -0.76026565), (0.5382063, 0.7321588, 0.41746554), (0.80954886, -0.31130691, -0.49771343)144.34027, -69.17376, 50.25899

-
Components

#1: Protein CAPSID PROTEIN


Mass: 26009.625 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: COLLECTED FROM RICE FIELD IN THE IVORY COAST AND WAS PROPAGATED UNDER CONTAINED CONDITIONS IN A SUSCEPTIBLE RICE VARIETY IR8 (ORYZA SATIVA L.)
Source: (natural) Rice yellow mottle virus / Genus: Sobemovirus / References: UniProt: Q86527
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 3.6% (w/v) PEG 8000, 200 mM lithium sulfate, 50 mM sodium citrate, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
136 mg/mlprotein1drop
250 mMsodium acetate1drop
3200 mMlithium sulfate1drop
450 mMsodium acetate1reservoir
5200 mMlithium sulfate1reservoir
63.6 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 23, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 739272 / Num. obs: 739272 / % possible obs: 48.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.83 Å / Redundancy: 1 % / Rmerge(I) obs: 0.257 / Num. unique all: 1399 / % possible all: 2.8
Reflection
*PLUS

-
Processing

Software
NameVersionClassification
GLRFphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→30 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: 60-fold non crystallographic symmetry constraints
RfactorNum. reflection% reflectionSelection details
Rfree0.219 56852 -RANDOM
Rwork0.218 ---
all0.246 738802 --
obs0.227 567810 37.2 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 3 199 4730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg28
X-RAY DIFFRACTIONx_torsion_impr_deg0.73
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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