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- PDB-1p5y: The structures of host range controlling regions of the capsids o... -

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Basic information

Entry
Database: PDB / ID: 1p5y
TitleThe structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants
ComponentsCoat protein VP2
KeywordsVIRUS / parvovirade / CPV / FPV / Icosahedral virus
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesCanine parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAgbandje-McKenna, M. / Govindasamy, L.
Citation
Journal: J.Virol. / Year: 2003
Title: Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants.
Authors: Govindasamy, L. / Hueffer, K. / Parrish, C.R. / Agbandje-McKenna, M.
#1: Journal: Science / Year: 1991
Title: The three-dimensional structure of canine parvovirus and its functional implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W. / Parrish, C.R.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure determination of monoclinic canine parvovirus
Authors: Tsao, J. / Chapman, M.S. / Wu, H. / Agbandje, M. / Keller, W. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: The canine parvovirus empty capsid structure
Authors: Wu, H. / Rossmann, M.G.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHORS STATE THE DENSITY AT POSITION 60 IS FOR GLU, NOT TYR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein VP2


Theoretical massNumber of molelcules
Total (without water)61,5641
Polymers61,5641
Non-polymers00
Water1,17165
1
A: Coat protein VP2
x 60


Theoretical massNumber of molelcules
Total (without water)3,693,86460
Polymers3,693,86460
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Coat protein VP2
x 5


  • icosahedral pentamer
  • 308 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)307,8225
Polymers307,8225
Non-polymers00
Water905
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Coat protein VP2
x 6


  • icosahedral 23 hexamer
  • 369 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)369,3866
Polymers369,3866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Coat protein VP2
x 60


  • crystal asymmetric unit, crystal frame
  • 3.69 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,693,86460
Polymers3,693,86460
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)440.450, 246.810, 443.650
Angle α, β, γ (deg.)90.00, 93.54, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.76441548, -0.56487232, -0.31078648), (0.00128917, 0.48338404, -0.87540745), (0.64472266, 0.66877435, 0.37023446)57.06483, 96.36764, 6.99745
3generate(0.38323173, -0.91269343, 0.14185957), (-0.56278639, -0.35251814, -0.74766466), (0.7323967, 0.20669218, -0.64874758)44.07595, 136.89817, 110.82734
4generate(0.38323173, -0.56278639, 0.7323967), (-0.91269343, -0.35251814, 0.20669218), (0.14185957, -0.74766466, -0.64874758)-21.01646, 65.57977, 168.0003
5generate(0.76441548, 0.00128917, 0.64472266), (-0.56487232, 0.48338404, 0.66877435), (-0.31078648, -0.87540745, 0.37023446)-48.25689, -19.02795, 99.50524
6generate(0.1622655, -0.12338851, 0.97900214), (-0.12338851, -0.98690082, -0.1039329), (0.97900214, -0.1039329, -0.17536468)-26.80602, 23.40244, 34.77348
7generate(0.75506405, 0.50342819, 0.42004563), (-0.16260027, -0.47686101, 0.86380827), (0.63516882, -0.72053011, -0.27820304)-22.58651, -79.47127, 79.3972
8generate(0.84864459, 0.09775012, -0.51985312), (0.43200785, 0.43903421, 0.78779324), (0.30524019, -0.8931371, 0.33035519)71.95453, -128.65955, 44.2605
9generate(0.313682, -0.77978942, -0.54178599), (0.83870763, 0.49504877, -0.22692781), (0.44516639, -0.38321688, 0.80930322)126.16459, -56.18586, -22.07889
10generate(-0.11052361, -0.91646062, 0.3845575), (0.4954538, -0.38622755, -0.77804487), (0.86157418, 0.10453814, 0.49675116)65.12722, 37.79362, -27.94219
11generate(-0.80690479, -0.51241788, -0.29382406), (-0.51241788, 0.35980629, 0.77972261), (-0.29382406, 0.77972261, -0.5529015)207.32207, -36.33562, 199.61578
12generate(-0.80690614, 0.01160155, 0.59056574), (0.11146852, 0.98483378, 0.13295562), (-0.58006659, 0.1731122, -0.79596163)109.83966, -25.4469, 254.11989
13generate(-0.23604548, 0.85636216, 0.45926722), (0.17219739, 0.50200476, -0.84754898), (-0.95636321, -0.12097549, -0.26595928)69.04416, 76.75049, 232.1312
14generate(0.11676717, 0.8544335, -0.50626952), (-0.41415651, -0.42142747, -0.80676717), (-0.90268478, 0.30387874, 0.3046603)141.31357, 129.02324, 164.03733
15generate(-0.23604329, 0.00848091, -0.97170553), (-0.83727202, -0.50931096, 0.19894198), (-0.49321307, 0.86054077, 0.12732026)226.77402, 59.13218, 143.9417
16generate(-0.35536071, 0.6358064, -0.68517807), (0.6358064, -0.37290547, -0.67578971), (-0.68517807, -0.67578971, -0.27173382)206.74286, 12.93429, 206.51314
17generate(-0.71257339, 0.04984257, -0.69982489), (0.04984257, -0.99135681, -0.12135645), (-0.69982489, -0.12135645, 0.70393021)242.94093, 8.55165, 100.38786
18generate(-0.99583084, -0.04141885, -0.08127368), (-0.04141885, -0.58852083, 0.80742041), (-0.08127368, 0.80742041, 0.58435167)202.18427, -84.988, 53.68335
19generate(-0.81368089, 0.48814232, 0.31565882), (0.48814232, 0.27889684, 0.8270028), (0.31565882, 0.8270028, -0.46521595)140.7972, -138.41604, 130.94365
20generate(-0.41784858, 0.90669054, -0.05757463), (0.90669054, 0.41215446, -0.08967147), (-0.05757463, -0.08967147, -0.99430588)143.61457, -77.89674, 225.39766
21generate(-0.37233104, -0.75662383, -0.53748486), (0.0161203, 0.5737643, -0.81886181), (0.92795998, -0.31355209, -0.20143326)192.10666, 88.69897, 42.58859
22generate(-0.6321197, -0.51487648, 0.57907417), (-0.51487648, -0.27939118, -0.81045838), (0.57907417, -0.81045838, -0.08848911)94.18457, 139.18124, 63.91668
23generate(-0.11052362, 0.4954538, 0.86157418), (-0.91646062, -0.38622755, 0.10453814), (0.3845575, -0.77804487, 0.49675116)12.54737, 77.20449, 18.24029
24generate(0.47162916, 0.8781249, -0.08039025), (-0.63365649, 0.40089943, 0.66163366), (0.6132254, -0.26110592, 0.7455054)60.0149, -11.58152, -31.31736
25generate(0.30982327, 0.10429837, -0.94505629), (-0.05728978, 0.99420702, 0.09094111), (0.94906661, 0.0259664, 0.3140037)170.98864, -4.47754, -16.26928
26generate(-0.49325662, 0.84851641, -0.19161892), (-0.86984762, -0.48313084, 0.09974826), (-0.00793898, 0.21588075, 0.97638746)165.69031, 73.21966, 3.37126
27generate(-0.49950017, 0.56063648, -0.66044403), (-0.60123786, 0.32452418, 0.73020346), (0.62370875, 0.76182071, 0.174976)217.97138, -22.27825, 30.55436
28generate(-0.80690614, 0.11146852, -0.58006659), (0.01160155, 0.98483378, 0.1731122), (0.59056574, 0.13295562, -0.79596163)238.87328, -20.20459, 140.78545
29generate(-0.99064992, 0.12174739, -0.0615655), (0.12174739, 0.58527254, -0.80164433), (-0.0615655, -0.80164433, -0.59462262)199.51029, 76.5749, 181.7289
30generate(-0.79680386, 0.57726803, 0.17850836), (-0.42301816, -0.32197949, -0.84698574), (-0.43146176, -0.75039378, 0.50074936)154.28072, 134.31427, 96.80226
31generate(0.84606927, -0.50053803, -0.1833807), (-0.06641333, -0.44030139, 0.89539039), (-0.52891972, -0.74538337, -0.40576787)35.11615, -92.26475, 206.15903
32generate(0.52787348, -0.84251351, 0.10733398), (0.52594347, 0.42349451, 0.73758787), (-0.66688309, -0.33290147, 0.666666)33.87808, -132.21998, 101.30614
33generate(0.47162916, -0.63365649, 0.6132254), (0.8781249, 0.40089943, -0.26110592), (-0.08039025, 0.66163366, 0.7455054)-16.43888, -56.2347, 35.8346
34generate(0.75506405, -0.16260027, 0.63516882), (0.50342819, -0.47686101, -0.72053011), (0.42004563, 0.86380827, -0.27820304)-46.29841, 30.68201, 100.22385
35generate(0.98648076, -0.08032854, 0.14283918), (-0.08032854, -0.99675171, -0.00577608), (0.14283918, -0.00577608, -0.98972906)-14.43565, 8.41421, 205.49014
36generate(0.0195184, 0.40864545, 0.91248448), (0.92014065, 0.34966793, -0.17627684), (-0.39110129, 0.8430547, -0.36918633)-5.6542, -69.65276, 188.78351
37generate(0.6037464, 0.7967535, -0.02596412), (0.59017087, -0.46862751, -0.65733295), (-0.53589983, 0.38153913, -0.75315288)41.22487, 15.3181, 245.12522
38generate(0.44580059, 0.02673416, -0.89473299), (0.02673416, -0.99950566, -0.01654442), (-0.89473298, -0.01654442, -0.44629493)152.27714, -0.76408, 246.04206
39generate(-0.23604329, -0.83727202, -0.49321307), (0.00848091, -0.50931096, 0.86054077), (-0.97170553, 0.19894198, 0.12732026)174.03213, -95.67428, 190.267
40generate(-0.49950017, -0.60123786, 0.62370875), (0.56063648, 0.32452418, 0.76182071), (-0.66044403, 0.73020346, 0.174976)76.4252, -138.24982, 154.87927
41generate(-0.37233104, 0.0161203, 0.92795998), (-0.75662383, 0.5737643, -0.31355209), (-0.53748486, -0.81886181, -0.20143326)30.57691, 107.81392, 184.46538
42generate(0.313682, 0.83870763, 0.44516639), (-0.77978942, 0.49504877, -0.38321688), (-0.54178599, -0.22692781, 0.80930322)17.37672, 117.73555, 73.47259
43generate(0.52787348, 0.52594347, -0.66688309), (-0.84251351, 0.42349451, -0.33290147), (0.10733398, 0.73758787, 0.666666)119.21624, 118.26214, 26.35022
44generate(-0.02576195, -0.48994274, -0.87137388), (-0.85811353, 0.45798709, -0.23214004), (0.51281331, 0.74175733, -0.43222513)195.35671, 108.66595, 108.21979
45generate(-0.58211894, -0.80503079, 0.11429335), (-0.80503079, 0.55085892, -0.22018147), (0.11429335, -0.22018147, -0.96873998)140.57459, 102.2086, 205.94033
46generate(0.84606927, -0.06641333, -0.52891972), (-0.50053803, -0.44030139, -0.74538337), (-0.1833807, 0.89539039, -0.40576787)73.20327, 130.62018, 172.70531
47generate(0.3056563, -0.86375219, -0.40063247), (-0.86375219, -0.42858787, 0.26503696), (-0.40063247, 0.26503696, -0.87706843)111.38289, 54.41047, 245.68804
48generate(-0.02576195, -0.85811353, 0.51281331), (-0.48994274, 0.45798709, 0.74175733), (-0.87137388, -0.23214004, -0.43222513)42.78395, -34.32682, 242.22976
49generate(0.30982327, -0.05728978, 0.94906661), (0.10429837, 0.99420702, 0.0259664), (-0.94505629, 0.09094111, 0.3140037)-37.79215, -12.95978, 167.10969
50generate(0.84864459, 0.43200785, 0.30524019), (0.09775012, 0.43903421, -0.8931371), (-0.51985312, 0.78779324, 0.33035519)-18.99197, 88.98308, 124.14122
51generate(0.0195184, 0.92014065, -0.39110129), (0.40864545, 0.34966793, 0.8430547), (0.91248448, -0.17627684, -0.36918633)138.03418, -132.48893, 62.5775
52generate(-0.23604548, 0.17219739, -0.95636321), (0.85636216, 0.50200476, -0.12097549), (0.45926722, -0.84754898, -0.26595928)225.08307, -69.57374, 95.07753
53generate(-0.79680386, -0.42301816, -0.43146176), (0.57726803, -0.32197949, -0.75039378), (0.17850836, -0.84698574, 0.50074936)221.51532, 26.82493, 37.7482
54generate(-0.88780772, -0.04293834, 0.4582071), (-0.04293834, -0.98356659, -0.17536549), (0.4582071, -0.17536549, 0.87137432)132.26145, 23.48738, -30.1833
55generate(-0.38329282, 0.78717945, 0.48315124), (-0.14715283, -0.56846566, 0.80943983), (0.91182929, 0.2391554, 0.33372449)80.66726, -74.97399, -14.83795
56generate(-0.49325662, -0.86984762, -0.00793898), (0.84851641, -0.48313084, 0.21588075), (-0.19161892, 0.09974826, 0.97638746)145.44455, -105.94406, 21.15421
57generate(-0.38329282, -0.14715283, 0.91182929), (0.78717945, -0.56846566, 0.2391554), (0.48315124, 0.80943983, 0.33372449)33.41623, -102.57117, 26.66424
58generate(0.29469233, 0.75518822, 0.58553154), (0.75518822, -0.55950211, 0.34153791), (0.58553154, 0.34153791, -0.73519023)3.74339, -110.75913, 134.57421
59generate(0.6037464, 0.59017087, -0.53589983), (0.7967535, -0.46862751, 0.38153913), (-0.02596412, -0.65733295, -0.75315288)97.4329, -119.19244, 195.75622
60generate(0.11676717, -0.41415651, -0.90268478), (0.8544335, -0.42142747, 0.30387874), (-0.50626952, -0.80676717, 0.3046603)185.00903, -116.21657, 125.65881

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Components

#1: Protein Coat protein VP2


Mass: 61564.398 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 190-737 / Mutation: N93D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus / Genus: ParvovirusParvoviridae / Species: Feline panleukopenia virus
Cell line (production host): NLFK Nordisk Laboratory feline kidney
References: UniProt: P30129, UniProt: P17455*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 15

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG8000, CaCl2, Tris.HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 %PEG80001reservoir
28 mM1reservoirCaCl2
320 mMTris-HCl1reservoirpH7.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: 0.2 collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 474357 / % possible obs: 61.2 % / Rsym value: 0.143
Reflection shellResolution: 3.2→3.6 Å / Num. unique all: 42698 / Rsym value: 0.258 / % possible all: 55.25
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 25 Å / % possible obs: 70.5 % / Rmerge(I) obs: 0.143
Reflection shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.31 Å / % possible obs: 54.8 % / Rmerge(I) obs: 0.297

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→25 Å / σ(F): 2
RfactorNum. reflection
Rfree0.253 -
Rwork0.252 -
obs-474357
Displacement parametersBiso mean: 37.74 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 0 65 4393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 3.2→3.6 Å
RfactorNum. reflection% reflection
Rfree0.273 --
Rwork0.272 --
obs-474357 55.25 %
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 8508415 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.6 Å

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