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- PDB-1cwp: STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MO... -

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Basic information

Entry
Database: PDB / ID: 1cwp
TitleSTRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MOTTLE VIRUS DETERMINED BY X-RAY CRYSTALLOGRAPHY AND CRYO-ELECTRON MICROSCOPY
Components
  • Coat protein
  • RNA (5'-R(*AP*U)-3')
  • RNA (5'-R(*AP*UP*AP*U)-3')
KeywordsVirus/RNA / BROMOVIRUS / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


T=3 icosahedral viral capsid / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Satellite virus coat domain / Bromovirus coat protein / Bromovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / Capsid protein
Similarity search - Component
Biological speciesCowpea chlorotic mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSpeir, J.A. / Johnson, J.E. / Munshi, S. / Wang, G. / Timothy, S. / Baker, T.S.
Citation
Journal: Structure / Year: 1995
Title: Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy.
Authors: Speir, J.A. / Munshi, S. / Wang, G. / Baker, T.S. / Johnson, J.E.
#1: Journal: Thesis, Purdue University / Year: 1994
Title: The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle
Authors: Speir, J.A.
#2: Journal: Virology / Year: 1993
Title: Preliminary X-Ray Data Analysis of Crystalline Cowpea Chlorotic Mottle Virus
Authors: Speir, J.A. / Munshi, S. / Baker, T.S. / Johnson, J.E.
#3: Journal: Virology / Year: 1967
Title: A Study of the Self-Assembly Process in a Small Spherical Virus: Formation of Organized Structures from Protein Subunits in Vitro
Authors: Bancroft, J.B. / Hills, G.J. / Markham, R.
History
DepositionMay 22, 1995Processing site: NDB
Revision 1.0May 22, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA (5'-R(*AP*UP*AP*U)-3')
E: RNA (5'-R(*AP*U)-3')
F: RNA (5'-R(*AP*UP*AP*U)-3')
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)64,0516
Polymers64,0516
Non-polymers00
Water0
1
D: RNA (5'-R(*AP*UP*AP*U)-3')
E: RNA (5'-R(*AP*U)-3')
F: RNA (5'-R(*AP*UP*AP*U)-3')
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,843,045360
Polymers3,843,045360
Non-polymers00
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
D: RNA (5'-R(*AP*UP*AP*U)-3')
E: RNA (5'-R(*AP*U)-3')
F: RNA (5'-R(*AP*UP*AP*U)-3')
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 320 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)320,25430
Polymers320,25430
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
D: RNA (5'-R(*AP*UP*AP*U)-3')
E: RNA (5'-R(*AP*U)-3')
F: RNA (5'-R(*AP*UP*AP*U)-3')
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 384 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)384,30436
Polymers384,30436
Non-polymers00
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
D: RNA (5'-R(*AP*UP*AP*U)-3')
E: RNA (5'-R(*AP*U)-3')
F: RNA (5'-R(*AP*UP*AP*U)-3')
A: Coat protein
B: Coat protein
C: Coat protein
x 60


  • crystal asymmetric unit, crystal frame
  • 3.84 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)3,843,045360
Polymers3,843,045360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)381.300, 381.300, 408.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.60429271, -0.76665636, -0.21476661), (0.31715375, 0.48056874, -0.81800351), (0.73063516, 0.42682884, 0.53317254)1.03963, 2.706, 1.16656
3generate(-0.0348943, -0.92338452, 0.38283803), (-0.25359424, -0.36134911, -0.89735796), (0.96644247, -0.12745208, -0.22179058)-0.65725, 3.38189, 3.70313
4generate(-0.03422631, -0.25359149, 0.96694463), (-0.92348966, -0.36225171, -0.1283982), (0.38154424, -0.89684537, -0.22155598)-2.7456, 1.09361, 4.10425
5generate(0.60537354, 0.31709153, 0.73033771), (-0.76675979, 0.47910832, 0.42619952), (-0.21575005, -0.81807565, 0.53355213)-2.3394, -0.99651, 1.81559
6generate(0.80796932, -0.27946529, 0.51900697), (-0.2803258, -0.95666888, -0.08047208), (0.51799738, -0.080069, -0.85130044)-0.09423, 4.40275, 2.69898
7generate(0.77882124, -0.53220996, 0.33179901), (-0.53160569, -0.27917941, 0.79985762), (-0.33436218, -0.79896422, -0.49964184)0.59497, 1.42869, 2.02774
8generate(0.54426764, -0.71123034, 0.44499093), (0.17461586, 0.61479629, 0.769003), (-0.82050302, -0.34087789, 0.45897006)0.35156, 1.05364, -1.06474
9generate(0.42845362, -0.56912636, 0.70215534), (0.86236468, 0.48981418, -0.1303959), (-0.26859503, 0.66113026, 0.69976619)-0.48808, 3.79591, -2.30476
10generate(0.59143022, -0.30228088, 0.74789976), (0.58119526, -0.48140471, -0.65540037), (0.55864371, 0.82231902, -0.11002551)-0.7636, 5.86577, 0.02135
11generate(-0.82731305, 0.41585836, -0.37767927), (0.41581303, 0.00134566, -0.90941421), (-0.3776585, -0.90946332, -0.17403261)-5.9253, 4.2877, 2.0119
12generate(-0.64399397, 0.67290894, -0.36386258), (-0.41275043, -0.70630323, -0.5752782), (-0.64381032, -0.22180749, 0.73226321)-6.10067, 3.66274, -1.04475
13generate(-0.44159606, 0.66179403, -0.606135), (-0.89374727, -0.26853484, 0.359681), (0.07562029, 0.69953859, 0.7101309)-5.37376, 0.65127, -1.46006
14generate(-0.49982637, 0.39787405, -0.76968428), (-0.36245621, 0.70966981, 0.60338155), (0.78640468, 0.58130596, -0.20984344)-4.74913, -0.58495, 1.33993
15generate(-0.73821258, 0.24587745, -0.62849087), (0.44689657, 0.87646513, -0.18096243), (0.50626299, -0.41311191, -0.75628654)-5.09, 1.66248, 3.48572
16generate(-0.98065627, -0.13639307, -0.14132769), (-0.13548723, -0.04467678, 0.98988629), (-0.14033888, 0.98953231, 0.02533305)-5.03576, 1.79995, -2.42636
17generate(-0.73911999, 0.62595738, 0.24683019), (0.62720237, 0.5049139, 0.59342408), (0.24753734, 0.59394287, -0.76579391)-6.58923, 2.69297, 0.13497
18generate(-0.06777728, 0.97282084, -0.22169396), (0.97272566, 0.01508766, -0.23132605), (-0.22155974, -0.23120862, -0.94731039)-5.37585, 5.40359, 1.10618
19generate(0.10559906, 0.42484379, -0.89941569), (0.42358119, -0.83723228, -0.34458745), (-0.89935389, -0.34559085, -0.26836678)-3.07248, 6.18583, -0.85491
20generate(-0.45859118, -0.2606881, -0.84974661), (-0.26133204, -0.87416874, 0.41016328), (-0.84915664, 0.40886854, 0.33275992)-2.86229, 3.95866, -3.03814
21generate(-0.34454072, -0.86142677, 0.37398978), (0.77002286, -0.48591804, -0.41238419), (0.5379179, 0.14573959, 0.83045877)-1.67049, 6.2607, 1.20132
22generate(-0.2081581, 0.00979918, 0.97804704), (0.00990608, -0.99987741, 0.01223554), (0.9780441, 0.01210346, 0.20803551)-3.92343, 5.26527, 3.12371
23generate(0.59191499, 0.58175359, 0.55815747), (-0.30218899, -0.48288191, 0.82229938), (0.74686163, -0.65521163, -0.10903308)-2.97236, 2.58417, 4.41595
24generate(0.95000472, 0.06401491, -0.30540582), (0.26504243, 0.35059825, 0.89832665), (0.16385682, -0.93399891, 0.31743102)-0.13164, 1.92259, 3.29221
25generate(0.37124326, -0.82791961, -0.41922772), (0.92770579, 0.34872182, 0.13525023), (0.03472249, -0.43898384, 0.89806891)0.67296, 4.19481, 1.30546
26generate(0.15682754, 0.89044237, -0.4278759), (0.54475628, 0.2826872, 0.7898129), (0.82394206, -0.35624791, -0.43951474)-4.42128, 2.93575, 4.03368
27generate(0.0645557, 0.12505617, -0.99019798), (0.99591263, 0.05532469, 0.07287197), (0.06379189, -0.99047959, -0.1198804)-2.34784, 5.18841, 3.41354
28generate(-0.64480089, -0.41203901, -0.64410716), (0.672612, -0.70583158, -0.22029125), (-0.36317417, -0.57606841, 0.73259848)-3.09746, 6.45851, 0.65977
29generate(-0.99093553, 0.02140412, 0.13211081), (0.02164486, -0.94888952, 0.31546486), (0.13309644, 0.31428348, 0.93982505)-5.63418, 4.99081, -0.42202
30generate(-0.49550192, 0.82638189, 0.26574908), (-0.05737432, -0.33795132, 0.93974356), (0.86677462, 0.45014002, 0.21541924)-6.45235, 2.81362, 1.66317
31generate(-0.21438986, -0.48456932, 0.84843322), (-0.68336062, 0.69461485, 0.2228474), (-0.69805589, -0.53137801, -0.480225)-2.57009, -1.21506, 0.30969
32generate(0.33665794, 0.29363025, 0.89478447), (-0.02982999, 0.95283065, -0.30261823), (-0.94122788, 0.07483144, 0.3285454)-3.11447, 0.2141, -2.41415
33generate(0.95032687, 0.26492839, 0.16458105), (0.06306425, 0.35160379, -0.93436005), (-0.30499726, 0.89779265, 0.31610333)-0.92609, 2.40842, -2.80692
34generate(0.77854733, -0.5310099, -0.33306074), (-0.53305458, -0.27819064, -0.79933235), (0.33138689, 0.80020119, -0.5003567)0.97079, 2.33544, -0.32581
35generate(0.05871281, -0.99422496, 0.08958314), (-0.99437052, -0.06619814, -0.08413881), (0.0884633, -0.08307486, -0.99251466)-0.04526, 0.096, 1.60035
36generate(0.40210304, 0.45555371, -0.7945471), (-0.63141851, -0.49138401, -0.60027611), (-0.66380406, 0.74188633, 0.08928097)-2.39343, 2.50901, -3.26017
37generate(-0.19305555, -0.42848559, -0.88263354), (-0.97598872, -0.00827793, 0.21751072), (-0.10060811, 0.90354469, -0.41670051)-1.66955, -0.17738, -1.83858
38generate(-0.89744097, -0.43464297, -0.07863135), (-0.43348726, 0.83710969, 0.33235192), (-0.0786902, 0.33348738, -0.93966872)-4.05939, -0.9607, 0.01571
39generate(-0.73761652, 0.44559087, 0.50635575), (0.24636728, 0.8764819, -0.41445916), (-0.62834015, -0.18048576, -0.75689938)-6.26027, 1.24156, -0.25986
40generate(0.06554585, 0.99576268, 0.06389549), (0.12403904, 0.05542764, -0.99085498), (-0.98996041, 0.07191868, -0.12097349)-5.23065, 3.38596, -2.28447
41generate(-0.3434342, 0.76988453, 0.53696717), (-0.86130107, -0.48730266, 0.14589753), (0.37360683, -0.41316366, 0.83073686)-6.03879, 1.43679, 2.21282
42generate(0.42896408, 0.86247152, -0.2697139), (-0.56842996, 0.48841279, 0.66138256), (0.70169703, -0.13039914, 0.70065712)-3.68612, -0.60709, 2.45232
43generate(0.33569348, -0.02951285, -0.94143594), (0.29463322, 0.95280351, 0.07518742), (0.89459856, -0.30156558, 0.32953699)-1.22094, 0.89515, 3.64632
44generate(-0.49434918, -0.67337651, -0.54990192), (0.53516448, 0.26409731, -0.80258613), (0.68572804, -0.69011677, 0.23025187)-2.05006, 3.86746, 4.14476
45generate(-0.91407317, -0.17932176, 0.36380144), (-0.17924219, -0.62593725, -0.75888487), (0.36373745, -0.75908818, 0.54001042)-5.02765, 4.20221, 3.2588
46generate(-0.21515521, -0.68354106, -0.69731933), (-0.48372679, 0.69520917, -0.53200963), (0.8480028, 0.22433441, -0.48005397)-1.16756, -0.23374, 2.60069
47generate(-0.85629035, -0.46117436, 0.23355562), (-0.46052932, 0.47787097, -0.7484481), (0.2328461, -0.74721951, -0.62158061)-4.05437, 0.52397, 3.52934
48generate(-0.49306925, 0.53454274, 0.68567027), (-0.67357844, 0.26325835, -0.69104578), (-0.55042492, -0.80291182, 0.2298109)-5.92008, 0.4652, 1.02432
49generate(0.37254889, 0.92756305, 0.03421753), (-0.82844751, 0.34795866, -0.43913072), (-0.41935634, 0.13422236, 0.89752644)-4.18633, -0.32884, -1.45251
50generate(0.54430921, 0.17474587, -0.82051704), (-0.71111274, 0.61491895, -0.34084097), (0.44491952, 0.76909545, 0.45880583)-1.24912, -0.76081, -0.47826
51generate(0.4014654, -0.63013592, -0.66388575), (0.45483938, -0.49152345, 0.7430646), (-0.79462347, -0.60071315, 0.09005805)0.37752, 4.74438, -0.10107
52generate(-0.44230563, -0.89397521, 0.07526637), (0.66187674, -0.26775491, 0.70056522), (-0.60490403, 0.35895854, 0.71006054)-1.68473, 4.75401, -2.44766
53generate(-0.4958174, -0.05839426, 0.8663973), (0.8269054, -0.33708521, 0.45039756), (0.26710115, 0.93933209, 0.21486862)-4.47586, 5.53482, -1.27686
54generate(0.31488153, 0.72186246, 0.61619098), (0.72186136, -0.60370223, 0.33828482), (0.61631054, 0.33835097, -0.7111793)-4.13863, 6.00776, 1.79332
55generate(0.8694328, 0.36850669, -0.32957596), (0.49191192, -0.69915031, 0.51916299), (-0.03987136, -0.61344933, -0.78831648)-1.13908, 5.51924, 2.52
56generate(0.157124, 0.54379244, 0.82423792), (0.89018848, 0.28361693, -0.3569525), (-0.42698616, 0.7895424, -0.44074093)-4.22646, 4.54298, -2.42792
57generate(0.8696319, 0.49267805, -0.0391081), (0.36708254, -0.69852885, -0.61349968), (-0.32963911, 0.51866011, -0.78913704)-1.63008, 5.8195, -1.24947
58generate(0.65319316, -0.44663562, -0.61063163), (-0.44796018, -0.87897665, 0.1654608), (-0.61127478, 0.16514531, -0.77421651)0.56158, 3.59522, -1.10926
59generate(-0.19308124, -0.97604901, -0.10050659), (-0.42857834, -0.00835374, 0.90343203), (-0.88268225, 0.21754344, -0.41659901)-0.68028, 0.94402, -2.20105
60generate(-0.49966884, -0.3639308, 0.78629156), (0.39844302, 0.7101686, 0.58056285), (-0.76878561, 0.60344206, -0.21049976)-3.63945, 1.52976, -3.01602
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW WILL GENERATE THE ADDITIONAL CHAINS OF THE FULL ASYMMETRIC UNIT WHEN APPLIED TO THE COORDINATES PRESENTED IN THIS ENTRY.

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Components

#1: RNA chain RNA (5'-R(*AP*UP*AP*U)-3')


Mass: 1225.786 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*AP*U)-3')


Mass: 590.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Coat protein / CCMV


Mass: 20336.252 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: COWPEA PLANT / Source: (natural) Cowpea chlorotic mottle virus / Genus: Bromovirus / Variant: CALIFORNIA BLACKEYE / References: UniProt: P03601

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 25 %
Crystal grow
*PLUS
Method: other / Details: Speir, J.A., (1993) Virology, 193, 234.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.19→30 Å / Num. obs: 633883 / % possible obs: 65 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.131
Reflection
*PLUS
Highest resolution: 3.19 Å / Lowest resolution: 30 Å / % possible obs: 65 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
PURDUEDATA PROCESSING PACKAGEdata reduction
RefinementResolution: 3.2→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.31 --
obs0.31 552678 57 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 210 0 0 3784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.97
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 7 Å / σ(F): 1 / Rfactor obs: 0.31 / Rfactor Rwork: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.103
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.539
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.969

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