[English] 日本語
Yorodumi
- PDB-1cwp: STRUCTURES OF THE NATIVE AND SWOLLEN FORMS OF COWPEA CHLOROTIC MO... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

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

-
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

-
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

+
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