[English] 日本語
Yorodumi
- PDB-1c8g: FELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c8g
TitleFELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE
ComponentsFELINE PANLEUKOPENIA VIRUS CAPSID
KeywordsVIRUS / beta barrel / protein-DNA complex / double complex / Icosahedral virus
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / clathrin-dependent endocytosis of virus by host cell / 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 VP1/VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesFeline panleukopenia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsRossmann, M.G. / Simpson, A.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Host range and variability of calcium binding by surface loops in the capsids of canine and feline parvoviruses.
Authors: Simpson, A.A. / Chandrasekar, V. / Hebert, B. / Sullivan, G.M. / Rossmann, M.G. / Parrish, C.R.
#1: Journal: Protein Sci. / Year: 1993
Title: Structure Determination of Feline Panleukopenia Virus Empty Particles
Authors: Agbandje, M. / McKenna, R. / Rossmann, M.G. / Strassheim, M.L. / Parrish, C.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structural Refinement of the DNA-Containing Capsid of Canine Parvovirus using RSRef, a Resolution-Dependent Stereochemically Restrained Real-Space Refinement Method
Authors: Chapman, M.S. / Rossmann, M.G.
#3: Journal: Virology / Year: 1996
Title: Structural Analysis of a Mutation in Canine Parvovirus which Controls Antigenicity and Host Range
Authors: Llamas-Saiz, A.L. / Agbandje-McKenna, M. / Parker, J.S. / Wahid, A.T. / Parrish, C.R. / Rossmann, M.G.
#4: 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.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Advisory
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7013
Polymers61,6211
Non-polymers802
Water00
1
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,702,039180
Polymers3,697,23060
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: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 5


  • icosahedral pentamer
  • 309 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)308,50315
Polymers308,1035
Non-polymers40110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: FELINE PANLEUKOPENIA VIRUS CAPSID
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 370 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)370,20418
Polymers369,7236
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
Unit cell
Length a, b, c (Å)266.17, 250.12, 379.1
Angle α, β, γ (deg.)90.00, 94.11, 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(0.45393618, 0.52041026, 0.72326696), (-0.84999798, 0.49641118, 0.17629356), (-0.26729284, -0.69480146, 0.66768663)-40.43364, 28.41263, 46.23874
3generate(-0.42961369, -0.00795643, 0.90297769), (-0.85491533, -0.31841263, -0.4095525), (0.29077809, -0.9479188, 0.12999234)-10.55875, 85.03708, 68.17822
4generate(-0.42961372, -0.85491526, 0.29077807), (-0.00795646, -0.31841262, -0.94791884), (0.90297773, -0.40955245, 0.12999236)48.33858, 91.62029, 35.49882
5generate(0.45393613, -0.84999792, -0.26729283), (0.52041028, 0.49641119, -0.69480147), (0.72326699, 0.17629358, 0.66768666)54.86425, 39.06448, -6.63764
6generate(0.17810825, -0.88967211, 0.42042944), (-0.8896722, -0.32814617, -0.31749578), (0.42042943, -0.31749574, -0.84996208)2.56037, 77.91296, 157.6973
7generate(0.72469149, -0.64106881, 0.25269147), (-0.04006647, -0.40529344, -0.91330824), (0.68790764, 0.65174225, -0.31939805)-10.47899, 89.88154, 92.37575
8generate(0.80632826, -0.11666724, 0.57984782), (0.57043173, 0.41252471, -0.71023307), (-0.15634062, 0.90344457, 0.39918101)-46.31122, 37.7559, 68.31028
9generate(0.31019932, -0.04117254, 0.94977955), (0.09813465, 0.99511138, 0.01108675), (-0.94559294, 0.08976716, 0.31272327)-55.4174, -6.42811, 118.75857
10generate(-0.078062, -0.51891582, 0.85125356), (-0.8042592, 0.53735161, 0.25381175), (-0.58912944, -0.66481544, -0.45928961)-25.21309, 18.39032, 174.00278
11generate(-0.72509807, 0.03912104, -0.68753352), (0.03912104, -0.99443272, -0.09784227), (-0.68753351, -0.09784227, 0.71953078)161.12715, 5.13777, 64.71708
12generate(-0.17862827, 0.11977094, -0.97659962), (0.88917679, -0.40530757, -0.2123451), (-0.42125603, -0.90630053, -0.03409815)159.76635, -29.22259, 123.0068
13generate(0.07814719, 0.64503851, -0.76014359), (0.80489846, 0.4090752, 0.42987909), (0.58824445, -0.64543223, -0.48722239)125.23521, -86.50967, 112.71268
14generate(-0.30962665, 0.8890218, -0.3373003), (-0.09724416, 0.3232663, 0.94129831), (0.94587258, 0.32425151, -0.01363963)105.25459, -87.55467, 48.06084
15generate(-0.80605952, 0.51454422, -0.2924248), (-0.57052064, -0.5441493, 0.61514856), (0.15739844, 0.66268072, 0.73217484)127.43703, -30.91344, 18.39792
16generate(-0.45301018, 0.85055107, 0.26710408), (0.85055115, 0.32257889, 0.41533804), (0.26710408, 0.415338, -0.8695687)53.89648, -87.67072, 168.80162
17generate(-1, 0.00088761, 0.0006412), (0.00088765, 0.31418984, 0.94935978), (0.00064123, 0.94935974, -0.31419043)108.73028, -93.69158, 129.59471
18generate(-0.45486176, -0.52041484, -0.72268192), (-0.52041485, -0.50318728, 0.68990648), (-0.72268193, 0.68990646, -0.04195096)149.21876, -40.90331, 142.01482
19generate(0.42904105, 0.00706599, -0.90325732), (0.00706598, -0.99996506, -0.00446621), (-0.90325738, -0.00446622, -0.429076)119.40822, -2.25751, 188.89778
20generate(0.43018539, 0.85436951, -0.29153593), (0.85436956, -0.4896135, -0.17415884), (-0.29153598, -0.17415886, -0.94057188)60.49581, -31.16136, 205.45293
21generate(-0.49203517, 0.5641021, 0.66309137), (-0.38165561, 0.54480637, -0.74667601), (-0.78245792, -0.62046339, -0.05277121)16.95929, 93.26269, 144.81118
22generate(-0.88007778, -0.43675041, 0.18631202), (-0.43675045, 0.59062206, -0.67853862), (0.18631203, -0.67853859, -0.71054428)83.5422, 89.64844, 156.37973
23generate(-0.07806205, -0.80425916, -0.58912941), (-0.51891587, 0.53735161, -0.66481547), (0.85125359, 0.25381176, -0.45928957)115.33256, 92.7142, 96.71272
24generate(0.80565354, -0.03053955, -0.59159923), (-0.51460206, 0.45861296, -0.72447148), (0.29344013, 0.88811117, 0.35376748)68.39717, 98.2232, 48.26793
25generate(0.54980408, 0.81515421, 0.18231577), (-0.42977054, 0.46322026, -0.77506407), (-0.71624912, 0.34777941, 0.60500964)7.59915, 98.56218, 77.99441
26generate(-0.31071835, 0.04211334, -0.94956862), (-0.86659966, 0.39783867, 0.30121332), (0.39046025, 0.91648831, -0.08712032)164.21809, 16.98419, 86.14379
27generate(0.07697034, 0.51896618, -0.85132227), (-0.81205516, -0.46277924, -0.3555304), (-0.57848253, 0.71868589, 0.3858089)134.07125, 77.25534, 92.36756
28generate(-0.17862824, 0.88917673, -0.421256), (0.11977093, -0.40530759, -0.90630056), (-0.97659966, -0.21234512, -0.03409816)106.34018, 80.50163, 154.01679
29generate(-0.72428553, 0.64112658, -0.25370678), (0.64112663, 0.49082976, -0.58995152), (-0.2537068, -0.58995153, -0.76654424)119.34827, 22.2368, 185.89433
30generate(-0.8059217, 0.11761262, -0.58022193), (0.03151609, 0.98720145, 0.1563331), (0.59118269, 0.1077059, -0.79931373)155.11878, -17.01913, 143.94651
31generate(-0.07705552, -0.64508887, 0.76021229), (0.81141591, -0.48364757, -0.32816044), (0.57936752, 0.59156178, 0.5607031)-16.50937, -13.75599, 12.13297
32generate(0.31014665, -0.88852642, 0.33812685), (0.86714543, 0.41018746, 0.28249803), (-0.38970236, 0.20558935, 0.89769987)3.42886, -75.47991, 31.44107
33generate(0.80565356, -0.51460199, 0.29344012), (-0.03053953, 0.45861298, 0.8881112), (-0.59159928, -0.72447144, 0.35376745)-18.72231, -85.8249, 94.548
34generate(0.72469151, -0.04006642, 0.68790763), (-0.64106886, -0.40529344, 0.65174225), (0.25269144, -0.9133082, -0.31939807)-52.35071, -30.49453, 114.24213
35generate(0.17914729, -0.12071175, 0.97638869), (-0.12071178, -0.98764248, -0.09995497), (0.97638872, -0.09995494, -0.1915048)-50.98304, 14.04651, 63.30685
36generate(0.87980903, 0.03887343, -0.47373504), (0.43683935, -0.45899747, 0.77362313), (-0.18736985, -0.8875867, -0.42081157)52.91599, -101.11089, 148.12806
37generate(0.49296079, 0.80631066, 0.32688339), (0.38166018, -0.53803028, 0.75157099), (0.78187286, -0.24573666, -0.57296449)-3.45831, -96.04386, 111.02764
38generate(-0.54896327, 0.42968442, 0.71694529), (0.42968447, -0.590657, 0.68300483), (0.71694534, 0.6830048, 0.13962028)14.63357, -92.01093, 45.93849
39generate(-0.80605952, -0.57052061, 0.15739838), (0.51454428, -0.54414929, 0.66268075), (-0.29242477, 0.61514856, 0.73217483)82.18927, -94.58547, 42.81161
40generate(0.07697033, -0.81205509, -0.57848254), (0.51896624, -0.46277922, 0.71868594), (-0.8513223, -0.35553037, 0.38580889)105.8491, -100.20956, 105.96824
41generate(-0.49203522, -0.38165558, -0.7824579), (0.56410213, 0.54480638, -0.62046339), (0.66309139, -0.74667596, -0.05277117)157.24745, 29.47315, 66.0333
42generate(0.31019927, 0.09813462, -0.94559291), (-0.04117253, 0.99511138, 0.08976718), (0.94977958, 0.01108675, 0.31272333)130.11851, -6.54561, 15.567
43generate(0.31014665, 0.86714535, -0.38970236), (-0.88852649, 0.41018744, 0.20558934), (0.33812689, 0.282498, 0.89769989)76.64127, 27.54359, -8.06111
44generate(-0.49212036, 0.86262991, 0.11699191), (-0.80694537, -0.40162045, -0.4330592), (-0.32658345, -0.30752333, 0.8937408)70.71944, 84.63065, 27.80222
45generate(-0.98789601, 0.0908285, -0.12574437), (0.09082849, -0.31842137, -0.94358786), (-0.12574435, -0.94358782, 0.30631737)120.5368, 85.82318, 73.59508
46generate(-0.07705551, 0.81141587, 0.57936748), (-0.64508892, -0.48364758, 0.59156177), (0.76021234, -0.32816044, 0.5607031)2.86024, -24.48046, 1.23346
47generate(-0.87954091, -0.03984994, 0.4741516), (-0.03984996, -0.98681694, -0.15685756), (0.47415167, -0.15685754, 0.86635785)55.81956, 15.2142, -12.90239
48generate(-0.49212039, -0.8069453, -0.32658347), (0.86262997, -0.40162043, -0.30752332), (0.11699194, -0.43305915, 0.89374081)112.17453, -18.46548, 3.5285
49generate(0.54980404, -0.42977049, -0.7162491), (0.81515428, 0.46322028, 0.34777946), (0.18231576, -0.77506402, 0.60500966)94.0445, -78.97533, 27.81919
50generate(0.80632825, 0.57043171, -0.15634061), (-0.11666724, 0.41252471, 0.9034446), (0.57984782, -0.71023306, 0.39918102)26.48455, -82.6928, 26.40078
51generate(0.87980905, 0.43683931, -0.18736979), (0.0388734, -0.45899748, -0.88758673), (-0.47373508, 0.77362309, -0.42081157)25.36797, 83.00983, 165.62388
52generate(0.07814723, 0.80489838, 0.58824446), (0.64503855, 0.40907519, -0.64543224), (-0.76014363, 0.42987904, -0.48722242)-6.4579, 27.35582, 187.30158
53generate(-0.80592167, 0.03151606, 0.59118267), (0.11761266, 0.98720145, 0.10770591), (-0.58022195, 0.15633307, -0.79931376)40.45129, -16.94651, 207.7224
54generate(-0.55064448, -0.81451957, -0.18261568), (-0.81451961, 0.47643045, 0.3310164), (-0.18261569, 0.3310164, -0.92578596)101.26863, 11.32716, 198.66546
55generate(0.4911944, -0.56401603, -0.66378756), (-0.86318315, -0.41736964, -0.28410828), (-0.11680318, 0.71252261, -0.69185873)91.94663, 73.10357, 172.64714
56generate(-0.31071832, -0.86659961, 0.39046021), (0.04211338, 0.39783869, 0.91648834), (-0.94956864, 0.30121331, -0.08712036)32.10834, -92.62252, 158.32536
57generate(0.49119441, -0.86318306, -0.11680316), (-0.56401606, -0.41736963, 0.71252262), (-0.66378762, -0.28410825, -0.69185875)38.10383, -40.64441, 201.2498
58generate(0.98789541, -0.09171611, 0.12510316), (-0.09171614, -0.99576847, -0.00577192), (0.12510311, -0.00577192, -0.99212694)-11.68308, 3.2484, 188.02621
59generate(0.4929608, 0.38166015, 0.78187287), (0.8063107, -0.53803028, -0.24573666), (0.32688337, 0.75157095, -0.5729645)-48.44857, -21.60247, 136.92914
60generate(-0.30962663, -0.09724418, 0.94587254), (0.88902189, 0.3232663, 0.32425154), (-0.33730029, 0.94129827, -0.01363967)-21.38398, -80.85396, 118.573

-
Components

#1: Protein FELINE PANLEUKOPENIA VIRUS CAPSID


Mass: 61620.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Feline panleukopenia virus / Genus: Parvovirus / References: UniProt: P24840
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Source detailsVIRUS GROWN IN A CELL CULTURE OF NORDEN LABORATORY FELINE KIDNEY CELLS

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM bis-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlvirus1drop
220 mMBis-Tris1drop
320 mMTris-HCl1drop
40.75-1.50 %PEG80001reservoir
58 mM1reservoiror 5mM EDTACaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 584157 / Num. obs: 358402 / % possible obs: 37.4 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.15 / Num. unique all: 34921 / % possible all: 36.8
Reflection shell
*PLUS
% possible obs: 36.8 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SnBphasing
GLRFphasing
TRANSFmodel building
ENVELOPEmodel building
CNS0.5refinement
TRANSFphasing
ENVELOPEphasing
RefinementResolution: 3→9 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
Details: restrained least squares with strictly enforced icosahedral symmetry
RfactorNum. reflection% reflection
obs0.245 358402 55.3 %
Rfree-0 -
all-584157 -
Refinement stepCycle: LAST / Resolution: 3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 2 0 4352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010194
X-RAY DIFFRACTIONc_angle_deg1.66476
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.317

+
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