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- PDB-4qpi: Crystal structure of hepatitis A virus -

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Basic information

Entry
Database: PDB / ID: 4qpi
TitleCrystal structure of hepatitis A virus
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
KeywordsVIRUS / evolution / insect picorna-like viruses / ICOSAHEDRAL / domain swap / beta-barrel / PICORNAVIRUS / pathogen / liver
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman hepatitis A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. ...Wang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
CitationJournal: Nature / Year: 2015
Title: Hepatitis A virus and the origins of picornaviruses.
Authors: Wang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,33313
Polymers83,5543
Non-polymers77910
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,059,998780
Polymers5,013,270180
Non-polymers46,728600
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: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 422 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)421,66665
Polymers417,77215
Non-polymers3,89450
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 506 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)506,00078
Polymers501,32718
Non-polymers4,67360
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
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.06 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,059,998780
Polymers5,013,270180
Non-polymers46,728600
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)291.479, 423.261, 314.827
Angle α, β, γ (deg.)90.00, 100.152, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.3186, -0.2471, -0.9151), (0.07693, 0.969, -0.2349), (0.9448, 0.00445, 0.3278)236.8, 8.38, -126.9
3generate(-0.7804, -0.324, -0.5348), (-0.1234, 0.9183, -0.3762), (0.613, -0.2276, -0.7566)425.7, 64.75, 54.81
4generate(-0.7795, -0.1266, 0.6135), (-0.3241, 0.9196, -0.2221), (-0.536, -0.3719, -0.7578)306, 90.61, 294.2
5generate(0.3213, 0.0751, 0.944), (-0.246, 0.9692, 0.006628), (-0.9145, -0.2344, 0.3299)42.85, 50.48, 260
6generate(-0.1693, 0.2813, -0.9446), (0.8665, 0.4991, -0.00667), (0.4695, -0.8196, -0.3282)277.5, -114.3, 109.9
7generate(-0.9244, 0.31, -0.2224), (0.3089, 0.2661, -0.9131), (-0.2238, -0.9128, -0.3417)359.4, 95.72, 255.7
8generate(-0.4821, 0.5255, 0.7011), (-0.7429, 0.179, -0.645), (-0.4644, -0.8318, 0.3041)171.5, 286.7, 238.6
9generate(0.5482, 0.6324, 0.5474), (-0.8331, 0.3547, 0.4245), (0.07432, -0.6887, 0.7212)-26.78, 194.4, 83.21
10generate(0.7399, 0.4823, -0.4691), (0.1607, 0.5504, 0.8193), (0.6533, -0.6815, 0.3297)39.09, -53.31, 3.345
11generate(-0.1682, 0.8671, 0.4689), (0.2807, 0.4982, -0.8204), (-0.9449, -0.006352, -0.3272)94.22, 68.99, 298.2
12generate(0.4541, 0.8845, 0.1067), (-0.6467, 0.4096, -0.6434), (-0.6128, 0.2232, 0.7581)2.584, 243.6, 116.2
13generate(0.3112, 0.7457, -0.5892), (-0.7828, 0.5526, 0.2859), (0.5388, 0.3723, 0.7557)104.7, 175.4, -123.1
14generate(-0.4001, 0.6441, -0.652), (0.05769, 0.7277, 0.6834), (0.9147, 0.2358, -0.3283)259.2, -40.81, -88.61
15generate(-0.6952, 0.7188, -0.000672), (0.7188, 0.6952, -0.0026), (-0.001402, -0.002291, -1)252.7, -107.1, 171.7
16generate(-0.9882, -0.05879, 0.1416), (-0.05431, -0.7294, -0.6819), (0.1434, -0.6815, 0.7176)379.6, 252.3, 68.81
17generate(-0.1861, 0.1903, 0.9639), (-0.716, -0.6981, -0.000367), (0.6729, -0.6902, 0.2661)127.3, 319.2, 5.843
18generate(0.8653, 0.2349, 0.4428), (-0.2824, -0.5014, 0.8178), (0.4141, -0.8327, -0.3675)-37.35, 144, 125.5
19generate(0.7125, 0.01841, -0.7014), (0.6448, -0.4114, 0.6442), (-0.2767, -0.9113, -0.305)113.4, -30.83, 262.6
20generate(-0.4337, -0.1624, -0.8863), (0.7835, -0.5538, -0.2819), (-0.445, -0.8167, 0.3674)371.1, 36.47, 227.6
21generate(0.1851, -0.4251, 0.886), (-0.9411, 0.1829, 0.2844), (-0.2829, -0.8865, -0.3662)126.9, 245.5, 266.4
22generate(0.8642, -0.451, 0.2232), (-0.02101, 0.4109, 0.9114), (-0.5028, -0.7923, 0.3456)54.72, -11.01, 238
23generate(0.455, -0.6449, -0.6141), (0.8842, 0.409, 0.2257), (0.1056, -0.6457, 0.7563)227, -128, 68.47
24generate(-0.4828, -0.7424, -0.4644), (0.5257, 0.1784, -0.8317), (0.7004, -0.6457, 0.3042)406.5, 56.26, -8.118
25generate(-0.6485, -0.6043, 0.4629), (-0.6042, 0.03871, -0.7959), (0.463, -0.7958, -0.3902)344.5, 287.5, 113.6
26generate(-0.03204, 0.9611, 0.2744), (-0.3055, -0.2708, 0.9129), (0.9517, -0.05457, 0.3023)74.53, 116.1, -119
27generate(0.3214, 0.9412, -0.1044), (0.7429, -0.1822, 0.6441), (0.5871, -0.2846, -0.7578)40.31, -74.03, 67.14
28generate(0.07528, 0.8323, -0.5492), (0.8319, -0.3561, -0.4256), (-0.5498, -0.4248, -0.7192)137.7, 18.53, 299.5
29generate(-0.4323, 0.7844, -0.4447), (-0.1621, -0.5527, -0.8174), (-0.887, -0.2813, 0.3661)232.4, 265.9, 256.8
30generate(-0.4988, 0.8643, 0.06507), (-0.8658, -0.5003, 0.008467), (0.03987, -0.05212, 0.9978)193.4, 326.5, -1.679
31generate(-0.6179, 0.606, 0.501), (0.606, -0.03894, 0.7945), (0.5009, 0.7945, -0.3432)206.9, -75.51, -66.65
32generate(0.3237, 0.7421, 0.587), (0.9403, -0.1835, -0.2866), (-0.105, 0.6447, -0.7572)1.972, -32.87, 102.5
33generate(0.7146, 0.6426, -0.2765), (0.01814, -0.4121, -0.9109), (-0.6993, 0.6459, -0.3062)10.46, 223.8, 179.2
34generate(0.01683, 0.451, -0.8924), (-0.8846, -0.4092, -0.2235), (-0.466, 0.7932, 0.3921)219.9, 340.1, 57.92
35generate(-0.804, 0.4267, -0.4142), (-0.5236, -0.1777, 0.8332), (0.2819, 0.8868, 0.3662)340.9, 155.4, -94.99
36generate(0.8653, -0.2817, 0.4147), (0.2363, -0.5003, -0.833), (0.4421, 0.8188, -0.3663)21, 184.5, -56.22
37generate(0.6476, -0.4841, -0.5885), (-0.7486, -0.5485, -0.3726), (-0.1424, 0.6818, -0.7176)170.6, 341.5, 101.7
38generate(-0.3859, -0.6333, -0.6708), (-0.6333, -0.3469, 0.6918), (-0.6709, 0.6918, -0.2672)394.1, 207, 164.7
39generate(-0.8064, -0.5203, 0.2811), (0.4246, -0.1786, 0.8876), (-0.4116, 0.8351, 0.3649)382.7, -33.41, 45.23
40generate(-0.03339, -0.3046, 0.9519), (0.9605, -0.2731, -0.05369), (0.2763, 0.9125, 0.3017)152.2, -47.05, -91.24
41generate(-0.1982, -0.2334, -0.952), (-0.8623, 0.5034, 0.05606), (0.4661, 0.832, -0.301)339.7, 215.6, -67.9
42generate(-0.9802, -0.1829, -0.07622), (-0.1841, 0.6984, 0.6916), (-0.07324, 0.6919, -0.7182)411.3, 8.569, 87.78
43generate(-0.4, 0.05902, 0.9146), (0.6452, 0.7269, 0.2353), (-0.6509, 0.6842, -0.3288)187.5, -116.5, 167.7
44generate(0.7396, 0.1598, 0.6538), (0.4828, 0.5509, -0.6808), (-0.4689, 0.8191, 0.3303)-22.4, 12.52, 61.23
45generate(0.8656, -0.02014, -0.5003), (-0.449, 0.4112, -0.7933), (0.2217, 0.9113, 0.3469)71.56, 217.9, -84.39
46generate(0.6472, -0.7486, -0.1438), (-0.4842, -0.5494, 0.6809), (-0.5888, -0.3711, -0.7181)160.2, 199.9, 300.7
47generate(0.01704, -0.8856, -0.4641), (0.4462, -0.4086, 0.7962), (-0.8948, -0.2206, 0.3882)324.7, -5.515, 249.2
48generate(-0.4999, -0.8652, 0.03856), (0.8636, -0.5013, -0.05431), (0.06632, 0.006145, 0.9978)380.2, -3.995, -14.14
49generate(-0.1893, -0.7177, 0.6702), (0.1863, -0.6964, -0.6931), (0.9641, -0.006339, 0.2655)249.8, 203.2, -124.7
50generate(0.5207, -0.6457, 0.5585), (-0.6451, -0.7261, -0.238), (0.5592, -0.2364, -0.7946)113.6, 328.8, 69.86
51generate(-0.8268, -0.0711, -0.558), (-0.07651, -0.9686, 0.2368), (-0.5573, 0.2384, 0.7953)410.5, 203.5, 100.4
52generate(-0.7975, 0.1321, 0.5886), (0.1255, -0.9181, 0.3761), (0.5901, 0.3738, 0.7156)285.3, 147, -129.8
53generate(0.3086, 0.3239, 0.8944), (0.3259, -0.9193, 0.2205), (0.8936, 0.2234, -0.3892)23.2, 121.5, -77.88
54generate(0.9676, 0.2434, -0.06699), (0.2434, -0.9699, -0.008201), (-0.06697, -0.008367, -0.9977)-14.08, 162.4, 184.9
55generate(0.2659, -0.002072, -0.964), (-0.001462, -1, 0.001746), (-0.964, 0.000945, -0.2659)225.2, 212.3, 295.3
56generate(0.3113, -0.7855, 0.5349), (0.747, 0.5502, 0.3732), (-0.5875, 0.2834, 0.758)171.6, -129.3, 104.1
57generate(0.5458, -0.8343, 0.07778), (0.6329, 0.3496, -0.6908), (0.5492, 0.4263, 0.7188)170.5, 4.943, -128.4
58generate(0.1828, -0.9425, -0.2798), (-0.4226, 0.1816, -0.8879), (0.8877, 0.2805, -0.3651)282.9, 245, -86.11
59generate(-0.2774, -0.9599, -0.03978), (-0.96, 0.2753, 0.05163), (-0.03861, 0.05251, -0.9979)353.6, 259.1, 172.4
60generate(-0.1956, -0.8637, 0.4646), (-0.2386, 0.5014, 0.8317), (-0.9512, 0.05181, -0.3041)284.2, 28.05, 290.1

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Components

#1: Protein Capsid protein VP1 / / HAV


Mass: 30820.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: Q8QXR6*PLUS
#2: Protein Capsid protein VP2 / / HAV


Mass: 24898.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: P08617*PLUS
#3: Protein Capsid protein VP3 / / HAV


Mass: 27835.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: P08617*PLUS
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 32

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% MPD and 0.5 M ammonium sulphate as precipitants and 0.1 M HEPES-Na buffer at pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 654559 / % possible obs: 44.9 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.41 / Net I/σ(I): 1.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 6711 / % possible all: 9.1

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QPG

4qpg


Resolution: 3.01→49.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 20281281.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.321 6633 1 %RANDOM
Rwork0.318 ---
obs0.318 650017 44 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: -11.0715 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-15.33 Å20 Å2-25.74 Å2
2---20.21 Å2-0 Å2
3---4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.61 Å
Luzzati d res low-6 Å
Luzzati sigma a1.08 Å1.03 Å
Refinement stepCycle: LAST / Resolution: 3.01→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5729 0 38 0 5767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.726
X-RAY DIFFRACTIONc_mcangle_it10.2412
X-RAY DIFFRACTIONc_scbond_it11.438
X-RAY DIFFRACTIONc_scangle_it15.4616
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.01→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 247 1 %
Rwork0.414 24173 -
obs--9.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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