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- PDB-1ohg: STRUCTURE OF THE DSDNA BACTERIOPHAGE HK97 MATURE EMPTY CAPSID -

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Basic information

Entry
Database: PDB / ID: 1ohg
TitleSTRUCTURE OF THE DSDNA BACTERIOPHAGE HK97 MATURE EMPTY CAPSID
ComponentsMAJOR CAPSID PROTEIN
KeywordsVIRUS / VIRUS COAT PROTEIN / VIRUS/VIRAL PROTEIN / BACTERIOPHAGE / CAPSID / AUTO- CATALYTIC CROSS-LINK / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding
Similarity search - Function
Major capsid protein gp5 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / hypothetical protein PF0899 fold / Phage capsid / Phage capsid family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesBACTERIOPHAGE HK97 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsHelgstrand, C. / Wikoff, W.R. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Liljas, L.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Refined Structure of a Protein Catenane: The Hk97 Bacteriophage Capsid at 3.44A Resolution
Authors: Helgstrand, C. / Wikoff, W.R. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Liljas, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Increased Resolution Data from a Large Unit Cell Crystal Collected at a Third-Generation Synchrotron X-Ray Source
Authors: Wikoff, W.R. / Schildkamp, W. / Johnson, J.E.
#2: Journal: Science / Year: 2000
Title: Topologically Linked Protein Rings in the Bacteriophage Hk97 Capsid
Authors: Wikoff, W.R. / Liljas, L. / Duda, R.L. / Tsuruta, H. / Hendrix, R.W. / Johnson, J.E.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallographic Analysis of the DsDNA Bacteriophage Hk97 Mature Empty Capsid
Authors: Wikoff, W.R. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E.
History
SupersessionMay 26, 2003ID: 1FH6
DepositionMay 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,7649
Polymers215,6327
Non-polymers1322
Water0
1
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)12,945,826540
Polymers12,937,935420
Non-polymers7,891120
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 1.08 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,078,81945
Polymers1,078,16135
Non-polymers65810
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.29 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,294,58354
Polymers1,293,79342
Non-polymers78912
Water0
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: MAJOR CAPSID PROTEIN
B: MAJOR CAPSID PROTEIN
C: MAJOR CAPSID PROTEIN
D: MAJOR CAPSID PROTEIN
E: MAJOR CAPSID PROTEIN
F: MAJOR CAPSID PROTEIN
G: MAJOR CAPSID PROTEIN
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 12.9 MDa, 420 polymers
Theoretical massNumber of molelcules
Total (without water)12,945,826540
Polymers12,937,935420
Non-polymers7,891120
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)579.700, 626.650, 787.200
Angle α, β, γ (deg.)90.00, 89.90, 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(0.72852, -0.599085, 0.332199), (0.59313, 0.309038, -0.743433), (0.342717, 0.738642, 0.580476)-77.82879, 180.45061, 98.34317
3generate(0.289256, -0.376209, 0.880226), (0.36062, -0.808962, -0.464257), (0.886727, 0.451716, -0.098329)-209.9644, 116.94261, 262.04422
4generate(0.289256, 0.36062, 0.886727), (-0.376209, -0.808962, 0.451716), (0.880226, -0.464257, -0.098329)-213.79991, -102.7581, 264.87387
5generate(0.72852, 0.59313, 0.342717), (-0.599085, 0.309038, 0.738642), (0.332199, -0.743433, 0.580476)-84.03478, -175.03261, 102.92163
6generate(-0.345888, 0.571437, 0.744192), (0.571437, -0.500788, 0.650131), (0.744192, 0.650131, -0.153324)146.84574, -632.4387, 356.55516
7generate(0.341997, 0.933504, -0.107743), (0.342082, -0.016887, 0.939518), (0.875224, -0.35817, -0.32511)350.06811, -703.34454, 400.87389
8generate(0.765916, 0.004019, -0.642928), (0.561186, 0.483813, 0.671561), (0.313756, -0.875162, 0.368305)481.30636, -640.62047, 236.15191
9generate(0.340026, -0.932501, -0.121756), (0.925955, 0.309362, 0.216568), (-0.164283, -0.186379, 0.968645)359.1937, -530.94903, 90.02939
10generate(-0.347106, -0.581817, 0.735531), (0.932291, -0.299155, 0.203323), (0.101741, 0.756304, 0.646261)152.48566, -525.89241, 164.44269
11generate(-0.38008, -0.911827, 0.155275), (-0.911827, 0.341187, -0.228391), (0.155275, -0.228391, -0.961107)509.24708, 531.77345, 1089.63179
12generate(-0.764512, 0.060603, 0.641754), (-0.54019, 0.483002, -0.689133), (-0.351732, -0.873519, -0.336524)389.55868, 641.84653, 941.81528
13generate(-0.301077, 0.950763, 0.073498), (-0.343233, -0.036137, -0.938555), (-0.889687, -0.307804, 0.337214)523.10778, 703.27545, 778.46827
14generate(0.369775, 0.528482, -0.764182), (-0.593145, -0.498798, -0.631965), (-0.715154, 0.686955, 0.129023)725.33407, 631.16753, 825.33078
15generate(0.320949, -0.622663, -0.713641), (-0.944555, -0.265599, -0.193059), (-0.069332, 0.736035, -0.673383)716.76769, 525.17346, 1017.64041
16generate(-0.274032, 0.34039, -0.899467), (0.34039, -0.840398, -0.42174), (-0.899467, -0.42174, 0.114431)1085.47313, 100.66176, 914.18888
17generate(-0.306005, -0.395022, -0.866209), (-0.395022, -0.775153, 0.493047), (-0.866209, 0.493047, 0.081158)1079.76795, -118.95609, 919.34349
18generate(-0.754095, -0.578573, -0.310796), (-0.578573, 0.361285, 0.73125), (-0.310796, 0.73125, -0.60719)947.1162, -179.60108, 1083.71143
19generate(-0.999058, 0.043399, -0.000789), (0.043399, 0.998397, -0.036319), (-0.000789, -0.036319, -0.99934)870.83809, 2.53611, 1180.14179
20generate(-0.702362, 0.61135, -0.364608), (0.61135, 0.255716, -0.748906), (-0.364608, -0.748906, -0.553354)956.34737, 175.74807, 1075.37109
21generate(-0.361584, -0.926595, 0.103338), (0.609969, -0.318929, -0.725412), (0.705121, -0.199265, 0.680513)531.84219, 162.48498, -118.4766
22generate(-0.777597, 0.006597, 0.628728), (0.006597, -0.999804, 0.018649), (0.628728, 0.018649, 0.777401)402.94189, -13.87839, -142.38885
23generate(-0.347106, 0.932291, 0.101741), (-0.581817, -0.299155, 0.756304), (0.735531, 0.203323, 0.646261)526.48283, -192.97313, -111.50472
24generate(0.334964, 0.57121, -0.749345), (-0.342105, 0.814746, 0.468139), (0.877931, 0.099545, 0.468324)731.73564, -127.2964, -68.50502
25generate(0.326016, -0.577645, -0.748358), (0.394459, 0.802524, -0.447612), (0.859136, -0.149268, 0.489493)735.0479, 92.38879, -72.81388
26generate(-0.327519, 0.324589, -0.887341), (-0.933074, 0.036662, 0.357811), (0.148672, 0.945145, 0.290858)1101.60524, 195.10992, 353.7306
27generate(-0.350188, -0.358905, -0.865191), (-0.53539, 0.834615, -0.129521), (0.768587, 0.417858, -0.484426)1098.40399, 309.53377, 541.31539
28generate(-0.764512, -0.54019, -0.351732), (0.060603, 0.483002, -0.873519), (0.641754, -0.689133, -0.336524)975.8084, 489.07176, 509.25997
29generate(-0.99791, 0.031264, -0.056547), (0.031264, -0.532259, -0.846004), (-0.056547, -0.846004, 0.530169)903.24141, 485.6085, 301.86383
30generate(-0.727834, 0.565726, -0.387571), (-0.582863, -0.808113, -0.085001), (-0.361288, 0.164035, 0.917912)980.98813, 303.93009, 205.74139
31generate(0.998371, -0.010041, 0.056162), (-0.053667, -0.499323, 0.864752), (0.01936, -0.866358, -0.499048)-32.43149, -486.9203, 876.14948
32generate(0.740625, -0.559729, 0.371723), (-0.038895, 0.516584, 0.855353), (-0.670791, -0.647954, 0.360824)-106.42227, -487.80409, 669.22992
33generate(0.334964, -0.342105, 0.877931), (0.57121, 0.814746, 0.099545), (-0.749345, 0.468139, 0.468324)-228.51126, -307.44092, 639.99769
34generate(0.341997, 0.342082, 0.875224), (0.933504, -0.016887, -0.35817), (-0.107743, 0.939518, -0.32511)-229.97563, -195.08655, 828.85073
35generate(0.752006, 0.547309, 0.367343), (0.547309, -0.829026, 0.114754), (0.367343, 0.114754, -0.922979)-108.79167, -306.01091, 974.80057
36generate(-0.309267, 0.612047, 0.727841), (0.376773, 0.78159, -0.497151), (-0.873153, 0.120478, -0.472323)140.55, 129.32191, 1248.97235
37generate(0.38716, 0.912037, -0.13526), (0.567689, -0.351394, -0.74448), (-0.726524, 0.211447, -0.653799)346.64233, 192.14522, 1292.21936
38generate(0.776655, -0.049996, -0.62794), (-0.049996, -0.998593, 0.017671), (-0.62794, 0.017671, -0.778061)467.78597, 11.33879, 1322.62289
39generate(0.320949, -0.944555, -0.069332), (-0.622663, -0.265599, 0.736035), (-0.713641, -0.193059, -0.673383)336.56452, -163.22904, 1298.16628
40generate(-0.350188, -0.53539, 0.768587), (-0.358905, 0.834615, 0.417858), (-0.865191, -0.129521, -0.484426)134.32158, -90.31146, 1252.64775
41generate(-0.361584, 0.609969, 0.705121), (-0.926595, -0.318929, -0.199265), (0.103338, -0.725412, 0.680513)176.73543, 521.01518, 143.53383
42generate(0.340026, 0.925955, -0.164283), (-0.932501, 0.309362, -0.186379), (-0.121756, 0.216568, 0.968645)384.2901, 515.98367, 71.51395
43generate(0.740625, -0.038895, -0.670791), (-0.559729, 0.516584, -0.647954), (0.371723, 0.855353, 0.360824)508.75937, 626.05456, 215.32953
44generate(0.286599, -0.951193, -0.114427), (-0.323437, 0.016363, -0.946108), (0.901804, 0.308163, -0.302961)378.13095, 699.11361, 376.23232
45generate(-0.394604, -0.550173, 0.735933), (-0.550173, -0.500013, -0.668803), (0.735933, -0.668803, -0.105383)172.92886, 634.1957, 331.86014
46generate(0.998371, -0.053667, 0.01936), (-0.010041, -0.499323, -0.866358), (0.056162, 0.864752, -0.499048)-10.71507, 515.60291, 860.12784
47generate(0.702137, -0.600394, 0.382793), (-0.600394, -0.788223, -0.135022), (0.382793, -0.135022, -0.913914)-96.1974, 341.0809, 962.72394
48generate(0.286599, -0.323437, 0.901804), (-0.951193, 0.016363, 0.308163), (-0.114427, -0.946108, -0.302961)-221.54027, 232.29496, 818.68955
49generate(0.326016, 0.394459, 0.859136), (-0.577645, 0.802524, -0.149268), (-0.748358, -0.447612, 0.489493)-213.52408, 339.58356, 627.07531
50generate(0.765916, 0.561186, 0.313756), (0.004019, 0.483813, -0.875162), (-0.642928, 0.671561, 0.368305)-83.22695, 514.6775, 652.68558
51generate(-0.309267, 0.376773, -0.873153), (0.612047, 0.78159, 0.120478), (0.727841, -0.497151, -0.472323)1085.28648, -337.57357, 551.91281
52generate(-0.301077, -0.343233, -0.889687), (0.950763, -0.036137, -0.307804), (0.073498, -0.938555, 0.337214)1091.4766, -232.32181, 359.10495
53generate(-0.727834, -0.582863, -0.361288), (0.565726, -0.808113, 0.164035), (-0.387571, -0.085001, 0.917912)965.4777, -343.1099, 217.18456
54generate(-0.999775, -0.010956, -0.018185), (-0.010956, -0.467493, 0.883929), (-0.018185, 0.883929, 0.467268)881.41597, -516.83246, 322.2808
55generate(-0.741086, 0.582132, -0.334535), (0.017672, 0.514998, 0.857009), (0.671177, 0.629206, -0.391945)955.46187, -513.41081, 529.15423
56generate(-0.327519, -0.933074, 0.148672), (0.324589, 0.036662, 0.945145), (-0.887341, 0.357811, 0.290858)490.25911, -699.04801, 804.80134
57generate(-0.741086, 0.017672, 0.671177), (0.582132, 0.514998, 0.629206), (-0.334535, 0.857009, -0.391945)361.99665, -624.74625, 967.03299
58generate(-0.29939, 0.945195, 0.130276), (0.945195, 0.275166, 0.175756), (0.130276, 0.175756, -0.975776)488.86913, -515.2431, 1109.17219
59generate(0.38716, 0.567689, -0.726524), (0.912037, -0.351394, 0.211447), (-0.13526, -0.74448, -0.653799)695.54311, -521.8682, 1034.7874
60generate(0.369775, -0.593145, -0.715154), (0.528482, -0.498798, 0.686955), (-0.764182, -0.631965, 0.129023)696.40216, -635.46588, 846.67586

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Components

#1: Protein
MAJOR CAPSID PROTEIN / GP5 / HEAD PROTEIN


Mass: 30804.607 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: CLEAVED FORM, RESIDUES 104-385 / Source: (gene. exp.) BACTERIOPHAGE HK97 (virus) / Plasmid: PT7-HD2.9B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49861
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Compound detailsEACH SUBUNIT IS COVALENTLY CROSS-LINKED TO ITS NEIGHBORING SUBUNITS, VIA AN AMINE BOND BETWEEN ...EACH SUBUNIT IS COVALENTLY CROSS-LINKED TO ITS NEIGHBORING SUBUNITS, VIA AN AMINE BOND BETWEEN LYS169 OF ONE SUBUNIT AND ASN356 OF THE NEIGHBOR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 61

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Sample preparation

CrystalDescription: STARTING MODEL WAS A VERY LOW RESOLUTION MODEL BASED UPON A CRYOEM RECONSTRUCTION BETWEEN 200-50 A RESOLUTION
Crystal growpH: 5
Details: 0.85 M AMMONIUM SULFATE, 1.5% PEG 8000, 50 MM CITRATE PH 5.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Wikoff, W.R., (1998) Virology, 243, 113.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMpotassium phosphate1reservoirpH7.0
21.0-1.5 %PEG80001reservoir
30.9 Mammonium sulfate1reservoir
420 mMTris-HCl1droppH7.5
5100 mM1dropKCl
61 mM2-mercaptoethanol1drop
727-30 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3.44→190 Å / Num. obs: 4797606 / % possible obs: 63 % / Redundancy: 1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYO EM RECONSTRUCTION

Resolution: 3.45→190.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 28838671.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.374 4792 0.1 %RANDOM
Rwork0.373 ---
obs0.373 4797606 65.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 263.253 Å2 / ksol: 0.446891 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.86 Å0.83 Å
Luzzati d res low-5 Å
Luzzati sigma a1.29 Å1.13 Å
Refinement stepCycle: LAST / Resolution: 3.45→190.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15064 0 6 0 15070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.44→3.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.554 335 0.1 %
Rwork0.494 313578 -
obs--25.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.363
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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