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- PDB-1m1c: Structure of the L-A virus -

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Basic information

Entry
Database: PDB / ID: 1m1c
TitleStructure of the L-A virus
ComponentsMajor coat protein
KeywordsVIRUS / dsRNA virus structure / RNA-protein interaction / mRNA decapping / L-A virus / quai-equivalence / Icosahedral virus
Function / homologyMajor capsid protein / Major capsid protein / Major coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / viral capsid / Alpha-Beta Complex / Alpha Beta / Major capsid protein
Function and homology information
Biological speciesSaccharomyces cerevisiae virus L-A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNaitow, H. / Tang, J. / Canady, M. / Wickner, R.B. / Johnson, J.E.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: L-A virus at 3.4 A resolution reveals particle architecture and mRNA decapping mechanism.
Authors: Naitow, H. / Tang, J. / Canady, M. / Wickner, R.B. / Johnson, J.E.
#1: Journal: To be Published
Title: LA virus: a virus capsid with enzymatic mRNA decapping activity
Authors: Tang, J. / Naitow, H. / Tang, L. / Wickner, R.B. / Johnson, J.E.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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

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Assembly

Deposited unit
A: Major coat protein
B: Major coat protein


Theoretical massNumber of molelcules
Total (without water)152,1402
Polymers152,1402
Non-polymers00
Water0
1
A: Major coat protein
B: Major coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)9,128,404120
Polymers9,128,404120
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
A: Major coat protein
B: Major coat protein
x 5


  • icosahedral pentamer
  • 761 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)760,70010
Polymers760,70010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major coat protein
B: Major coat protein
x 6


  • icosahedral 23 hexamer
  • 913 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)912,84012
Polymers912,84012
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
A: Major coat protein
B: Major coat protein
x 60


  • crystal asymmetric unit, crystal frame
  • 9.13 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)9,128,404120
Polymers9,128,404120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)407.0, 403.2, 572.0
Angle α, β, γ (deg.)90.0, 90.46, 90.0
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(0.30996941, -0.92237983, -0.23050905), (0.90861227, 0.35877093, -0.21379231), (0.27989766, -0.14317428, 0.94929365)103.57934, -62.26488, -21.3518
3generate(-0.80652354, -0.58382963, -0.09307382), (0.54778572, -0.67875949, -0.4890975), (0.22237488, -0.44545316, 0.86724904)198.03941, 14.0746, -3.71459
4generate(-0.80652354, 0.54778572, 0.22237488), (-0.58382963, -0.67875949, -0.44545316), (-0.09307382, -0.4890975, 0.86724904)152.83961, 123.51987, 28.53761
5generate(0.30996941, 0.90861227, 0.27989766), (-0.92237983, 0.35877093, -0.14317428), (-0.23050905, -0.21379231, 0.94929365)30.44452, 114.82129, 30.83335
6generate(-0.73613012, -0.44874488, 0.50669565), (-0.44874488, -0.23685127, -0.86170152), (0.50669565, -0.86170152, -0.02701861)104.90545, 169.34916, 95.34951
7generate(-0.49408999, 0.44544917, 0.74662582), (-0.5954914, 0.45231136, -0.66393104), (-0.63345487, -0.77265094, 0.04177863)45.77976, 156.01486, 202.06334
8generate(0.46056662, 0.50865524, 0.72742576), (0.04055879, 0.80660327, -0.58970005), (-0.88669802, 0.30109967, 0.3508641)-49.0754, 80.34727, 183.66747
9generate(0.80853673, -0.3464753, 0.4756293), (0.58040595, 0.33640508, -0.74159326), (0.09693964, 0.87566346, 0.47309219)-48.57342, 46.91643, 65.58437
10generate(0.06893747, -0.93818111, 0.33921059), (0.27799965, -0.3084853, -0.90969941), (0.95810428, 0.1570128, 0.23954783)46.59198, 101.92262, 11.00086
11generate(-0.46521927, -0.5058051, -0.72645181), (-0.5058051, -0.52160057, 0.68709101), (-0.72645181, 0.68709101, -0.01318016)253.89578, -46.73176, 219.44433
12generate(-0.80711663, 0.35164992, -0.47424159), (-0.43840162, 0.18103554, 0.88035797), (0.39543239, 0.91845984, 0.0080471)252.71362, -81.31595, 101.69872
13generate(-0.06340715, 0.93852906, -0.33932689), (0.27501016, 0.34327848, 0.89806976), (0.95934819, -0.0363743, -0.27987133)157.34349, -156.79468, 85.29773
14generate(0.73812795, 0.4437853, -0.50815523), (0.6485194, -0.25908597, 0.71574929), (0.18598312, -0.85786308, -0.47904197)99.58366, -168.85891, 192.90698
15generate(0.48979439, -0.4488623, -0.74741159), (0.16594903, -0.79361062, 0.58535725), (-0.85589857, -0.41073693, -0.31421777)159.25626, -100.83628, 275.81413
16generate(0.20134939, 0.95454997, 0.21975616), (0.95454997, -0.24154816, 0.17461051), (0.21975616, 0.17461051, -0.95980123)50.16725, -122.6123, 258.33714
17generate(0.99123721, 0.12528074, -0.04187518), (0.12528074, -0.99211783, -0.00263462), (-0.04187518, -0.00263462, -0.99911938)6.89576, -12.42893, 290.72072
18generate(0.40936407, -0.86335467, -0.29502505), (-0.86335467, -0.47112226, 0.18072779), (-0.29502505, 0.18072779, -0.93824181)102.66097, 62.37791, 307.88036
19generate(-0.74014113, -0.64509572, -0.18984894), (-0.64509572, 0.60144038, 0.47129713), (-0.18984894, 0.47129713, -0.86129925)205.11862, -1.57228, 286.10202
20generate(-0.86870127, 0.47843114, 0.12830334), (0.47843114, 0.74332498, 0.46751644), (0.12830334, 0.46751644, -0.87462371)172.67571, -115.90252, 255.48263
21generate(-0.30707855, -0.61953835, 0.72240916), (0.92215423, -0.38132946, 0.06495704), (0.23523252, 0.68611957, 0.68840801)30.1305, -103.58846, 20.59421
22generate(-0.45590448, -0.0424597, 0.88901534), (-0.0424597, -0.99668656, -0.06937629), (0.88901534, -0.06937629, 0.45259104)21.47425, 14.28414, -12.46047
23generate(0.06893747, 0.27799965, 0.95810428), (-0.93818111, -0.3084853, 0.1570128), (0.33921059, -0.90969941, 0.23954783)-42.08636, 73.42607, 74.27923
24generate(0.54213355, -0.10102422, 0.83419741), (-0.52715346, 0.73220358, 0.43126228), (-0.65437027, -0.6735518, 0.34369686)-72.71273, -7.89481, 160.94198
25generate(0.30974287, -0.65573322, 0.68852981), (0.62259702, 0.68718341, 0.37436869), (-0.71863225, 0.31271857, 0.62110771)-28.08025, -117.29581, 127.76281
26generate(0.87010601, -0.3379627, 0.35874328), (-0.47479241, -0.3794672, 0.79408867), (-0.13224104, -0.86126991, -0.49063881)-38.12065, -65.23366, 227.10452
27generate(0.0630406, -0.97518224, 0.21223923), (-0.26969612, 0.18810407, 0.94439444), (-0.96087975, -0.11677529, -0.25114467)65.38774, -107.74009, 277.50997
28generate(-0.80711663, -0.43840162, 0.39543239), (0.35164992, 0.18103554, 0.91845984), (-0.47424159, 0.88035797, 0.0080471)128.10535, -167.55183, 190.61607
29generate(-0.53783795, 0.53056659, 0.65515604), (0.53056659, -0.39090433, 0.75212559), (0.65515604, 0.75212559, -0.07125772)63.35858, -162.01109, 86.50724
30generate(0.49874264, 0.59264126, 0.63248092), (0.01979714, -0.73731407, 0.67525998), (0.866524, -0.32425964, -0.37946257)-39.37474, -98.77499, 109.05835
31generate(-0.06857092, 0.97483429, -0.21212293), (-0.28331369, -0.22289725, -0.9327648), (-0.95657273, -0.00386321, 0.29146817)139.64527, 162.61725, 199.32241
32generate(0.8051188, 0.44336119, -0.39397281), (-0.55142444, 0.31490171, -0.77250761), (-0.21843718, 0.83920663, 0.49801348)76.37401, 167.06669, 94.25841
33generate(0.54213355, -0.52715346, -0.65437027), (-0.10102422, 0.73220358, -0.6735518), (0.83419741, 0.43126228, 0.34369686)140.57388, 106.83762, 8.74625
34generate(-0.49408999, -0.5954914, -0.63345487), (0.44544917, 0.45231136, -0.77265094), (0.74662582, -0.66393104, 0.04177863)243.52284, 65.16458, 60.96083
35generate(-0.87152611, 0.33278808, -0.36013099), (0.33278808, -0.13797341, -0.93285338), (-0.36013099, -0.93285338, 0.00949953)242.94892, 99.63829, 178.74337
36generate(-0.49445654, -0.01733324, -0.86902951), (-0.16404813, 0.98369391, 0.07371909), (0.85358125, 0.17901355, -0.48923737)277.31336, 6.20997, 126.10983
37generate(-0.41225492, 0.57428075, -0.70728177), (0.86358026, 0.49368079, -0.10251055), (0.29030159, -0.65305505, -0.69945985)245.73247, -73.60564, 213.82305
38generate(0.19604561, 0.68755542, -0.6991664), (0.68755542, -0.60475382, -0.40192084), (-0.6991664, -0.40192084, -0.59129179)182.3756, -12.70675, 299.48942
39generate(0.48979439, 0.16594903, -0.85589857), (-0.4488623, -0.79361062, -0.41073693), (-0.74741159, 0.58535725, -0.31421777)174.79979, 104.74644, 264.72092
40generate(0.0630406, -0.26969612, -0.96087975), (-0.97518223, 0.18810407, -0.11677529), (0.21223923, 0.94439444, -0.25114467)233.47454, 116.43762, 157.56645
41generate(-0.30707855, 0.92215423, 0.23523252), (-0.61953835, -0.38132946, 0.68611957), (0.72240916, 0.06495704, 0.68840801)99.93254, -34.96442, -29.21497
42generate(0.80853673, 0.58040595, 0.09693964), (-0.3464753, 0.33640508, 0.87566346), (0.4756293, -0.74159326, 0.47309219)5.68509, -90.04225, 26.8684
43generate(0.8051188, -0.55142444, -0.21843718), (0.44336119, 0.31490171, 0.83920663), (-0.39397281, -0.77250761, 0.49801348)51.22405, -165.57314, 112.20761
44generate(-0.31260887, -0.90918581, -0.2750579), (0.65844394, -0.41612264, 0.62713119), (-0.6846366, 0.01493657, 0.72873152)173.61612, -157.17597, 108.86677
45generate(-0.99998464, 0.00153589, 0.0053254), (0.00153589, -0.84641717, 0.53251819), (0.0053254, 0.53251819, 0.84640181)203.71963, -76.45534, 21.46281
46generate(-0.06857092, -0.28331369, -0.95657273), (0.97483429, -0.22289725, -0.00386321), (-0.21212293, -0.9327648, 0.29146817)246.31368, -99.11403, 123.20947
47generate(-0.54641966, 0.09856033, -0.8316919), (0.09856033, -0.97858342, -0.18072173), (-0.8316919, -0.18072173, 0.52500308)277.27619, 15.81981, 153.09303
48generate(-0.31260887, 0.65844394, -0.6846366), (-0.90918581, -0.41612264, 0.01493657), (-0.2750579, 0.62713119, 0.72873152)232.29968, 90.81874, 66.98979
49generate(0.30974287, 0.62259702, -0.71863225), (-0.65573322, 0.68718341, 0.31271857), (0.68852981, 0.37436869, 0.62110771)173.54016, 22.23678, -16.1085
50generate(0.46056662, 0.04055879, -0.88669802), (0.50865524, 0.80660327, 0.30109967), (0.72742576, -0.58970005, 0.3508641)182.20128, -95.14813, 18.63718
51generate(-0.49445654, -0.16404813, 0.85358125), (-0.01733324, 0.98369391, 0.17901355), (-0.86902951, 0.07371909, -0.48923737)30.49315, -23.87734, 302.23334
52generate(-0.06340715, 0.27501016, 0.95934819), (0.93852906, 0.34327848, -0.0363743), (-0.33932689, 0.89806976, -0.27987133)-28.73339, -90.74455, 218.07583
53generate(0.49874264, 0.01979714, 0.866524), (0.59264126, -0.73731407, -0.32425964), (0.63248092, 0.67525998, -0.37946257)-72.90835, -14.12987, 132.98613
54generate(0.41512093, -0.57699146, 0.70338856), (-0.57699146, -0.76474155, -0.28679471), (0.70338856, -0.28679471, -0.65037937)-40.98343, 100.08781, 164.55531
55generate(-0.19870993, -0.69061409, 0.6953895), (-0.95397643, 0.29889987, 0.02424522), (-0.22459592, -0.65856743, -0.71822393)22.92221, 94.06354, 269.15584
56generate(0.87010601, -0.47479241, -0.13224104), (-0.3379627, -0.3794672, -0.86126991), (0.35874328, 0.79408867, -0.49063881)32.2291, 157.9609, 176.90313
57generate(-0.19870993, -0.95397643, -0.22459592), (-0.69061409, 0.29889987, -0.65856742), (0.6953895, 0.02424522, -0.71822393)154.74058, 164.97209, 175.09371
58generate(-0.99125257, -0.12681663, 0.03654978), (-0.12681663, 0.838535, -0.52988357), (0.03654978, -0.52988357, -0.84728243)198.35309, 88.88938, 260.94744
59generate(-0.41225492, 0.86358026, 0.29030159), (0.57428075, 0.49368079, -0.65305505), (-0.70728177, -0.10251055, -0.69945985)102.79562, 34.85649, 315.81739
60generate(0.73812795, 0.6485194, 0.18598312), (0.4437853, -0.25908597, -0.85786308), (-0.50815523, 0.71574929, -0.47904197)0.12535, 77.54503, 263.87515

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Components

#1: Protein Major coat protein / gag protein


Mass: 76070.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae virus L-A (L1) / Genus: Totivirus / References: UniProt: P32503

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Experimental details

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Experiment

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

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5 % PEG 8000, 1.0 M LiCl in 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: Naitow, H., (2001) J. Struct. Biol., 135, 1.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.0-6.0 %PEG80001reservoir
21.0 M1reservoirLiCl
30.1 MHEPES1reservoirpH7.0
44-56 mg/mlvirus1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9648 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9648 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 1768471 / Num. obs: 1768471 / % possible obs: 35.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.3
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.5 / % possible all: 21.4
Reflection
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 89.5 Å / Num. obs: 2105482 / % possible obs: 83.8 % / Redundancy: 2.4 % / Num. measured all: 5151654
Reflection shell
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 3.9 Å / % possible obs: 70.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→30 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 64536 RANDOM
Rwork0.266 --
all-831462 -
obs-645314 -
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 0 0 10302
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.323
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.627

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