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- PDB-1f8v: THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF D... -

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Basic information

Entry
Database: PDB / ID: 1f8v
TitleTHE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA
Components
  • (MATURE CAPSID PROTEIN ...) x 2
  • RNA
KeywordsVirus/RNA / nodavirus / coat protein / nucleoprotein / protein-RNA interactions / RNA duplex / RNA cage / gamma polypeptide / beta-sandwich / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


nodavirus endopeptidase / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / metal ion binding
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein alpha
Similarity search - Component
Biological speciesPariacato virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, electron density averaging / Resolution: 3 Å
AuthorsTang, L. / Johnson, K.N. / Ball, L.A. / Lin, T. / Yeager, M. / Johnson, J.E.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA.
Authors: Tang, L. / Johnson, K.N. / Ball, L.A. / Lin, T. / Yeager, M. / Johnson, J.E.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA
A: MATURE CAPSID PROTEIN BETA
D: MATURE CAPSID PROTEIN GAMMA
B: MATURE CAPSID PROTEIN BETA
E: MATURE CAPSID PROTEIN GAMMA
C: MATURE CAPSID PROTEIN BETA
F: MATURE CAPSID PROTEIN GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8799
Polymers135,7437
Non-polymers1362
Water3,945219
1
R: RNA
A: MATURE CAPSID PROTEIN BETA
D: MATURE CAPSID PROTEIN GAMMA
B: MATURE CAPSID PROTEIN BETA
E: MATURE CAPSID PROTEIN GAMMA
C: MATURE CAPSID PROTEIN BETA
F: MATURE CAPSID PROTEIN GAMMA
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,152,733540
Polymers8,144,564420
Non-polymers8,168120
Water6,485360
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
R: RNA
A: MATURE CAPSID PROTEIN BETA
D: MATURE CAPSID PROTEIN GAMMA
B: MATURE CAPSID PROTEIN BETA
E: MATURE CAPSID PROTEIN GAMMA
C: MATURE CAPSID PROTEIN BETA
F: MATURE CAPSID PROTEIN GAMMA
hetero molecules
x 5


  • icosahedral pentamer
  • 679 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)679,39445
Polymers678,71435
Non-polymers68110
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: RNA
A: MATURE CAPSID PROTEIN BETA
D: MATURE CAPSID PROTEIN GAMMA
B: MATURE CAPSID PROTEIN BETA
E: MATURE CAPSID PROTEIN GAMMA
C: MATURE CAPSID PROTEIN BETA
F: MATURE CAPSID PROTEIN GAMMA
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 815 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)815,27354
Polymers814,45642
Non-polymers81712
Water64936
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
R: RNA
A: MATURE CAPSID PROTEIN BETA
D: MATURE CAPSID PROTEIN GAMMA
B: MATURE CAPSID PROTEIN BETA
E: MATURE CAPSID PROTEIN GAMMA
C: MATURE CAPSID PROTEIN BETA
F: MATURE CAPSID PROTEIN GAMMA
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.15 MDa, 420 polymers
Theoretical massNumber of molelcules
Total (without water)8,152,733540
Polymers8,144,564420
Non-polymers8,168120
Water6,485360
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)329.332, 346.944, 424.893
Angle α, β, γ (deg.)90.00, 90.83, 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(0.75690705, -0.29018534, -0.58556314), (-0.36817222, 0.5509484, -0.74893597), (0.53994531, 0.78246299, 0.31017854)82.0333, 109.73846, 27.109
3generate(0.36357439, -0.83770196, -0.40751575), (-0.8859005, -0.17563236, -0.42934086), (0.28808672, 0.51711575, -0.80597602)96.40636, 119.6934, 165.67741
4generate(0.36357439, -0.8859005, 0.28808672), (-0.83770196, -0.17563236, 0.51711575), (-0.40751575, -0.42934086, -0.80597602)23.25609, 16.10743, 224.2084
5generate(0.75690705, -0.36817222, 0.53994531), (-0.29018534, 0.5509484, 0.78246299), (-0.58556314, -0.74893597, 0.31017854)-36.32631, -57.86716, 121.81412
6generate(0.25325907, -0.62212273, 0.74082599), (-0.62212274, -0.69117582, -0.36774894), (0.74082599, -0.36774894, -0.56208324)-15.07202, 91.02093, 101.93397
7generate(0.8207474, 0.16341933, 0.54741924), (-0.41498166, -0.48802125, 0.76787074), (0.39263715, -0.85739686, -0.33272615)-42.48408, -45.83173, 107.11266
8generate(0.85663949, 0.28020206, -0.43319233), (0.28018153, 0.45237751, 0.84667166), (0.43320561, -0.84666487, 0.30901699)57.61791, -112.61253, 36.21269
9generate(0.31133368, -0.43316431, -0.84583687), (0.50267494, 0.83042133, -0.24024638), (0.80646714, -0.3503842, 0.47627898)146.89641, -17.03268, -12.78458
10generate(-0.06157592, -0.9908317, -0.12025364), (-0.05497977, 0.1236665, -0.99079959), (0.99658699, -0.05439788, -0.06209058)101.97156, 108.81972, 27.83341
11generate(-0.87443506, -0.24540121, -0.41849918), (-0.24540122, -0.52039354, 0.81790514), (-0.41849918, 0.81790514, 0.3948286)201.73282, -65.36262, 98.85476
12generate(-0.79748282, -0.2089153, 0.56601727), (0.44747258, 0.42448235, 0.78713597), (-0.40470908, 0.88100462, -0.24503352)91.72498, -120.42828, 164.98295
13generate(-0.22108519, 0.55920384, 0.79900714), (0.60742291, 0.71992265, -0.33578086), (-0.76299328, 0.41109906, -0.49883746)18.72295, -15.80012, 221.8208
14generate(0.0581959, 0.99744165, -0.04151366), (0.01340386, -0.04236109, -0.99901245), (-0.99821519, 0.05758198, -0.01583481)83.61306, 103.9293, 190.82033
15generate(-0.34559653, 0.50016838, -0.79397395), (-0.51367043, -0.80891865, -0.28599529), (-0.78530613, 0.30900196, 0.53648119)196.71938, 73.29799, 114.82314
16generate(-0.378824, 0.86752395, -0.32232681), (0.86752395, 0.21156936, -0.4501562), (-0.32232681, -0.4501562, -0.83274536)149.91639, -25.65831, 219.85532
17generate(-0.78017162, 0.3356813, -0.52787337), (0.3356813, -0.4874095, -0.80607074), (-0.52787337, -0.80607075, 0.26758112)205.30299, 56.52155, 121.43945
18generate(-0.99912868, -0.00170394, 0.04170095), (-0.00170394, -0.9966678, -0.08154995), (0.04170095, -0.08154995, 0.99579648)163.82996, 8.71925, -3.06685
19generate(-0.73310397, 0.32162316, 0.59926381), (0.32162316, -0.61242788, 0.72214308), (0.59926381, 0.72214308, 0.34553185)82.81163, -103.00405, 18.3999
20generate(-0.34973459, 0.85883554, 0.37428228), (0.85883554, 0.13430375, 0.49433189), (0.37428228, 0.49433189, -0.78456915)74.21256, -124.25056, 156.17338
21generate(-0.38245567, -0.36366914, -0.84939533), (-0.44166871, 0.8794137, -0.17765217), (0.8115765, 0.30720726, -0.49695803)205.64903, 55.84599, 89.13209
22generate(-0.61421754, -0.75400031, 0.23285264), (-0.75400031, 0.4736711, -0.45510353), (0.23285264, -0.45510353, -0.85945357)111.34018, 111.30397, 175.9488
23generate(-0.06157592, -0.05497977, 0.99658699), (-0.9908317, 0.1236665, -0.05439788), (-0.12025365, -0.99079959, -0.06209058)-15.47654, 89.09337, 121.80918
24generate(0.51173724, 0.76736985, 0.38635282), (-0.82486995, 0.31309436, 0.47070318), (0.24023854, -0.55956718, 0.79320238)0.45527, 19.90848, 1.53234
25generate(0.31342266, 0.57658933, -0.75452699), (-0.48546856, 0.78017182, 0.39452784), (0.81614124, 0.24264517, 0.52443951)137.11839, -0.63954, -18.66321
26generate(-0.49986766, 0.80165791, 0.32783672), (-0.79056921, -0.26772595, -0.55074781), (-0.35374094, -0.53447863, 0.7675936)91.72967, 124.43909, 54.20538
27generate(-0.49648763, 0.84324651, -0.20599845), (-0.79719184, -0.34903136, 0.49260762), (0.34348974, 0.40879388, 0.84551899)147.58391, 15.27603, -12.65732
28generate(-0.79748282, 0.44747258, -0.40470908), (-0.2089153, 0.42448235, 0.88100462), (0.56601727, 0.78713597, -0.24503352)193.80755, -75.06831, 83.30186
29generate(-0.98688811, 0.16128224, 0.00631617), (0.16128224, 0.98384553, 0.07769173), (0.00631617, 0.07769173, -0.99695742)166.52109, -21.74112, 209.4706
30generate(-0.80295182, 0.38018082, 0.45905437), (-0.19819965, 0.55603728, -0.80717993), (-0.56212567, -0.73911101, -0.37111944)103.43349, 101.56123, 191.48798
31generate(0.77914874, -0.41161864, -0.47275504), (0.2447487, -0.49455779, 0.83397282), (-0.57708345, -0.76549506, -0.28459095)68.29877, -108.29563, 183.64717
32generate(0.48602786, -0.8227915, -0.29460325), (0.81763417, 0.30905456, 0.48575677), (-0.30862806, -0.47696901, 0.82295157)74.2286, -119.88193, 44.58788
33generate(0.51173724, -0.82486995, 0.24023854), (0.76736985, 0.31309436, -0.55956718), (0.38635282, 0.47070318, 0.79320238)15.8208, -5.72515, -10.76234
34generate(0.8207474, -0.41498166, 0.39263715), (0.16341933, -0.48802125, -0.85739686), (0.54741925, 0.76787074, -0.33272615)-26.20704, 76.41392, 94.08862
35generate(0.9860168, -0.1595783, -0.04801712), (-0.1595783, -0.98717773, 0.00385822), (-0.04801711, 0.00385822, -0.99883906)6.22614, 13.02187, 214.24031
36generate(0.10317458, -0.02637013, 0.99431364), (0.98748921, -0.11712996, -0.10557284), (0.11924789, 0.99276643, 0.01395538)-29.10029, -71.98944, 93.65942
37generate(0.6246773, 0.7335453, 0.26774907), (0.73355798, -0.4336943, -0.52326087), (-0.26771431, 0.52327866, -0.80901699)3.4245, -6.69808, 212.76469
38generate(0.3473215, 0.43237715, -0.83211644), (0.43237715, -0.86124322, -0.26703955), (-0.83211644, -0.26703955, -0.48607829)142.42538, -8.29992, 226.29535
39generate(-0.34559653, -0.51367043, -0.78530613), (0.50016838, -0.80891865, 0.30900196), (-0.79397395, -0.28599529, 0.53648119)195.80786, -74.58128, 115.55249
40generate(-0.49648763, -0.79719184, 0.34348974), (0.84324651, -0.34903136, 0.40879388), (-0.20599845, 0.49260762, 0.84551899)89.79917, -113.94356, 33.57897
41generate(-0.38245567, -0.44166871, 0.8115765), (-0.36366914, 0.8794137, 0.30720726), (-0.84939533, -0.17765217, -0.49695803)30.97955, -1.70554, 228.8934
42generate(0.31133368, 0.50267494, 0.80646714), (-0.43316431, 0.83042133, -0.3503842), (-0.84583687, -0.24024638, 0.47627898)-26.86156, 73.29506, 126.24738
43generate(0.48602786, 0.81763417, -0.30862806), (-0.8227915, 0.30905456, -0.47696901), (-0.29460325, 0.48575677, 0.82295157)75.70346, 119.39176, 43.40778
44generate(-0.09979455, 0.06794604, -0.99268544), (-0.99409916, 0.03582455, 0.10238874), (0.04251941, 0.9970456, 0.06397)196.93325, 72.88047, 94.8561
45generate(-0.63654689, -0.71034594, -0.30036095), (-0.71034594, 0.38832588, 0.58703633), (-0.30036095, 0.58703633, -0.75177899)169.29235, -1.96177, 209.49251
46generate(0.77914874, 0.2447487, -0.57708345), (-0.41161864, -0.49455779, -0.76549506), (-0.47275504, 0.83397282, -0.28459095)79.27005, 115.1356, 174.86853
47generate(0.18804, -0.54280008, -0.8185408), (-0.54280008, -0.75200168, 0.37398068), (-0.8185408, 0.37398068, -0.43603832)154.40038, 6.34534, 219.89079
48generate(-0.09979455, -0.99409916, 0.04251941), (0.06794604, 0.03582455, 0.9970456), (-0.99268544, 0.10238874, 0.06397)88.07006, -110.5676, 181.96268
49generate(0.31342266, -0.48546856, 0.81614124), (0.57658933, 0.78017182, 0.24264517), (-0.75452699, 0.39452784, 0.52443951)-28.05467, -74.03352, 113.49957
50generate(0.85663949, 0.28018153, 0.43320561), (0.28020206, 0.45237751, -0.84666487), (-0.43319233, 0.84667166, 0.30901699)-33.49337, 65.45873, 109.11514
51generate(0.10317458, 0.98748921, 0.11924789), (-0.02637013, -0.11712996, 0.99276643), (0.99431364, -0.10557284, 0.01395538)62.92252, -102.18143, 20.02763
52generate(-0.22108519, 0.60742291, -0.76299328), (0.55920384, 0.71992265, 0.41109906), (0.79900714, -0.33578086, -0.49883746)182.9845, -90.28541, 90.38737
53generate(-0.80295182, -0.19819965, -0.56212567), (0.38018082, 0.55603728, -0.73911101), (0.45905437, -0.80717993, -0.37111944)210.82182, 45.73562, 105.5615
54generate(-0.83830541, -0.31603546, 0.44425851), (-0.31603546, -0.38230207, -0.86831257), (0.44425851, -0.86831257, 0.22060748)107.96424, 117.90521, 44.57989
55generate(-0.27828849, 0.41676055, 0.86537053), (-0.56729777, -0.7983423, 0.20204656), (0.77506694, -0.43469554, 0.45859681)16.55744, 26.48745, -8.28295
56generate(-0.49986766, -0.79056921, -0.35374094), (0.80165791, -0.26772595, -0.53447863), (0.32783672, -0.55074781, 0.7675936)163.40507, -11.24863, -3.1455
57generate(-0.27828849, -0.56729777, 0.77506694), (0.41676055, -0.7983423, -0.43469554), (0.86537053, 0.20204656, 0.45859681)26.05386, 10.645, -15.88149
58generate(0.41671851, 0.37466464, 0.82823432), (0.37466464, -0.90091638, 0.21903442), (0.82823432, 0.21903442, -0.51580213)-38.01815, -54.55977, 89.71209
59generate(0.6246773, 0.73355798, -0.26771431), (0.7335453, -0.4336943, 0.52327866), (0.26774907, -0.52326087, -0.80901699)59.73437, -116.75217, 167.7085
60generate(0.0581959, 0.01340386, -0.99821519), (0.99744165, -0.04236109, 0.05758198), (-0.04151366, -0.99901245, -0.01583481)184.22077, -89.98441, 110.31936

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Components

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RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA


Mass: 7701.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pariacato virus / Genus: Alphanodavirus

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MATURE CAPSID PROTEIN ... , 2 types, 6 molecules ABCDEF

#2: Protein MATURE CAPSID PROTEIN BETA


Mass: 38432.504 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pariacato virus / Genus: Alphanodavirus / References: UniProt: Q9J7Z0
#3: Protein/peptide MATURE CAPSID PROTEIN GAMMA


Mass: 4247.958 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pariacato virus / Genus: Alphanodavirus / References: UniProt: Q9J7Z0

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Non-polymers , 3 types, 221 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 7.5
Details: PEG 8000, lithium sulphate, calcium chloride, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Li2SO411
3CaCl211
4Tris-HCl11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
175 mM1reservoirLi2SO4
25 mM1reservoirCaCl2
34 %(w/v)PEG80001reservoir
450 mM1reservoir
520 mg/mlprotein1drop
650 mMTris-HCl1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-210.98
SYNCHROTRONAPS 14-ID-B21
Detector
TypeIDDetectorDate
OTHER1CCDNov 14, 1999
OTHER2CCDApr 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
211
ReflectionResolution: 3→207 Å / Num. all: 1505825 / Num. obs: 1505825 / % possible obs: 81.2 % / Redundancy: 2.14 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.3 / Num. unique all: 76058 / % possible all: 82.2
Reflection
*PLUS
Num. measured all: 3226875
Reflection shell
*PLUS
% possible obs: 82.2 % / Num. unique obs: 76058 / Num. measured obs: 136241

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Processing

Software
NameVersionClassification
GLRFphasing
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement, electron density averaging
Starting model: crystal structure of flock house virus

Resolution: 3→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: throughtout / σ(F): 3 / Stereochemistry target values: Engh & Huber
Details: The asymmetric unit of the crystal unit cell contains a virus particle. The 60-fold strict non-crystallographic symmetry was used in the electron density averaging and refinement. A BULK ...Details: The asymmetric unit of the crystal unit cell contains a virus particle. The 60-fold strict non-crystallographic symmetry was used in the electron density averaging and refinement. A BULK SOLVENT MODEL WAS USED FOR DATA(3-20A, F>3SIGMA). All data(3-20A, F>3*sigma, working and testing sets) were used in the last cycle of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 123840 10 %RANDOM
Rwork0.219 ---
obs0.218 1237980 65.6 %-
all-1464339 --
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7985 509 6 219 8719
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.211.5
X-RAY DIFFRACTIONx_mcangle_it2.172
X-RAY DIFFRACTIONx_scbond_it1.742
X-RAY DIFFRACTIONx_scangle_it2.762.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.305 10208 10 %
Rwork0.304 101838 -
obs--43.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM.SO4TOP.SO4
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5PARAM.CATOP.CA
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / % reflection Rfree: 10 % / Rfactor Rwork: 0.304 / Rfactor obs: 0.304

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