[English] 日本語
Yorodumi
- PDB-2w0c: X-ray structure of the entire lipid-containing bacteriophage PM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w0c
TitleX-ray structure of the entire lipid-containing bacteriophage PM2
Components
  • MAJOR CAPSID PROTEIN P2
  • PROTEIN 2
  • PROTEIN P3
  • PROTEIN P6
KeywordsVIRUS / MEMBER OF PRD1-ADENO VIRAL LINEAGE / MEMBRANE-CONTAINING BACTERIOPHAGE / VIRUS VIRION / MEMBRANE / TRANSMEMBRANE / CAPSID PROTEIN
Function / homology
Function and homology information


viral inner membrane / viral capsid, major subunit / virion component => GO:0044423 / virion component / membrane => GO:0016020 / virion membrane
Similarity search - Function
Viral coat protein P2, N-terminal / Viral coat protein P2 N-terminal domain
Similarity search - Domain/homology
Major capsid protein P2 / Protein P6 / Spike protein P1 / Protein P3
Similarity search - Component
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsAbrescia, N.G.A. / Grimes, J.M. / Kivela, H.M. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
Citation
Journal: Mol.Cell / Year: 2008
Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2
Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.M. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Preliminary Crystallographic Analysis of the Major Capsid Protein P2 of the Lipid-Containing Bacteriophage Pm2.
Authors: Abrescia, N.G.A. / Kivela, H.M. / Grimes, J.M. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
#2: Journal: J.Struct.Biol. / Year: 2008
Title: Selenomethionine Labeling of Large Biological Macromolecular Complexes: Probing the Structure of Marine Bacterial Virus Pm2.
Authors: Kivela, H.M. / Abrescia, N.G.A. / Bamford, J.K.H. / Grimes, J.M. / Stuart, D.I. / Bamford, D.H.
History
DepositionAug 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,75227
Polymers397,31116
Non-polymers44111
Water00
1
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)23,865,0901620
Polymers23,838,639960
Non-polymers26,451660
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 CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 5


  • icosahedral pentamer
  • 1.99 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,988,758135
Polymers1,986,55380
Non-polymers2,20455
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.39 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)2,386,509162
Polymers2,383,86496
Non-polymers2,64566
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 CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 23.9 MDa, 960 polymers
Theoretical massNumber of molelcules
Total (without water)23,865,0901620
Polymers23,838,639960
Non-polymers26,451660
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)946.900, 677.600, 1067.600
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.438676, 0.122701, -0.890229), (-0.610434, 0.76769, -0.194991), (0.659495, 0.628964, 0.411668)340.15449, 179.20263, 3.48827
3generate(-0.469566, -0.4119, -0.780926), (-0.865003, 0.391806, 0.313462), (0.176856, 0.822695, -0.540274)508.25494, 108.45263, 341.96649
4generate(-0.469566, -0.865003, 0.176856), (-0.4119, 0.391806, 0.822695), (-0.780926, 0.313462, -0.540274)271.99224, -114.47591, 547.66927
5generate(0.438676, -0.610434, 0.659495), (0.122701, 0.76769, 0.628964), (-0.890229, -0.194991, 0.411668)-42.12659, -181.50332, 336.32235
6generate(-0.762275, -0.330162, -0.556713), (-0.330162, -0.541457, 0.773186), (-0.556713, 0.773186, 0.303732)515.81567, -119.82934, 291.32649
7generate(-0.499999, -0.697147, 0.513797), (0.695602, 0.030124, 0.717795), (-0.515886, 0.716295, 0.469875)195.41646, -326.46893, 241.57454
8generate(0.545072, -0.273383, 0.792565), (0.760137, 0.559944, -0.329626), (-0.353678, 0.782128, 0.513018)-97.79865, -81.95449, 196.09466
9generate(0.928684, 0.355502, -0.105658), (-0.225742, 0.31581, -0.921577), (-0.294255, 0.879706, 0.37354)41.38366, 275.80334, 217.7385
10generate(0.1207, 0.320411, -0.939558), (-0.899584, -0.364893, -0.240001), (-0.419737, 0.874179, 0.244194)420.61817, 252.39539, 276.59501
11generate(-0.858366, -0.412463, 0.305094), (-0.412463, 0.201164, -0.888486), (0.305094, -0.888486, -0.342799)323.86941, 307.74251, 265.69377
12generate(0.076445, -0.230073, 0.970166), (-0.889687, -0.455003, -0.037799), (0.450125, -0.860255, -0.239476)-40.95784, 200.39121, 209.058
13generate(0.813799, 0.442955, 0.376195), (-0.137463, -0.482241, 0.865186), (0.564655, -0.7558, -0.331558)-52.80017, -183.90951, 207.1749
14generate(0.334697, 0.676519, -0.655972), (0.804661, 0.157092, 0.572576), (0.490406, -0.719475, -0.49179)304.70811, -314.06912, 262.64686
15generate(-0.698757, 0.147841, -0.699915), (0.634701, 0.57946, -0.511253), (0.329989, -0.801479, -0.498737)537.50271, -10.21146, 298.81351
16generate(0.620641, 0.742625, 0.251619), (0.742625, -0.659707, 0.115299), (0.251619, 0.115299, -0.960934)19.41793, -187.95733, 429.66623
17generate(-0.015122, 0.804519, -0.593734), (0.804519, -0.342811, -0.485005), (-0.593734, -0.485005, -0.642067)364.48989, -53.16908, 532.56569
18generate(-0.889304, 0.242328, -0.387833), (0.242328, -0.469508, -0.849022), (-0.387833, -0.849022, 0.358813)501.44689, 157.36721, 241.45044
19generate(-0.793816, -0.167018, 0.584775), (-0.167018, -0.864708, -0.473693), (0.584775, -0.473693, 0.658524)241.019, 152.69754, -41.36812
20generate(0.139382, 0.142182, 0.979978), (0.142182, -0.982257, 0.12229), (0.979978, 0.12229, -0.157125)-56.89128, -60.72477, 74.95563
21generate(0.641647, -0.58844, -0.491964), (-0.682824, -0.146101, -0.715825), (0.349344, 0.795232, -0.495546)198.31257, 323.21518, 293.88695
22generate(0.316231, -0.682436, -0.658998), (-0.682436, -0.646172, 0.341676), (-0.658998, 0.341676, -0.670059)309.40559, 62.2709, 553.49677
23generate(0.1207, -0.899584, -0.419738), (0.320411, -0.364893, 0.874179), (-0.939558, -0.240001, 0.244194)292.3798, -284.46677, 388.22748
24generate(0.32527, -0.939792, -0.104832), (0.939817, 0.309017, 0.145784), (-0.104611, -0.145942, 0.983747)170.76427, -237.81816, 26.47563
25generate(0.647233, -0.747494, -0.14947), (0.319784, 0.444238, -0.836894), (0.691973, 0.493867, 0.526562)112.62752, 137.74994, -31.83002
26generate(-0.020948, -0.273612, -0.961612), (0.967246, -0.248916, 0.049754), (-0.252974, -0.929073, 0.269865)456.4743, -220.0278, 234.42616
27generate(-0.476345, -0.817439, -0.323864), (0.609067, -0.041115, -0.792052), (0.634139, -0.574545, 0.517461)396.96224, 64.55239, -17.17523
28generate(0.076445, -0.889687, 0.450125), (-0.230073, -0.455003, -0.860255), (0.970166, -0.037799, -0.239476)87.31419, 261.59852, 97.37493
29generate(0.873486, -0.390512, 0.290729), (-0.390512, -0.918601, -0.0606), (0.290729, -0.0606, -0.954884)-44.54677, 98.79953, 419.77222
30generate(0.813293, -0.009756, -0.581772), (0.349472, -0.791233, 0.501817), (-0.465213, -0.611437, -0.640094)183.60673, -198.8619, 504.47454
31generate(-0.458153, 0.054074, 0.887227), (0.42798, 0.88825, 0.166867), (-0.779056, 0.456166, -0.430097)94.32278, -133.08243, 520.09182
32generate(0.351133, 0.54333, 0.76256), (-0.244426, 0.839368, -0.485507), (-0.90386, -0.015912, 0.427533)-48.73496, 172.25578, 335.33822
33generate(0.32527, 0.939817, -0.104611), (-0.939792, 0.309017, -0.145942), (-0.104832, 0.145784, 0.983747)170.73061, 237.83669, 26.52623
34generate(-0.499999, 0.695602, -0.515886), (-0.697147, 0.030124, 0.716295), (0.513797, 0.717795, 0.469875)449.42552, -26.97028, 20.42353
35generate(-0.984181, 0.148183, 0.097104), (0.148183, 0.38811, 0.909622), (0.097104, 0.909622, -0.403929)402.20289, -256.2109, 325.46384
36generate(-0.162545, 0.807978, 0.566349), (-0.712402, -0.493233, 0.499204), (0.682687, -0.322325, 0.655778)109.99335, 29.85089, -61.71843
37generate(-0.191018, 0.956545, 0.220302), (0.317795, -0.152081, 0.935883), (0.928719, 0.248781, -0.274935)201.47014, -299.12323, 115.02675
38generate(-0.522415, 0.849455, 0.074223), (0.849455, 0.51088, 0.132017), (0.074223, 0.132017, -0.988465)308.67841, -215.0126, 474.55786
39generate(-0.698757, 0.634701, 0.329989), (0.147841, 0.57946, -0.801479), (-0.699915, -0.511253, -0.498737)283.45999, 165.94475, 520.01512
40generate(-0.476345, 0.609067, 0.634139), (-0.817439, -0.041115, -0.574545), (-0.323864, -0.792052, 0.517461)160.66587, 317.2787, 188.57814
41generate(0.641647, -0.682824, 0.349344), (-0.58844, -0.146101, 0.795232), (-0.491964, -0.715825, -0.495546)-9.21512, -69.79119, 474.56269
42generate(0.928684, -0.225742, -0.294255), (0.355502, 0.31581, 0.879706), (-0.105658, -0.921577, 0.37354)87.89869, -293.35925, 177.21262
43generate(0.351133, -0.244426, -0.90386), (0.54333, 0.839368, -0.015912), (0.76256, -0.485507, 0.427533)362.3148, -112.77096, -22.57351
44generate(-0.292852, -0.713054, -0.637018), (-0.284527, 0.701034, -0.653908), (0.912843, -0.010249, -0.408182)434.79948, 222.4068, 151.30194
45generate(-0.113304, -0.983999, 0.137505), (-0.983999, 0.09198, -0.152594), (0.137505, -0.152594, -0.978676)205.18136, 248.96976, 458.54901
46generate(-0.458153, 0.42798, -0.779056), (0.054074, 0.88825, 0.456166), (0.887227, 0.166867, -0.430097)505.35174, -124.13829, 162.21136
47generate(-0.976018, -0.217658, 0.003697), (-0.217658, 0.975448, -0.03355), (0.003697, -0.03355, -0.99943)423.48653, 55.02319, 492.40839
48generate(-0.292852, -0.284527, 0.912843), (-0.713054, 0.701034, -0.010249), (-0.637018, -0.653908, -0.408182)52.49759, 155.67171, 484.16729
49generate(0.647233, 0.319784, 0.691973), (-0.747494, 0.444238, 0.493867), (-0.14947, -0.836894, 0.526562)-94.92097, 38.71443, 148.87698
50generate(0.545072, 0.760137, -0.353678), (-0.273383, 0.559944, 0.782128), (0.792565, -0.329626, 0.513018)184.95828, -134.21766, -50.10272
51generate(-0.162545, -0.712402, 0.682687), (0.807978, -0.493233, -0.322325), (0.566349, 0.499204, 0.655778)81.27915, -94.04215, -36.72266
52generate(0.813799, -0.137463, 0.564655), (0.442955, -0.482241, -0.7558), (0.376195, 0.865186, -0.331558)-99.2944, 91.2822, 247.66951
53generate(0.813293, 0.349472, -0.465213), (-0.009756, -0.791233, -0.611437), (-0.581772, 0.501817, -0.640094)154.85886, 152.89992, 529.52091
54generate(-0.163364, 0.075476, -0.983675), (0.075476, -0.993191, -0.088741), (-0.983675, -0.088741, 0.156555)492.50776, 5.65741, 419.32248
55generate(-0.766465, -0.580799, -0.274233), (0.580863, -0.809017, 0.089941), (-0.274097, -0.090355, 0.957448)447.033, -146.96118, 69.3647
56generate(-0.020948, 0.967246, -0.252974), (-0.273612, -0.248916, -0.929073), (-0.961612, 0.049754, 0.269865)281.68724, 287.92747, 386.63511
57generate(-0.766465, 0.580863, -0.274097), (-0.580799, -0.809017, -0.090355), (-0.274233, 0.089941, 0.957448)447.01219, 147.00969, 69.39598
58generate(-0.871574, 0.17948, 0.45623), (0.17948, -0.749169, 0.637599), (0.45623, 0.637599, 0.620743)289.43176, -195.84484, -4.42819
59generate(-0.191018, 0.317795, 0.928719), (0.956545, -0.152081, 0.248781), (0.220302, 0.935883, -0.274935)26.71674, -266.82281, 267.1851
60generate(0.334697, 0.804661, 0.490406), (0.676519, 0.157092, -0.719475), (-0.655972, 0.572576, -0.49179)21.93037, 32.16492, 508.87551

-
Components

#1: Protein
MAJOR CAPSID PROTEIN P2


Mass: 30233.723 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: P15794
#2: Protein PROTEIN 2


Mass: 37540.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR3
#3: Protein
PROTEIN P3 / PROTEIN III


Mass: 10767.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR6
#4: Protein PROTEIN P6 / PROTEIN VI


Mass: 14363.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR1
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
Nonpolymer detailsCALCIUM (CA): THESE CALCIUM WERE DERIVED FROM ATOMIC STRUCTURE OF P2 AND P1

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 718

-
Sample preparation

CrystalDescription: THE STARTING MODEL FOR MANUAL MOLECULAR REPLACEMENT WAS A PRELIMINARY CRYO-EM RECONSTRUCTION OF PM2
Crystal growpH: 7.4
Details: 20MG/ML VIRUS WITH 20MM MOPS PH 7.4, 100MM NACL, 5MM CACL2 MIXED 1:1 WITH 1.5% PEG 8K, 500MM NACL, 2.5MM CACL2, 100MM MOPS PH 7.4

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1273.151
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-110.7291
SYNCHROTRONESRF ID2920.9756
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.72911
20.97561
ReflectionResolution: 7→96 Å / Num. obs: 874109 / % possible obs: 85.1 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 3.1
Reflection shellResolution: 7→7.25 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.45 / % possible all: 56.7

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7→96 Å / σ(F): 0
Details: THE ATOMIC MODELS COMPOSING THE ICOSAHEDRAL ASYMMETRIC UNIT WAS REFINED AS RIGID BODY AGAINST THE EXPERIMENTAL DATA USING STRICT 60-NCS AND AB AS TARGET FUNCTION IN XPLOR. FOR DETAILS PLEASE ...Details: THE ATOMIC MODELS COMPOSING THE ICOSAHEDRAL ASYMMETRIC UNIT WAS REFINED AS RIGID BODY AGAINST THE EXPERIMENTAL DATA USING STRICT 60-NCS AND AB AS TARGET FUNCTION IN XPLOR. FOR DETAILS PLEASE SEE PRIMARY REFERENCE. THE ATOMIC MODELS CORRESPONDING TO P3, P6 AND P1 (RESIDUES 1- 88) HAVE BEEN BUILT INTO THE AVERAGED VIRUS MAP AND THEN REGULARIZED. PLEASE REFER TO PRIMARY SEQUENCE FOR MORE DETAILS.
RfactorNum. reflection% reflection
Rwork0.419 --
obs0.419 851677 82.9 %
Refinement stepCycle: LAST / Resolution: 7→96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26436 0 11 0 26447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0
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_deg0
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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://pdbjlvh1.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