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- PDB-5abj: Structure of Coxsackievirus A16 in complex with GPP3 -

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Basic information

Entry
Database: PDB / ID: 5abj
TitleStructure of Coxsackievirus A16 in complex with GPP3
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / INHIBITOR
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / Few Secondary Structures / Irregular / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-YM2 / Genome polyprotein
Similarity search - Component
Biological speciesCOXSACKIEVIRUS A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsDe Colibus, L. / Wang, X. / Tijsma, A. / Neyts, J. / Spyrou, J.A.B. / Ren, J. / Grimes, J.M. / Puerstinger, G. / Leyssen, P. / Fry, E.E. ...De Colibus, L. / Wang, X. / Tijsma, A. / Neyts, J. / Spyrou, J.A.B. / Ren, J. / Grimes, J.M. / Puerstinger, G. / Leyssen, P. / Fry, E.E. / Rao, Z. / Stuart, D.I.
CitationJournal: Plos Pathog. / Year: 2015
Title: Structure Elucidation of Coxsackievirus A16 in Complex with Gpp3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses.
Authors: De Colibus, L. / Wang, X. / Tijsma, A. / Neyts, J. / Spyrou, J.A.B. / Ren, J. / Grimes, J.M. / Puerstinger, G. / Leyssen, P. / Fry, E.E. / Rao, Z. / Stuart, D.I.
History
DepositionAug 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2May 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_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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3107
Polymers94,8414
Non-polymers4693
Water18010
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,718,593420
Polymers5,690,456240
Non-polymers28,137180
Water4,324240
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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 477 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)476,54935
Polymers474,20520
Non-polymers2,34515
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,85942
Polymers569,04624
Non-polymers2,81418
Water43224
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
Unit cell
Length a, b, c (Å)491.600, 491.600, 709.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5442, -0.7743, -0.3229), (0.3058, 0.5415, -0.7831), (0.7812, 0.3275, 0.5314)208.9928, 157.1542, -54.2016
3generate(-0.1916, -0.9468, 0.2585), (-0.2823, -0.1991, -0.9384), (0.94, -0.2528, -0.2292)218.5985, 348.4402, 131.8616
4generate(-0.191, -0.2803, 0.9407), (-0.947, -0.1996, -0.2517), (0.2583, -0.9389, -0.2273)15.8549, 309.6709, 300.6837
5generate(0.5445, 0.3055, 0.7811), (-0.7737, 0.5425, 0.3272), (-0.3238, -0.7826, 0.5318)-119.3563, 94.289, 219.2667
6generate(-0.9246, -0.3529, 0.1438), (-0.3527, 0.6497, -0.6734), (0.1442, -0.6733, -0.7252)256.072, 205.9263, 370.169
7generate(-0.2771, -0.4785, 0.8332), (-0.5858, 0.7715, 0.2483), (-0.7616, -0.4193, -0.4942)69.7821, 56.6413, 409.7457
8generate(0.5491, -0.7211, 0.4224), (0.1933, 0.6013, 0.7753), (-0.8131, -0.344, 0.4696)70.0719, -111.7127, 236.6187
9generate(0.4115, -0.7467, -0.5226), (0.9093, 0.3757, 0.1791), (0.0626, -0.5489, 0.8336)257.2943, -67.1832, 89.0711
10generate(-0.4989, -0.5193, -0.6939), (0.5724, 0.4037, -0.7137), (0.6507, -0.7532, 0.0958)372.0846, 129.202, 172.329
11generate(0.2689, 0.5833, 0.7665), (0.5825, -0.7322, 0.3529), (0.7671, 0.3516, -0.5367)-117.1273, 79.4714, 133.0094
12generate(-0.5528, 0.7701, 0.3183), (-0.2016, -0.4942, 0.8456), (0.8086, 0.4033, 0.4284)40.6055, 60.1084, -48.8737
13generate(-0.4063, 0.6722, -0.6189), (-0.9111, -0.3495, 0.2185), (-0.0694, 0.6527, 0.7544)200.1883, 240.5788, -28.8911
14generate(0.5063, 0.4256, -0.75), (-0.5642, -0.4943, -0.6613), (-0.6522, 0.758, -0.0102)141.1036, 371.2492, 165.3929
15generate(0.923, 0.3698, 0.106), (0.3598, -0.7324, -0.578), (-0.1361, 0.5716, -0.8091)-54.8993, 271.5739, 265.7192
16generate(-0.3449, -0.2295, -0.9101), (-0.2298, -0.9195, 0.3189), (-0.9101, 0.3191, 0.2644)355.5363, 209.1319, 202.9122
17generate(0.2838, 0.4833, -0.8282), (0.4841, -0.8178, -0.3113), (-0.8277, -0.3126, -0.466)175.2078, 219.5869, 399.7695
18generate(0.0483, 0.997, -0.0607), (0.9971, -0.0517, -0.0564), (-0.0594, -0.0578, -0.9966)5.3259, 16.5397, 367.0351
19generate(-0.7264, 0.6017, 0.3321), (0.6011, 0.3219, 0.7315), (0.3332, 0.731, -0.5955)80.5741, -119.7409, 150.2859
20generate(-0.9686, -0.1568, -0.1928), (-0.157, -0.2154, 0.9638), (-0.1927, 0.9638, 0.1841)296.8756, -0.7667, 48.811
21generate(0.7227, -0.6085, -0.3276), (-0.5529, -0.2246, -0.8024), (0.4147, 0.7611, -0.4988)167.3967, 361.3089, 119.3562
22generate(0.6878, -0.4037, 0.6033), (-0.4041, -0.9033, -0.143), (0.603, -0.1448, -0.7845)-18.0178, 310.4191, 258.4294
23generate(0.4925, 0.5259, 0.6934), (-0.4812, -0.4994, 0.7205), (0.7252, -0.6885, 0.0071)-124.6698, 117.4311, 170.7599
24generate(0.4068, 0.8952, -0.1819), (-0.6783, 0.4294, 0.5963), (0.6119, -0.1192, 0.7819)-5.1252, 48.9729, -22.4454
25generate(0.5493, 0.1944, -0.8127), (-0.7222, 0.5996, -0.3448), (0.4203, 0.7763, 0.4697)175.3488, 199.6211, -54.2497
26generate(-0.4997, -0.4309, 0.7514), (0.4751, 0.589, 0.6538), (-0.7243, 0.6837, -0.0896)105.959, -123.5164, 197.4475
27generate(-0.4058, -0.9114, -0.0676), (0.6719, -0.3477, 0.654), (-0.6196, 0.22, 0.7535)298.3855, -32.1246, 92.9533
28generate(-0.5403, -0.2982, -0.7868), (0.7259, -0.6381, -0.2566), (-0.4256, -0.7098, 0.5613)366.1675, 157.7875, 217.7268
29generate(-0.719, 0.56, -0.4116), (0.5611, 0.1183, -0.8192), (-0.41, -0.82, -0.3993)216.1792, 184.1797, 399.0385
30generate(-0.6933, 0.4786, 0.5389), (0.4064, 0.8771, -0.2561), (-0.5952, 0.0415, -0.8025)55.0802, 10.075, 386.7554
31generate(-0.4142, 0.7513, 0.5138), (-0.8934, -0.4434, -0.0718), (0.1738, -0.4888, 0.8549)-8.9528, 301.3793, 64.6313
32generate(0.41, 0.9102, 0.0592), (-0.7464, 0.3721, -0.5518), (-0.5243, 0.1821, 0.8319)-50.1015, 267.0637, 71.8727
33generate(0.9705, 0.1485, 0.1898), (0.131, 0.3358, -0.9328), (-0.2023, 0.9302, 0.3065)-48.2311, 230.3575, 32.2624
34generate(0.4932, -0.4814, 0.7246), (0.5265, -0.4978, -0.6892), (0.6925, 0.7214, 0.008)-5.876, 241.8409, 0.5084
35generate(-0.3625, -0.1081, 0.9257), (-0.1074, -0.9818, -0.1567), (0.9258, -0.1563, 0.3443)18.2863, 285.8428, 20.6965
36generate(0.1897, 0.2886, -0.9385), (0.9723, 0.0777, 0.2205), (0.1366, -0.9543, -0.2659)230.2988, -45.3042, 324.4849
37generate(-0.6928, 0.4057, -0.5962), (0.4777, 0.8775, 0.042), (0.5402, -0.2557, -0.8017)264.5064, -51.4975, 282.8857
38generate(-0.9221, -0.3745, -0.0979), (-0.3745, 0.7995, 0.4697), (-0.0976, 0.4697, -0.8774)301.2119, -12.0661, 285.4429
39generate(-0.1805, -0.9746, -0.1324), (-0.408, -0.0483, 0.9117), (-0.895, 0.2185, -0.3889)289.7501, 18.852, 328.9019
40generate(0.5064, -0.5643, -0.652), (0.4249, -0.4946, 0.7582), (-0.7503, -0.661, -0.0106)245.9084, -1.9031, 352.8507
41generate(0.7226, -0.553, 0.4148), (-0.6086, -0.2242, 0.7612), (-0.3279, -0.8024, -0.4986)29.4738, 92.053, 404.3113
42generate(0.9706, 0.1317, -0.2014), (0.1469, 0.339, 0.9293), (0.1907, -0.9315, 0.3097)22.8859, -100.731, 213.4027
43generate(0.3538, 0.1103, -0.9288), (0.2269, 0.9532, 0.1996), (0.9074, -0.2814, 0.3122)230.3357, -57.6192, 43.9752
44generate(-0.2763, -0.5866, -0.7613), (-0.4803, 0.7704, -0.4193), (0.8324, 0.2498, -0.4946)364.7422, 161.6857, 130.076
45generate(-0.0482, -0.9964, 0.0694), (-0.9964, 0.0432, -0.0725), (0.0693, -0.0727, -0.9949)240.4734, 254.1419, 352.7082
46generate(0.1901, 0.9724, 0.1353), (0.2898, 0.076, -0.9541), (-0.938, 0.2206, -0.2674)-43.9336, 246.646, 312.5019
47generate(0.1822, 0.4002, 0.8981), (0.9498, 0.1646, -0.266), (-0.2543, 0.9015, -0.3502)-106.8749, 32.5219, 158.3284
48generate(-0.5526, -0.2009, 0.8089), (0.77, -0.4944, 0.4032), (0.3189, 0.8457, 0.4279)74.0294, 18.1207, -42.9779
49generate(-1, 0.0005, -0.0088), (-0.0016, -0.9917, 0.1289), (-0.0087, 0.1289, 0.9916)248.9911, 223.4298, -13.5332
50generate(-0.5414, 0.7252, -0.4254), (-0.2981, -0.6387, -0.7094), (-0.7861, -0.2572, 0.562)176.2138, 364.5669, 206.3088
51generate(-0.4988, 0.4743, -0.7254), (-0.4323, 0.5893, 0.6825), (0.7512, 0.6541, -0.0889)255.004, -16.3829, 18.5712
52generate(-0.1803, -0.4084, -0.8948), (-0.9746, -0.049, 0.2187), (-0.1332, 0.9115, -0.3892)354.4925, 211.3877, 149.1561
53generate(0.6984, -0.4803, -0.5306), (-0.4795, -0.8644, 0.1514), (-0.5314, 0.1487, -0.834)190.2333, 262.6969, 371.1817
54generate(0.9231, 0.3594, -0.1366), (0.3696, -0.7317, 0.5727), (0.1059, -0.5791, -0.8083)-10.7388, 66.9673, 377.7556
55generate(0.1824, 0.9493, -0.2562), (0.3992, 0.1666, 0.9016), (0.8985, -0.2667, -0.3486)29.062, -105.7035, 160.0234
56generate(-0.4121, -0.8944, 0.1737), (0.7514, -0.4415, -0.4904), (0.5153, -0.0716, 0.854)254.3673, 171.6864, -29.164
57generate(-0.9726, -0.1218, 0.1981), (-0.1226, -0.4552, -0.8819), (0.1975, -0.882, 0.4278)223.9219, 350.4967, 185.454
58generate(-0.4998, 0.57, 0.6522), (-0.5171, 0.4077, -0.7526), (-0.6949, -0.7134, 0.0909)0.0734, 269.872, 334.2295
59generate(0.3535, 0.2272, 0.9074), (0.1097, 0.9533, -0.2814), (-0.929, 0.199, 0.312)-108.3919, 42.0368, 211.877
60generate(0.4074, -0.6776, 0.6123), (0.8953, 0.4288, -0.1211), (-0.1805, 0.5975, 0.7813)48.7827, -18.9262, -13.0148

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 33078.301 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 566-862
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COXSACKIEVIRUS A16 / Description: NINGBO STRAIN, ISOLATED FROM CHINA / Cell: VERO CELL / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: I3W9E1
#2: Protein VP2


Mass: 27557.104 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COXSACKIEVIRUS A16 / Description: NINGBO STRAIN, ISOLATED FROM CHINA / Cell: VERO CELL / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: I3W9E1
#3: Protein VP3


Mass: 26654.295 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 324-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COXSACKIEVIRUS A16 / Description: NINGBO STRAIN, ISOLATED FROM CHINA / Cell: VERO CELL / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: I3W9E1
#4: Protein VP4


Mass: 7551.226 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COXSACKIEVIRUS A16 / Description: NINGBO STRAIN, ISOLATED FROM CHINA / Cell: VERO CELL / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: I3W9E1

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Non-polymers , 4 types, 13 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-YM2 / 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE


Mass: 410.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N4O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 15

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Sample preparation

CrystalDescription: NONE
Crystal growDetails: 3.2 M SODIUM CHLORIDE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 888041 / % possible obs: 40.5 % / Observed criterion σ(I): -3 / Redundancy: 1.3 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.58 / Net I/σ(I): 1.42
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 0.62 / % possible all: 36.1

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.75→49.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 35266018.59 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.307 8919 1 %RANDOM
Rwork0.305 ---
obs0.305 888030 40.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: -2.30348 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2--2.66 Å20 Å2
3----5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.5 Å
Luzzati d res low-10 Å
Luzzati sigma a0.52 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.75→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 32 10 6440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d25.5
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.75→2.85 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 798 0.9 %
Rwork0.37 77833 -
obs--36 %
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
X-RAY DIFFRACTION6GPP3-XPLO2D-PRODRG.25.06.15.PARGPP3-XPLO2D-PRODRG.25.06.15.TOP

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