[English] 日本語
Yorodumi
- PDB-3zfg: Human enterovirus 71 in complex with capsid binding inhibitor WIN51711 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zfg
TitleHuman enterovirus 71 in complex with capsid binding inhibitor WIN51711
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / EV71 / INHIBITOR / PICORNAVIRUS
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 / 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-W71 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ENTEROVIRUS 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPlevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of Human Enterovirus 71 in Complex with a Capsid-Binding Inhibitor.
Authors: Plevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Oct 24, 2018Group: Data collection / Refinement description / Category: struct_ncs_oper
Item: _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] ..._struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / 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_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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0015
Polymers94,6594
Non-polymers3421
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,700,057300
Polymers5,679,511240
Non-polymers20,54660
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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 475 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,00525
Polymers473,29320
Non-polymers1,7125
Water0
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
  • 570 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)570,00630
Polymers567,95124
Non-polymers2,0556
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
Unit cell
Length a, b, c (Å)592.500, 592.500, 592.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), ()1
2generate(0.56443163, -0.76531488, -0.30937047), (312.21477, 0.74410918, 0.30945715), (0.59206233, -272.9304, -0.35737721)-0.56438411, 0.74414522, 247.88406
3generate(-0.14033281, -0.4941963, -0.85794914), (620.62835, 0.43867907, -0.80786467), (0.39359287, 21.69402, -0.88761894)-0.32113034, 0.33016349, 474.80493
4generate(-0.14033281, 0.43867907, -0.88761894), (499.02365, -0.49419629, -0.80786467), (-0.32113034, 476.71233, -0.85794914)0.39359287, 0.33016349, 367.16569
5generate(0.56443163, 0.74410918, -0.35737721), (115.45424, -0.76531487, 0.30945714), (-0.56438411, 463.30469, -0.30937046)0.59206234, 0.74414522, 73.7201
6generate(-0.97893114, -0.01909326, -0.20329601), (379.97061, -0.01909326, -0.9826971), (0.18423317, 206.94088, -0.20329601)0.18423318, 0.96162824, 19.94319
7generate(-0.4940938, 0.85801906, 0.14026624), (29.15114, -0.8078515, -0.39346856), (-0.43881481, 514.85607, -0.32132112)-0.33012996, 0.88756236, 144.56065
8generate(0.30944973, 0.56449343, 0.76523724), (-324.52196, -0.59193809, 0.74415922), (-0.30957446, 261.24723, -0.7442111)-0.35717534, 0.56442504, 354.35451
9generate(0.3212296, -0.49402769, 0.80792832), (-192.2845, 0.33026199, 0.85802332), (0.39334845, -203.40683, -0.88754637)0.14047284, 0.43878107, 359.3968
10generate(-0.47503356, -0.8547041, 0.20934186), (243.11586, 0.68429956, -0.20923258), (0.69853835, -236.97, -0.55324247)0.4750817, 0.68426614, 152.71923
11generate(0.96168803, 0.20301066, 0.18423575), (-106.33463, 0.20301065, -0.97899089), (0.01906614, 248.26706, 0.18423576)0.01906614, -0.98269714, 858.65262
12generate(0.62802757, -0.77715078, -0.04022476), (184.1799, -0.62070427, -0.46908343), (-0.62824115, 583.57255, 0.46936934)0.41952044, -0.77697813, 667.37506
13generate(-0.20943099, -0.69843149, -0.68434795), (582.39638, -0.47487533, 0.68444232), (-0.5532017, 362.07567, 0.85477019)0.20912237, -0.47501132, 506.81873
14generate(-0.39334839, 0.33038115, -0.85797747), (537.99317, 0.43896683, 0.88745297), (0.14048252, -110.12242, 0.80782743)-0.32136508, -0.49410458, 598.86701
15generate(0.33044296, 0.88750303, -0.32116322), (112.334, 0.85792342, -0.14060528), (0.4941635, -180.46001, 0.39341436)-0.43882629, -0.80787167, 816.31232
16generate(-0.98275689, -0.1839174, 0.01906026), (304.76401, -0.1839174, 0.96168798), (-0.20329931, 123.19214, 0.01906026)-0.20329932, -0.9789311, 913.00424
17generate(-0.6983654, 0.6844466, 0.20932899), (52.85418, 0.6844466, 0.55309484), (0.47499363, -247.09814, 0.20932899)0.47499363, -0.85472944, 731.78028
18generate(0.04031407, 0.62813436, 0.77705985), (-300.10277, 0.62813435, -0.62073687), (0.4691833, -66.61685, 0.77705985)0.4691833, -0.4195772, 455.62188
19generate(0.2124516, -0.27503252, 0.93766808), (-266.33234, -0.27503253, -0.93761162), (-0.21270063, 415.217, 0.93766808)-0.21270063, -0.27483998, 466.17056
20generate(-0.41984103, -0.77690811, 0.46919857), (107.49589, -0.77690811, 0.04038072), (-0.62831774, 532.5254, 0.46919857)-0.62831774, -0.6205397, 748.8484
21generate(0.20313837, -0.97896101, 0.01923897), (248.16683, -0.18425095, -0.01892042), (0.98269711, -266.17145, -0.96165814)-0.2031683, -0.18421796, 698.84514
22generate(-0.62067172, -0.46926947, -0.62813437), (583.54689, -0.46926947, -0.4194637), (0.77706909, -74.93841, -0.62813436)0.77706909, 0.04013542, 408.38738
23generate(-0.47503356, 0.68429956, -0.55324246), (362.13742, -0.8547041, -0.20923258), (0.4750817, 85.65616, 0.20934185)0.69853836, 0.68426614, 10.13771
24generate(0.43878587, 0.88755289, 0.14041662), (-110.08121, -0.80789728, 0.32124068), (0.49407126, -6.32397, 0.39340684)-0.33023368, 0.85800744, 54.46364
25generate(0.85791917, -0.14039868, 0.4942296), (-180.51891, -0.39353445, 0.43886007), (0.80779483, -223.76539, -0.33031096)-0.88751905, 0.32125475, 480.10824
26generate(-0.18407813, 0.96168803, -0.20315357), (123.15007, -0.01904817, 0.2031564), (0.978961, -320.49868, 0.98272702)0.18407502, -0.01907827, 287.72559
27generate(0.68430383, 0.55313561, 0.47515184), (-247.15427, -0.2094392, -0.47506399), (0.85466334, -139.22453, 0.69847226)-0.68436481, -0.20923984, 539.57862
28generate(0.62802757, -0.62070427, 0.46936933), (-66.68947, -0.77715078, -0.46908342), (0.41952045, 136.90228, -0.04022475)-0.62824115, -0.77697814, 892.56871
29generate(-0.27513503, -0.93762481, -0.21250986), (415.14825, -0.93762481, 0.21283316), (0.27488501, 126.28388, -0.21250985)0.274885, -0.93769814, 858.87557
30generate(-0.77704395, 0.04034742, -0.62815187), (532.47554, -0.46909162, 0.62830022), (0.62063829, -156.40546, 0.41970912)0.77692401, -0.46929026, 485.06196
31generate(0.00016073, 0.99999998, -0.00014574), (0.04202, 1.497E-5, -0.00014575), (-0.99999999, 592.51894, -0.99999999)0.00016073, -1.498E-5, 592.48348
32generate(0.74425197, 0.30941638, 0.59190414), (-272.87432, 0.3572772, 0.56432754), (-0.74423613, 344.67934, -0.56430666)0.76537306, 0.30945448, 280.22113
33generate(0.43878587, -0.80789728, 0.39340684), (21.7666, 0.88755289, 0.32124068), (-0.33023369, 117.72014, 0.14041661)0.49407125, 0.85800744, -28.14849
34generate(-0.4940938, -0.80785151, -0.32132112), (476.78104, 0.85801905, -0.39346856), (-0.33012997, 225.29125, 0.14026623)-0.43881481, 0.88756236, 93.53095
35generate(-0.76517904, 0.30949045, -0.56454999), (463.35451, 0.30949045, -0.59209629), (-0.74406831, 518.73304, -0.56454999)-0.7440683, 0.35727534, 477.1026
36generate(-0.01922097, -0.98272699, 0.18406034), (207.04106, 0.20328414, -0.18409024), (-0.96165812, 572.55127, 0.9789311)0.01893254, 0.20331121, 212.54584
37generate(-0.80788407, -0.39328253, -0.43892161), (514.88169, 0.32143146, 0.33020015), (-0.8874963, 447.88369, 0.49396876)-0.85807734, -0.14035007, 563.41293
38generate(-0.59177988, 0.74430199, -0.30953372), (261.18544, 0.74430199, 0.35707532), (-0.56436846, 238.12149, -0.30953372)-0.56436846, -0.76529545, 917.04212
39generate(0.33044296, 0.85792342, 0.39341436), (-203.44809, 0.88750304, -0.14060529), (-0.4388263, 233.14891, -0.32116322)0.4941635, -0.80787166, 784.72989
40generate(0.68430382, -0.20943919, 0.69847226), (-236.91116, 0.55313561, -0.475064), (-0.68436481, 439.83788, 0.47515184)0.85466334, -0.20923983, 349.32724
41generate(0.20313838, -0.18425095, -0.96165815), (572.59558, -0.97896101, -0.01892042), (-0.20316829, 379.89275, 0.01923898)0.98269711, -0.18421795, 385.53126
42generate(0.32122961, 0.33026198, -0.88754637), (447.92634, -0.4940277, 0.85802332), (0.14047284, 29.04845, 0.80792832)0.39334845, 0.43878106, 77.66534
43generate(0.74425197, 0.3572772, -0.56430666), (238.07184, 0.30941638, 0.56432755), (0.76537306, -324.55397, 0.59190414)-0.74423613, 0.30945446, 331.32258
44generate(0.88760293, -0.14053941, -0.43864531), (233.04386, 0.32103881, -0.49413015), (0.8079415, -192.24797, -0.33029549)-0.85795341, -0.39347278, 795.95728
45generate(0.55317634, -0.47522221, -0.68422204), (439.7909, -0.47522221, -0.85459723), (0.20935002, 243.12405, -0.68422203)0.20935002, -0.69857911, 829.46009
46generate(0.00016074, 1.496E-5, -0.99999999), (592.4746, 0.99999998, -0.00014574), (0.00016073, -0.05089, -0.00014575)-0.99999999, -1.499E-5, 592.52782
47generate(0.35747906, 0.56426572, -0.74418608), (344.63665, 0.56426572, -0.76545067), (-0.30933714, 312.24349, -0.74418607)-0.30933714, -0.59202839, 865.409
48generate(0.88760293, 0.32103881, -0.3302955), (117.76975, -0.1405394, -0.49413016), (-0.85795341, 620.65059, -0.4386453)0.8079415, -0.39347277, 570.73623
49generate(0.85791918, -0.39353444, -0.33031096), (225.39626, -0.14039867, 0.43886006), (-0.88751905, 498.96229, 0.4942296)0.80779483, 0.32125475, 115.73726
50generate(0.30944974, -0.59193809, -0.7442111), (518.77999, 0.56449343, 0.74415922), (-0.35717534, 115.34767, 0.76523724)-0.30957446, 0.56442503, 129.20521
51generate(-0.01922097, 0.20328414, 0.97893111), (-320.4788, -0.98272699, -0.18409023), (0.01893254, 304.8419, 0.18406034)-0.96165812, 0.20331121, 469.27758
52generate(-0.209431, -0.47487533, 0.85477019), (-139.30088, -0.69843149, 0.68444232), (0.20912238, 52.95692, -0.68434795)-0.55320171, -0.47501132, 839.60728
53generate(-0.77704396, -0.46909162, 0.41970912), (136.80349, 0.04034742, 0.62830022), (0.77692401, -300.07072, -0.62815187)0.62063828, -0.46929025, 659.18158
54generate(-0.93763804, 0.21264239, 0.27498751), (126.26745, 0.21264239, -0.27493005), (0.93765488, -266.36881, 0.2749875)0.93765488, 0.21256809, 177.34266
55generate(-0.46927767, 0.62819346, 0.62060571), (-156.34854, -0.41965237, -0.77701497), (0.46919039, 107.48775, 0.77696226)-0.04025807, 0.62825865, 59.97553
56generate(-0.18407814, -0.01904816, 0.98272703), (-266.19139, 0.96168803, 0.2031564), (0.18407502, -106.28369, -0.20315358)0.978961, -0.01907826, 344.26339
57generate(-0.46927768, -0.41965237, 0.77696226), (-74.86212, 0.62819346, -0.77701497), (-0.04025808, 184.15122, 0.6206057)0.4691904, 0.62825866, 8.91843
58generate(-0.85481095, -0.20922439, 0.47489304), (85.75491, -0.20922439, -0.69849761), (-0.68434366, 582.37417, 0.47489304)-0.68434365, 0.55330856, 230.35968
59generate(-0.80788407, 0.32143146, 0.49396877), (-6.30758, -0.39328252, 0.33020015), (-0.85807734, 538.05457, -0.43892161)-0.8874963, -0.14035006, 702.56285
60generate(-0.3933484, 0.43896684, 0.80782743), (-223.82236, 0.33038115, 0.88745297), (-0.32136508, 112.44061, -0.85797747)0.14048251, -0.49410457, 772.95922

-
Components

#1: Protein VP1


Mass: 32832.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#2: Protein VP2


Mass: 27800.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#3: Protein VP3


Mass: 26524.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2, UniProt: B2ZUN0*PLUS
#5: Chemical ChemComp-W71 / 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / COMPOUND IV


Mass: 342.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O3
Nonpolymer details5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE (W71): WIN 51711

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 73.3 % / Description: NONE
Crystal growpH: 8.5
Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M ...Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M SODIUM ACETATE AND 0.1M BIS-TRIS PROPANE PH7.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.2→33.2 Å / Num. obs: 353681 / % possible obs: 66.8 % / Observed criterion σ(I): 0.8 / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Net I/σ(I): 2.5
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 0.81 / % possible all: 44

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
GLRFphasing
PHASERphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AED

4aed


Resolution: 3.2→33.2 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0
Isotropic thermal model: CONSTRAINED 2 B FACTORS PER RESIDUE
σ(F): 0.8
RfactorNum. reflection% reflection
Rwork0.2491 --
obs0.2491 353681 66.8 %
Solvent computationSolvent model: BULK SOLVENT
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 25 0 6532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008474
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_deg1.49016
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: CONSTRAINS
LS refinement shellResolution: 3.2→3.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3547 15538 -
obs--44 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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