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- PDB-5kwl: expanded poliovirus in complex with VHH 10E -

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Basic information

Entry
Database: PDB / ID: 5kwl
Titleexpanded poliovirus in complex with VHH 10E
Components
  • VHH 10E
  • VP1
  • VP2
  • VP3
KeywordsVIRUS/Immune System / poliovirus / VHH / nanobody / 80S / expanded / single domain antibody / VIRUS-Immune System complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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 ...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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Poliovirus type 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsStrauss, M. / Schotte, L. / Filman, D.J. / Hogle, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI020566 United States
CitationJournal: J Virol / Year: 2017
Title: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State.
Authors: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle /
Abstract: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs ...By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion.
IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The ...IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Other
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Database references / Other
Revision 1.4Feb 8, 2017Group: Database references
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.6Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.7Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
7: VHH 10E


Theoretical massNumber of molelcules
Total (without water)92,1274
Polymers92,1274
Non-polymers00
Water0
1
1: VP1
2: VP2
3: VP3
7: VHH 10E
x 60


Theoretical massNumber of molelcules
Total (without water)5,527,616240
Polymers5,527,616240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: VP1
2: VP2
3: VP3
7: VHH 10E
x 5


  • icosahedral pentamer
  • 461 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)460,63520
Polymers460,63520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1
2: VP2
3: VP3
7: VHH 10E
x 6


  • icosahedral 23 hexamer
  • 553 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)552,76224
Polymers552,76224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111
21A
31D
41E
51F
61V
71W
81X
122
22B
32G
42J
52L
62N
133
23C
33H
43I
53K
63M
73T
83U
147
24S
151
25A
35D
45E
55F
65V
75W
85X
162
26B
36G
46J
56L
66N
173
27C
37H
47I
57K
67M
77T
87U
187
28S
191
29A
39D
49E
59F
69V
79W
89X
1102
210B
310G
410J
510L
610N
1113
211C
311H
411I
511K
611M
711T
811U
1127
212S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111157 - 213
2111A57 - 213
3111D57 - 213
4111E57 - 213
5111F57 - 213
6111V57 - 213
7111W57 - 213
8111X57 - 213
12111232 - 279
2211A232 - 279
3211D232 - 279
4211E232 - 279
5211F232 - 279
6211V232 - 279
7211W232 - 279
8211X232 - 279
112121 - 43
2121B1 - 43
3121G1 - 43
4121J1 - 43
5121L1 - 43
6121N1 - 43
1221253 - 159
2221B53 - 159
3221G53 - 159
4221J53 - 159
5221L53 - 159
6221N53 - 159
13212174 - 269
2321B174 - 269
3321G174 - 269
4321J174 - 269
5321L174 - 269
6321N174 - 269
113131 - 231
2131C1 - 231
3131H1 - 231
4131I1 - 231
5131K1 - 231
6131M1 - 231
7131T1 - 231
8131U1 - 231
114171 - 124
2141S1 - 124
1151165 - 212
2151A65 - 212
3151D65 - 212
4151E65 - 212
5151F65 - 212
6151V65 - 212
7151W65 - 212
8151X65 - 212
12511232 - 279
2251A232 - 279
3251D232 - 279
4251E232 - 279
5251F232 - 279
6251V232 - 279
7251W232 - 279
8251X232 - 279
116121 - 43
2161B1 - 43
3161G1 - 43
4161J1 - 43
5161L1 - 43
6161N1 - 43
1261255 - 133
2261B55 - 133
3261G55 - 133
4261J55 - 133
5261L55 - 133
6261N55 - 133
13612140 - 159
2361B140 - 159
3361G140 - 159
4361J140 - 159
5361L140 - 159
6361N140 - 159
14612175 - 272
2461B175 - 272
3461G175 - 272
4461J175 - 272
5461L175 - 272
6461N175 - 272
117131 - 230
2171C1 - 230
3171H1 - 230
4171I1 - 230
5171K1 - 230
6171M1 - 230
7171T1 - 230
8171U1 - 230
118171 - 124
2181S1 - 124
1191171 - 212
2191A71 - 212
3191D71 - 212
4191E71 - 212
5191F71 - 212
6191V71 - 212
7191W71 - 212
8191X71 - 212
12911232 - 279
2291A232 - 279
3291D232 - 279
4291E232 - 279
5291F232 - 279
6291V232 - 279
7291W232 - 279
8291X232 - 279
1110121 - 42
21101B1 - 42
31101G1 - 42
41101J1 - 42
51101L1 - 42
61101N1 - 42
12101255 - 159
22101B55 - 159
32101G55 - 159
42101J55 - 159
52101L55 - 159
62101N55 - 159
131012175 - 268
23101B175 - 268
33101G175 - 268
43101J175 - 268
53101L175 - 268
63101N175 - 268
1111131 - 230
21111C1 - 230
31111H1 - 230
41111I1 - 230
51111K1 - 230
61111M1 - 230
71111T1 - 230
81111U1 - 230
1112171 - 124
21121S1 - 124

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)-0.05154, 0.01791, -0.00045
3given(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)-0.00914, 0.03233, -0.02408
4given(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)-0.00052, -0.00904, -0.00661
5given(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)0.12889, 0.06892, -0.05558
6given(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)-0.11564, -0.11264, 0.05872
7given(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)0.08254, -0.02893, -0.00391
8given(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)-0.1812, -0.17441, 0.14015
9given(1), (1), (1)
10given(0.309796, 0.808693, -0.500042), (-0.808811, 0.500624, 0.308544), (0.499851, 0.308853, 0.809172)-0.01852, -0.03142, 0.01647
11given(0.30849, -0.809106, 0.500182), (0.809023, 0.49974, 0.309421), (-0.500315, 0.309205, 0.80875)-0.04023, -0.03907, 0.03686
12given(-0.308865, 0.809192, 0.499811), (-0.809079, -0.499795, 0.309186), (0.499994, -0.30889, 0.809069)0.02191, -0.02136, -0.00739
13given(-0.309311, -0.808773, 0.500213), (0.80918, -0.500162, -0.308327), (0.499555, 0.309394, 0.809148)-0.01033, -0.09286, 0.03359
14given(-0.499825, 0.308647, 0.809266), (0.309273, -0.809154, 0.49962), (0.809027, 0.500006, 0.308979)-0.02726, 0.03577, 0.02027
15given(1), (1), (1)
16given(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)0.00324, -0.04093, 0.01727
17given(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)-0.04711, 0.00924, 0.01115
18given(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)0.00195, -0.06586, 0.01564
19given(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)-0.09558, 0.0211, 0.02025
20given(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)-0.07535, 0.05127, 0.01461
21given(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)-0.00478, 0.01621, 0.00163
22given(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)0.0676, 0.03751, -0.01401
23given(1), (1), (1)
24given(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)-0.08093, 0.36696, -0.02947
25given(1), (1), (1)
26given(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)-0.05154, 0.01791, -0.00045
27given(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)-0.00914, 0.03233, -0.02408
28given(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)-0.00052, -0.00904, -0.00661
29given(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)0.12889, 0.06892, -0.05558
30given(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)-0.11564, -0.11264, 0.05872
31given(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)0.08254, -0.02893, -0.00391
32given(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)-0.1812, -0.17441, 0.14015
33given(1), (1), (1)
34given(0.309797, 0.808693, -0.500041), (-0.808812, 0.500624, 0.308542), (0.499848, 0.308855, 0.809173)-0.01862, -0.03098, 0.01651
35given(0.308491, -0.809106, 0.500181), (0.809022, 0.499741, 0.309422), (-0.500316, 0.309204, 0.80875)-0.04018, -0.0391, 0.03692
36given(-0.308866, 0.80919, 0.499813), (-0.809078, -0.499798, 0.309185), (0.499995, -0.308891, 0.809068)0.02161, -0.02114, -0.00721
37given(-0.309312, -0.808773, 0.500212), (0.80918, -0.500162, -0.308327), (0.499554, 0.309393, 0.809149)-0.01019, -0.09283, 0.03359
38given(-0.499834, 0.308648, 0.80926), (0.309272, -0.809151, 0.499626), (0.809022, 0.500012, 0.308985)-0.0261, 0.03522, 0.01993
39given(1), (1), (1)
40given(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)0.00324, -0.04093, 0.01727
41given(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)-0.04711, 0.00924, 0.01115
42given(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)0.00195, -0.06586, 0.01564
43given(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)-0.09558, 0.0211, 0.02025
44given(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)-0.07535, 0.05127, 0.01461
45given(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)-0.00478, 0.01621, 0.00163
46given(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)0.0676, 0.03751, -0.01401
47given(1), (1), (1)
48given(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)-0.08093, 0.36696, -0.02947
49given(1), (1), (1)
50given(0.308947, 0.809174, -0.499789), (-0.809122, 0.499811, 0.309048), (0.499874, 0.308911, 0.809136)-0.05154, 0.01791, -0.00045
51given(-0.80873, 0.500307, -0.309271), (-0.500433, -0.30899, 0.808759), (0.309066, 0.808838, 0.50026)-0.00914, 0.03233, -0.02408
52given(-0.80905, -0.499954, 0.309005), (0.499923, -0.308921, 0.809101), (-0.309055, 0.809082, 0.499871)-0.00052, -0.00904, -0.00661
53given(0.3094, -0.809369, 0.499192), (0.809318, 0.499743, 0.308645), (-0.499275, 0.308511, 0.809658)0.12889, 0.06892, -0.05558
54given(-0.999999, 0.000787, 0.00123), (-0.000787, -1, 0.000644), (0.001231, 0.000643, 0.999999)-0.11564, -0.11264, 0.05872
55given(-0.308665, 0.809433, 0.499544), (-0.809159, -0.49952, 0.309421), (0.499988, -0.308703, 0.809145)0.08254, -0.02893, -0.00391
56given(-0.308718, -0.808202, 0.5015), (0.809535, -0.500066, -0.30755), (0.499346, 0.311036, 0.808647)-0.1812, -0.17441, 0.14015
57given(1), (1), (1)
58given(0.309796, 0.808693, -0.500042), (-0.808811, 0.500624, 0.308544), (0.499851, 0.308853, 0.809172)-0.01852, -0.03142, 0.01647
59given(0.30849, -0.809106, 0.500182), (0.809023, 0.49974, 0.309421), (-0.500315, 0.309205, 0.80875)-0.04023, -0.03907, 0.03686
60given(-0.308865, 0.809192, 0.499811), (-0.809079, -0.499795, 0.309186), (0.499994, -0.30889, 0.809069)0.02191, -0.02136, -0.00739
61given(-0.309311, -0.808773, 0.500213), (0.80918, -0.500162, -0.308327), (0.499555, 0.309394, 0.809148)-0.01033, -0.09286, 0.03359
62given(-0.499825, 0.308647, 0.809266), (0.309273, -0.809154, 0.49962), (0.809027, 0.500006, 0.308979)-0.02726, 0.03577, 0.02027
63given(1), (1), (1)
64given(0.308995, 0.808931, -0.500153), (-0.808837, 0.500156, 0.309236), (0.500305, 0.30899, 0.808839)0.00324, -0.04093, 0.01727
65given(0.309198, -0.808729, 0.500354), (0.808919, 0.500308, 0.308776), (-0.500047, 0.309273, 0.80889)-0.04711, 0.00924, 0.01115
66given(-1, 0.000124, -6.4E-5), (-0.000125, -1, 0.000423), (-6.4E-5, 0.000423, 1)0.00195, -0.06586, 0.01564
67given(-0.30896, 0.80865, 0.500628), (-0.808993, -0.50022, 0.308723), (0.500073, -0.309622, 0.80874)-0.09558, 0.0211, 0.02025
68given(-0.308695, -0.808937, 0.500329), (0.808875, -0.500014, -0.309366), (0.500429, 0.309204, 0.80868)-0.07535, 0.05127, 0.01461
69given(-0.808942, 0.500052, -0.30913), (-0.500145, -0.309015, 0.808928), (0.30898, 0.808986, 0.500074)-0.00478, 0.01621, 0.00163
70given(-0.808987, -0.500284, 0.308635), (0.499923, -0.309356, 0.808935), (-0.309219, 0.808712, 0.500368)0.0676, 0.03751, -0.01401
71given(1), (1), (1)
72given(0.311201, 0.808089, -0.500147), (-0.809773, 0.500934, 0.305505), (0.497415, 0.309932, 0.810259)-0.08093, 0.36696, -0.02947

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Components

#1: Protein VP1


Mass: 23645.768 Da / Num. of mol.: 1 / Fragment: UNP residues 650-858 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#2: Protein VP2


Mass: 29580.188 Da / Num. of mol.: 1 / Fragment: UNP residues 70-337 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#3: Protein VP3


Mass: 25664.455 Da / Num. of mol.: 1 / Fragment: UNP residues 342-571 / Source method: isolated from a natural source / Source: (natural) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / References: UniProt: P03300
#4: Antibody VHH 10E


Mass: 13236.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli K-12 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: expanded poliovirus (type 1) in complex with VHH 10E / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 9 MDa / Experimental value: NO
Source (natural)Organism: Poliovirus type 1 (strain Mahoney)
Buffer solutionpH: 7
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansSampling size: 5 µm / Width: 3800 / Height: 3700

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Processing

SoftwareName: REFMAC / Version: 5.8.0151 / Classification: refinement
EM software
IDNameVersionCategory
1e2boxer.pyparticle selection
4CTFFIND3CTF correction
7Cootmodel fitting
11RELION1.3classification
12GeFrealign and Frealign9.093D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13938 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with ...Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with the map. Refinement space: reciprocal, using both Fourier amplitudes and phases.
RefinementResolution: 4.5→98.6 Å / Cor.coef. Fo:Fc: 0.729 / SU B: 135.906 / SU ML: 1.653 / ESU R: 1.303
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.48055 --
obs0.48055 228405 99.94 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 24.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.87 Å20.51 Å2
2--0.34 Å2-1.05 Å2
3---0.28 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01940774
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.9991.94955596
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg1.67655010
ELECTRON MICROSCOPYr_dihedral_angle_2_deg18.48423.5691754
ELECTRON MICROSCOPYr_dihedral_angle_3_deg9.299156372
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.25615220
ELECTRON MICROSCOPYr_chiral_restr0.1420.26194
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02131120
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.5→4.743 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.524 33400 -
Rfree-0 -
obs--99.75 %

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