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- PDB-5ku2: expanded poliovirus in complex with VHH 7A -

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Basic information

Entry
Database: PDB / ID: 5ku2
Titleexpanded poliovirus in complex with VHH 7A
Components
  • VHH 7A
  • 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / 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) / Peptidase C3A/C3B, picornaviral ...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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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: 5.3 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 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references / Other
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.image_processing_id / _em_software.name
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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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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  • Deposited structure unit
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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
7: VHH 7A


Theoretical massNumber of molelcules
Total (without water)92,1134
Polymers92,1134
Non-polymers00
Water00
1
1: VP1
2: VP2
3: VP3
7: VHH 7A
x 60


Theoretical massNumber of molelcules
Total (without water)5,526,778240
Polymers5,526,778240
Non-polymers00
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
1: VP1
2: VP2
3: VP3
7: VHH 7A
x 5


  • icosahedral pentamer
  • 461 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)460,56520
Polymers460,56520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: VP1
2: VP2
3: VP3
7: VHH 7A
x 6


  • icosahedral 23 hexamer
  • 553 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)552,67824
Polymers552,67824
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
111
21A
31D
41E
51F
122
22B
32G
42J
52L
62N
133
23C
33H
43I
53K
63M
73T
83U
147
24S
151
25A
35D
45E
55F
162
26B
36G
46J
56L
66N
173
27C
37H
47I
57K
67M
77T
87U
187
28S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111171 - 213
2111A71 - 213
3111D71 - 213
4111E71 - 213
5111F71 - 213
12111232 - 279
2211A232 - 279
3211D232 - 279
4211E232 - 279
5211F232 - 279
1121210 - 43
2121B10 - 43
3121G10 - 43
4121J10 - 43
5121L10 - 43
6121N10 - 43
1221253 - 159
2221B53 - 159
3221G53 - 159
4221J53 - 159
5221L53 - 159
6221N53 - 159
13212175 - 268
2321B175 - 268
3321G175 - 268
4321J175 - 268
5321L175 - 268
6321N175 - 268
113131 - 175
2131C1 - 175
3131H1 - 175
4131I1 - 175
5131K1 - 175
6131M1 - 175
7131T1 - 175
8131U1 - 175
12313185 - 230
2231C185 - 230
3231H185 - 230
4231I185 - 230
5231K185 - 230
6231M185 - 230
7231T185 - 230
8231U185 - 230
114171 - 125
2141S1 - 125
1151171 - 213
2151A71 - 213
3151D71 - 213
4151E71 - 213
5151F71 - 213
12511232 - 279
2251A232 - 279
3251D232 - 279
4251E232 - 279
5251F232 - 279
1161210 - 43
2161B10 - 43
3161G10 - 43
4161J10 - 43
5161L10 - 43
6161N10 - 43
1261253 - 159
2261B53 - 159
3261G53 - 159
4261J53 - 159
5261L53 - 159
6261N53 - 159
13612175 - 268
2361B175 - 268
3361G175 - 268
4361J175 - 268
5361L175 - 268
6361N175 - 268
117131 - 175
2171C1 - 175
3171H1 - 175
4171I1 - 175
5171K1 - 175
6171M1 - 175
7171T1 - 175
8171U1 - 175
12713185 - 230
2271C185 - 230
3271H185 - 230
4271I185 - 230
5271K185 - 230
6271M185 - 230
7271T185 - 230
8271U185 - 230
118171 - 124
2181S1 - 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 7A


Mass: 13222.551 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)
Has protein modificationY

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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 in complex with VHH 7A / 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.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0151 / Classification: refinement
EM software
IDNameVersionCategory
1e2boxer.pyparticle selection
2SerialEMimage acquisition
7Cootmodel fitting
8Cootother
9RELION1.3initial Euler assignment
10FREALIGN9final Euler assignment
11Relion 1.3classification
12GeFrealign3D reconstruction
13CTFFIND3CTF correction
14REFMAC 5.8.01245model refinement
15FREALIGN9.093D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17654 / 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: 5.3→5.3 Å / Cor.coef. Fo:Fc: 0.732 / SU B: 101.898 / SU ML: 1.272 / ESU R: 1.448
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.47782 --
obs0.47782 177930 99.99 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 37.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.88 Å20.18 Å2
2---0.95 Å2-0.05 Å2
3---2.03 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.01935090
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg2.2041.95247827
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg1.77854335
ELECTRON MICROSCOPYr_dihedral_angle_2_deg18.83323.6561469
ELECTRON MICROSCOPYr_dihedral_angle_3_deg9.605155511
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.18715183
ELECTRON MICROSCOPYr_chiral_restr0.1640.25367
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02126619
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: 4.501→4.744 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.545 25966 -
Rfree-0 -
obs--99.98 %

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