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- PDB-7enp: wild type of O type Foot-and-mouth disease virus -

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Basic information

Entry
Database: PDB / ID: 7enp
Titlewild type of O type Foot-and-mouth disease virus
Components
  • VP1 of O type FMDV capsid protein
  • VP2 of O type FMDV capsid protein
  • VP3 of O type FMDV capsid protein
  • VP4 of O type FMDV capsid
KeywordsVIRUS / FMDV
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : ...L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Papain-like cysteine peptidase superfamily / 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 speciesFoot-and-mouth disease virus - type O
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDong, H. / Lu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31941011, 12034006 China
CitationJournal: J Virol / Year: 2021
Title: A Heat-Induced Mutation on VP1 of Foot-and-Mouth Disease Virus Serotype O Enhanced Capsid Stability and Immunogenicity.
Authors: Hu Dong / Yuanlu Lu / Yun Zhang / Suyu Mu / Nan Wang / Ping Du / Xiaoying Zhi / Xiaobo Wen / Xiangxi Wang / Shiqi Sun / Yanming Zhang / Huichen Guo /
Abstract: Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes a significant economic burden globally. Vaccination is the most effective FMD control ...Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes a significant economic burden globally. Vaccination is the most effective FMD control strategy. However, FMD virus (FMDV) particles are prone to dissociate when appropriate physical or chemical conditions are unavailable, such as an incomplete cold chain. Such degraded vaccines result in compromised herd vaccination. Therefore, thermostable FMD particles are needed for use in vaccines. This study generated thermostable FMDV mutants (M3 and M10) by serial passages at high temperature, subsequent amplification, and purification. Both mutants contained an alanine-to-threonine mutation at position 13 in VP1 (A1013T), although M3 contained 3 additional mutations. The selected mutants showed improved stability and immunogenicity in neutralizing antibody titers, compared with the wild-type (wt) virus. The sequencing analysis and cryo-electron microscopy showed that the mutation of alanine to threonine at the 13th amino acid in the VP1 protein (A1013T) is critical for the capsid stability of FMDV. Virus-like particles containing A1013T (VLP) also showed significantly improved stability to heat treatment. This study demonstrated that Thr at the 13th amino acid of VP1 could stabilize the capsid of FMDV. Our findings will facilitate the development of a stable vaccine against FMDV serotype O. Foot-and-mouth disease (FMD) serotype O is one of the global epidemic serotypes and causes significant economic loss. Vaccination plays a key role in the prevention and control of FMD. However, the success of vaccination mainly depends on the quality of the vaccine. Here, the thermostable FMD virus (FMDV) mutants (M3 and M10) were selected through thermal screening at high temperatures with improved stability and immunogenicity compared with the wild-type virus. The results of multisequence alignment and cryo-electron microscopy (cryo-EM) analysis showed that the Thr substitution at the 13th amino acid in the VP1 protein is critical for the capsid stability of FMDV. For thermolabile type O FMDV, this major discovery will aid the development of its thermostable vaccine.
History
DepositionApr 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Oct 13, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.4Oct 20, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.5Oct 27, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.6Dec 1, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.7Dec 8, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.8Jan 26, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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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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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
1: VP1 of O type FMDV capsid protein
2: VP2 of O type FMDV capsid protein
3: VP3 of O type FMDV capsid protein
4: VP4 of O type FMDV capsid


Theoretical massNumber of molelcules
Total (without water)80,3624
Polymers80,3624
Non-polymers00
Water0
1
1: VP1 of O type FMDV capsid protein
2: VP2 of O type FMDV capsid protein
3: VP3 of O type FMDV capsid protein
4: VP4 of O type FMDV capsid
x 60


Theoretical massNumber of molelcules
Total (without water)4,821,729240
Polymers4,821,729240
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 of O type FMDV capsid protein
2: VP2 of O type FMDV capsid protein
3: VP3 of O type FMDV capsid protein
4: VP4 of O type FMDV capsid
x 5


  • icosahedral pentamer
  • 402 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)401,81120
Polymers401,81120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1 of O type FMDV capsid protein
2: VP2 of O type FMDV capsid protein
3: VP3 of O type FMDV capsid protein
4: VP4 of O type FMDV capsid
x 6


  • icosahedral 23 hexamer
  • 482 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)482,17324
Polymers482,17324
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
6
1: VP1 of O type FMDV capsid protein
2: VP2 of O type FMDV capsid protein
3: VP3 of O type FMDV capsid protein
4: VP4 of O type FMDV capsid
x 60


  • crystal asymmetric unit, crystal frame
  • 4.82 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,821,729240
Polymers4,821,729240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.36180337, 0.58778524, 0.72360681), (-0.26286566, 0.809017, -0.52573106), (-0.89442718, -1.2E-7, 0.44721362)-162.37474, 236.27463, 349.06794
3generate(-0.67082048, 0.68819085, 0.27639324), (0.16245968, 0.5, -0.85065084), (-0.72360676, -0.52573125, -0.44721351)170.34421, 286.59171, 650.40823
4generate(-0.67082049, 0.16245968, -0.72360675), (0.68819086, 0.5, -0.52573125), (0.27639325, -0.85065083, -0.4472135)538.35058, 81.41474, 487.57883
5generate(0.36180336, -0.26286565, -0.89442717), (0.58778526, 0.80901699, -1.1E-7), (0.72360682, -0.52573105, 0.44721364)433.07206, -95.70868, 85.60444
6generate(-0.9472137, 0.16245968, -0.27639293), (0.16245968, -0.5, -0.85065084), (-0.27639293, -0.85065084, 0.4472137)497.14864, 527.79171, 405.17501
7generate(-0.13819683, -0.42532556, -0.89442708), (0.95105652, -0.30901699, -1.8E-7), (-0.27639308, -0.85065072, 0.44721383)592.85741, 86.34011, 405.17499
8generate(0.86180329, -0.42532556, -0.27639328), (0.42532558, 0.30901699, 0.85065073), (-0.27639328, -0.85065072, 0.44721371)202.58763, -141.10039, 405.17507
9generate(0.67082049, 0.16245968, 0.72360675), (-0.68819086, 0.49999999, 0.52573125), (-0.27639325, -0.85065084, 0.44721351)-134.32113, 159.78526, 405.17514
10generate(-0.4472135, 0.52573094, 0.72360697), (-0.85065092, -0.52573095), (-0.27639303, -0.85065091, 0.44721351)47.72759, 573.18331, 405.1751
11generate(-0.86180329, 0.42532556, 0.27639328), (0.42532558, 0.309017, 0.85065073), (0.27639329, 0.85065072, -0.4472137)279.81237, -141.10039, 77.22493
12generate(-0.67082048, -0.16245969, -0.72360675), (-0.68819086, 0.5, 0.52573124), (0.27639325, 0.85065084, -0.44721351)616.72113, 159.78526, 77.22487
13generate(0.44721351, -0.52573094, -0.72360696), (-0.85065092, -0.52573095), (0.27639302, 0.85065091, -0.44721351)434.67241, 573.18331, 77.22491
14generate(0.9472137, -0.16245968, 0.27639294), (0.16245968, -0.5, -0.85065084), (0.27639293, 0.85065084, -0.44721371)-14.74865, 527.79171, 77.22499
15generate(0.13819683, 0.42532556, 0.89442708), (0.95105653, -0.30901699, -1.8E-7), (0.27639309, 0.85065072, -0.44721383)-110.45742, 86.34011, 77.22501
16generate(0.809017, -0.58778524, -3.4E-7), (-0.58778526, -0.809017, 1.1E-7), (-3.6E-7, 1.2E-7, -1)187.83898, 578.10868, 482.40007
17generate(0.44721394, 0.89442702), (-1), (0.89442702, -0.44721394)-82.4038, 482.4, 133.33221
18generate(-0.63819632, 0.26286565, 0.723607), (0.26286566, -0.80901699, 0.52573107), (0.72360702, 0.52573106, 0.44721331)157.19575, 246.12537, -168.00819
19generate(-0.9472137, -0.16245969, -0.27639294), (-0.16245968, -0.5, 0.85065084), (-0.27639293, 0.85065083, 0.4472137)575.5192, 195.80829, -5.17895
20generate(-0.05278668, -0.68819085, -0.72360687), (-0.68819086, -0.5, 0.52573124), (-0.72360688, 0.52573124, -0.44721332)594.45776, 400.98526, 396.79546
21generate(-0.36180336, -0.26286566, 0.89442717), (-0.58778526, 0.80901699, 1.1E-7), (-0.72360682, -0.52573106, -0.44721363)176.13433, 187.83888, 650.40823
22generate(-0.86180329, -0.42532557, 0.27639328), (-0.42532558, 0.30901699, -0.85065073), (0.27639329, -0.85065072, -0.4472137)484.98942, 474.43059, 487.57884
23generate(-0.44721351, -0.8506509, -0.27639303), (0.52573095, -0.85065091), (0.72360698, -0.52573094, 0.44721351)620.9109, 319.5707, 85.6044
24generate(0.30901699, -0.95105651, 1.3E-7), (0.95105652, 0.309017, -1.8E-7), (1.4E-7, 1.9E-7, 1)396.0599, -62.72969, -8.0E-5
25generate(0.36180337, -0.58778525, 0.72360681), (0.26286566, 0.80901699, 0.52573106), (-0.89442718, 1.1E-7, 0.44721362)121.17286, -144.14443, 349.06788
26generate(0.05278668, -0.68819085, 0.72360687), (0.68819086, -0.5, -0.52573124), (0.72360688, 0.52573125, 0.44721331)219.92551, 322.61474, -168.00821
27generate(-0.44721351, -0.52573095, 0.72360696), (0.85065092, 0.52573095), (-0.27639303, 0.85065091, 0.4472135)301.3402, -90.78331, -5.1789
28generate(-0.67082047, -0.68819086, 0.27639324), (-0.16245968, 0.5, 0.85065084), (-0.72360676, 0.52573125, -0.44721351)502.32748, -45.39171, 396.79548
29generate(-0.30901699, -0.95105651, -1.3E-7), (-0.95105652, 0.30901699, 1.8E-7), (-1.4E-7, 1.9E-7, -1)545.12976, 396.05989, 482.39999
30generate(0.13819683, -0.95105651, 0.27639309), (-0.42532557, -0.30901699, -0.85065073), (0.89442708, 1.9E-7, -0.44721382)370.59574, 623.50039, 133.33212
31generate(0.4472135, 0.52573095, -0.72360697), (0.85065092, 0.52573095), (0.27639303, -0.85065091, -0.4472135)181.0598, -90.78331, 487.5789
32generate(0.67082048, 0.68819086, -0.27639325), (-0.16245968, 0.5, 0.85065084), (0.72360676, -0.52573124, 0.44721352)-19.92748, -45.39171, 85.60453
33generate(0.309017, 0.95105651, 1.3E-7), (-0.95105652, 0.30901699, 1.8E-7), (1.3E-7, -1.9E-7, 1)-62.72976, 396.05989, 1.0E-5
34generate(-0.13819683, 0.95105651, -0.27639309), (-0.42532558, -0.30901699, -0.85065073), (-0.89442708, -1.9E-7, 0.44721382)111.80426, 623.50039, 349.06789
35generate(-0.05278669, 0.68819086, -0.72360687), (0.68819086, -0.5, -0.52573125), (-0.72360688, -0.52573125, -0.44721331)262.47449, 322.61475, 650.40821
36generate(-0.13819683, 0.42532556, -0.89442708), (-0.95105652, -0.30901699, 1.8E-7), (-0.27639309, 0.85065072, 0.44721382)387.68036, 545.12969, -5.17891
37generate(0.63819632, 0.26286566, -0.723607), (-0.26286566, -0.80901699, -0.52573106), (-0.72360702, 0.52573105, -0.44721332)198.39786, 626.54443, 396.79554
38generate(0.80901699, 0.58778525, -3.5E-7), (0.58778526, -0.80901699, -1.1E-7), (-3.6E-7, -1.2E-7, -1)-95.70862, 294.56112, 482.40012
39generate(0.13819682, 0.95105651, 0.27639309), (0.42532558, -0.30901699, 0.85065073), (0.89442708, -1.8E-7, -0.44721382)-88.19392, 7.96941, 133.33221
40generate(-0.44721351, 0.8506509, -0.27639304), (-0.52573095, 0.85065091), (0.72360698, 0.52573094, 0.44721351)210.5569, 162.8293, -168.0082
41generate(-0.36180337, -0.58778525, -0.72360681), (-0.26286566, 0.80901699, -0.52573107), (0.89442718, 1.2E-7, -0.44721362)644.77474, 236.27463, 133.33207
42generate(0.67082048, -0.68819085, -0.27639324), (0.16245968, 0.5, -0.85065084), (0.72360676, 0.52573125, 0.44721351)312.05579, 286.59171, -168.00822
43generate(0.67082048, -0.16245969, 0.72360675), (0.68819086, 0.50000001, -0.52573124), (-0.27639325, 0.85065084, 0.4472135)-55.95058, 81.41474, -5.17883
44generate(-0.36180336, 0.26286565, 0.89442717), (0.58778525, 0.809017, -1.1E-7), (-0.72360682, 0.52573106, -0.44721364)49.32794, -95.70867, 396.79557
45generate(-1), (1), (-1)482.4, 482.40001
46generate(0.44721351, 0.8506509, 0.27639303), (0.52573095, -0.85065091), (-0.72360698, 0.52573094, -0.44721352)-138.5109, 319.5707, 396.7956
47generate(-0.309017, 0.95105651, -1.3E-7), (0.95105652, 0.309017, -1.8E-7), (-1.3E-7, -1.8E-7, -1)86.3401, -62.72969, 482.40008
48generate(-0.36180337, 0.58778525, -0.72360681), (0.26286566, 0.80901699, 0.52573106), (0.89442718, -1.1E-7, -0.44721362)361.22714, -144.14443, 133.33212
49generate(0.36180336, 0.26286565, -0.89442717), (-0.58778526, 0.80901699, 1.1E-7), (0.72360682, 0.52573106, 0.44721363)306.26567, 187.83888, -168.00822
50generate(0.86180329, 0.42532556, -0.27639328), (-0.42532558, 0.309017, -0.85065073), (-0.27639329, 0.85065072, 0.4472137)-2.58942, 474.43059, -5.17884
51generate(-0.13819683, -0.95105651, -0.27639309), (0.42532557, -0.309017, 0.85065073), (-0.89442708, 1.8E-7, 0.44721382)570.59392, 7.96941, 349.06779
52generate(0.44721352, -0.8506509, 0.27639303), (-0.52573095, 0.85065091), (-0.72360698, -0.52573094, -0.44721351)271.8431, 162.82931, 650.40821
53generate(0.13819683, -0.42532556, 0.89442708), (-0.95105652, -0.309017, 1.8E-7), (0.27639309, -0.85065072, -0.44721382)94.71964, 545.12969, 487.57892
54generate(-0.63819632, -0.26286565, 0.723607), (-0.26286566, -0.809017, -0.52573106), (0.72360702, -0.52573106, 0.44721332)284.00214, 626.54443, 85.60447
55generate(-0.809017, -0.58778525, 3.5E-7), (0.58778526, -0.80901699, -1.1E-7), (3.6E-7, 1.1E-7, 1)578.10862, 294.56112, -0.00011
56generate(0.05278669, 0.68819085, 0.72360687), (-0.68819086, -0.5, 0.52573125), (0.72360688, -0.52573125, 0.44721332)-112.05776, 400.98526, 85.60455
57generate(-0.80901699, 0.58778525, 3.4E-7), (-0.58778526, -0.809017, 1.2E-7), (3.6E-7, -1.2E-7, 1)294.56101, 578.10868, -6.0E-5
58generate(-0.44721394, -0.89442702), (-1), (-0.89442702, 0.44721394)564.8038, 482.4, 349.0678
59generate(0.63819632, -0.26286565, -0.723607), (0.26286566, -0.809017, 0.52573106), (-0.72360701, -0.52573106, -0.44721331)325.20425, 246.12537, 650.4082
60generate(0.9472137, 0.16245969, 0.27639293), (-0.16245968, -0.5, 0.85065084), (0.27639293, -0.85065084, -0.4472137)-93.1192, 195.80829, 487.57896

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Components

#1: Protein VP1 of O type FMDV capsid protein


Mass: 23205.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type O
#2: Protein VP2 of O type FMDV capsid protein


Mass: 24496.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type O
#3: Protein VP3 of O type FMDV capsid protein


Mass: 23882.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type O
#4: Protein VP4 of O type FMDV capsid


Mass: 8777.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type O / References: UniProt: Q1KL66

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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: Foot-and-mouth disease virus - type O / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Foot-and-mouth disease virus - type O
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1043 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045266
ELECTRON MICROSCOPYf_angle_d0.5837192
ELECTRON MICROSCOPYf_dihedral_angle_d9.09717
ELECTRON MICROSCOPYf_chiral_restr0.043810
ELECTRON MICROSCOPYf_plane_restr0.005934

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