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- PDB-5xs7: Structure of Coxsackievirus A6 (CVA6) virus A-particle in complex... -

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Basic information

Entry
Database: PDB / ID: 5xs7
TitleStructure of Coxsackievirus A6 (CVA6) virus A-particle in complex with the neutralizing antibody fragment 1D5
Components
  • (Genome polyprotein) x 3
  • Heavy chain of Fab 1D5
  • Light chain of Fab 1D5
KeywordsVIRUS / Coxsackievirus A6 / Immune-complex / Icosahedral
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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Jelly Rolls - #20 / Picornavirus coat protein / 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 ...Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Jelly Rolls - #20 / Picornavirus coat protein / 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 / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Coxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZheng, Q.B. / He, M.Z. / Xu, L.F. / Yu, H. / Li, S.W. / Cheng, T.
Funding support China, United States, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670933 China
National Natural Science Foundation of China81401669 China
National Science and Technology Major Projects for Major New Drugs Innovation and Development2017ZX09101005-005-003 China
National Science and Technology Major Project of Infectious Diseases2017ZX10304402-002-003 China
Natural Science Foundation of Fujian Province2015J05073 China
National Institutes of Health (GrantR37-GM33050 United States
CitationJournal: Nat Commun / Year: 2017
Title: Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.
Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng ...Authors: Longfa Xu / Qingbing Zheng / Shaowei Li / Maozhou He / Yangtao Wu / Yongchao Li / Rui Zhu / Hai Yu / Qiyang Hong / Jie Jiang / Zizhen Li / Shuxuan Li / Huan Zhao / Lisheng Yang / Wangheng Hou / Wei Wang / Xiangzhong Ye / Jun Zhang / Timothy S Baker / Tong Cheng / Z Hong Zhou / Xiaodong Yan / Ningshao Xia /
Abstract: Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the ...Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses. Our near-atomic resolution structure of CVA6 A-particle complexed with a neutralizing antibody maps an immune-dominant neutralizing epitope to the surface loops of VP1. The structure-guided cell-based inhibition studies further demonstrate that these loops could serve as excellent targets for designing anti-CVA6 vaccines.Coxsackievirus A6 (CVA6) causes hand, foot and mouth disease in children. Here the authors present the CVA6 procapsid and A-particle cryo-EM structures and identify an immune-dominant neutralizing epitope, which can be exploited for vaccine development.
History
DepositionJun 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / em_software / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_software.name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • 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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Structure viewerMolecule:
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Assembly

Deposited unit
L: Light chain of Fab 1D5
H: Heavy chain of Fab 1D5
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)112,9765
Polymers112,9765
Non-polymers00
Water00
1
L: Light chain of Fab 1D5
H: Heavy chain of Fab 1D5
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)6,778,545300
Polymers6,778,545300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area14380 Å2
ΔGint-93 kcal/mol
Surface area37020 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: Light chain of Fab 1D5
H: Heavy chain of Fab 1D5
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 5


  • icosahedral pentamer
  • 565 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)564,87925
Polymers564,87925
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
L: Light chain of Fab 1D5
H: Heavy chain of Fab 1D5
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 678 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)677,85530
Polymers677,85530
Non-polymers00
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
6
L: Light chain of Fab 1D5
H: Heavy chain of Fab 1D5
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
x 60


  • crystal asymmetric unit, crystal frame
  • 6.78 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)6,778,545300
Polymers6,778,545300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)0.564, 0.91257, 676.02055
3generate(0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5), (-0.30901699, -0.5, -0.80901699)338.74856, 548.10669, 883.9021
4generate(0.5, -0.80901699, -0.30901699), (-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.80901699)547.19411, 885.37868, 336.35942
5generate(0.80901699, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.30901699)337.83599, 546.63011, -209.92212
6generate(1), (-1), (-1)676.79998, 674.54398
7generate(0.80901699, -0.30901699, 0.5), (0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.30901699)0.564, 675.88741, -1.47657
8generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)338.74856, 128.69329, -209.35812
9generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)547.19411, -208.5787, 338.18456
10generate(0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699)337.83599, 130.16987, 884.4661
11generate(-1), (1), (-1)676.79998, 674.54398
12generate(-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699), (0.5, 0.80901699, -0.30901699)676.23598, 0.91257, -1.47657
13generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)338.05142, 548.10669, -209.35812
14generate(-0.5, 0.80901699, 0.30901699), (-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699)129.60587, 885.37868, 338.18456
15generate(-0.80901699, 0.30901699, 0.5), (-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699)338.96399, 546.63011, 884.4661
16generate(-1), (-1), (1)676.79998, 676.79998
17generate(-0.80901699, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699)676.23598, 675.88741, 676.02055
18generate(-0.5, 0.80901699, -0.30901699), (0.80901699, 0.30901699, -0.5), (-0.30901699, -0.5, -0.80901699)338.05142, 128.69329, 883.9021
19generate(-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699)129.60587, -208.5787, 336.35942
20generate(-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699)338.96399, 130.16987, -209.92212
21generate(-1), (1), (-1)676.79998, 1.128, 675.67198
22generate(0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5)675.88741, 677.14855, 675.10798
23generate(0.80901699, 0.30901699, -0.5), (-0.30901699, -0.5, -0.80901699), (-0.5, 0.80901699, -0.30901699)128.69329, 885.0301, 336.92342
24generate(0.80901699, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699)-208.5787, 337.48742, 128.47787
25generate(0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5)130.16987, -208.79412, 337.83599
26generate(1), (-1), (-1)675.67198, 675.67198
27generate(-0.30901699, 0.5, 0.80901699), (0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5)0.91257, -0.34857, 675.10798
28generate(-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699), (-0.5, 0.80901699, -0.30901699)548.10669, -208.23012, 336.92342
29generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)885.37868, 339.31256, 128.47787
30generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)546.63011, 885.5941, 337.83599
31generate(-1), (-1), (1)676.79998, 675.67198, -1.128
32generate(0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.30901699), (0.80901699, -0.30901699, 0.5)675.88741, -0.34857, -0.564
33generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)128.69329, -208.23012, 337.62056
34generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699)-208.5787, 339.31256, 546.06611
35generate(0.30901699, -0.5, 0.80901699), (-0.5, -0.80901699, -0.30901699), (0.80901699, -0.30901699, -0.5)130.16987, 885.5941, 336.70799
36generate(1), (1), (1)1.128, -1.128
37generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)0.91257, 677.14855, -0.564
38generate(-0.80901699, -0.30901699, 0.5), (-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699)548.10669, 885.0301, 337.62056
39generate(-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.80901699), (0.5, -0.80901699, -0.30901699)885.37868, 337.48742, 546.06611
40generate(-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.30901699), (0.80901699, -0.30901699, -0.5)546.63011, -208.79412, 336.70799
41generate(-1), (-1), (1)675.67198, 676.79998, -1.128
42generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)-0.34857, 676.23598, -0.21543
43generate(0.30901699, 0.5, 0.80901699), (-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5)-208.23012, 338.05142, 546.97869
44generate(-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699), (-0.80901699, -0.30901699, -0.5)339.31256, 129.60587, 884.25068
45generate(-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5), (-0.30901699, 0.5, -0.80901699)885.5941, 338.96399, 545.50211
46generate(1), (-1), (-1)1.128, 676.79998, 675.67198
47generate(-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699)677.14855, 676.23598, 674.75941
48generate(-0.30901699, -0.5, -0.80901699), (-0.5, 0.80901699, -0.30901699), (0.80901699, 0.30901699, -0.5)885.0301, 338.05142, 127.56529
49generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)337.48742, 129.60587, -209.7067
50generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)-208.79412, 338.96399, 129.04187
51generate(1), (1), (1)1.128, -1.128
52generate(-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699)677.14855, 0.564, -0.21543
53generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.80901699, 0.30901699), (-0.80901699, -0.30901699, 0.5)885.0301, 338.74856, 546.97869
54generate(0.30901699, 0.5, -0.80901699), (0.5, -0.80901699, -0.30901699), (-0.80901699, -0.30901699, -0.5)337.48742, 547.19411, 884.25068
55generate(0.5, 0.80901699, 0.30901699), (0.80901699, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699)-208.79412, 337.83599, 545.50211
56generate(-1), (1), (-1)675.67198, 675.67198
57generate(0.5, 0.80901699, -0.30901699), (0.80901699, -0.30901699, 0.5), (0.30901699, -0.5, -0.80901699)-0.34857, 0.564, 674.75941
58generate(0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5)-208.23012, 338.74856, 127.56529
59generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)339.31256, 547.19411, -209.7067
60generate(-0.5, -0.80901699, -0.30901699), (0.80901699, -0.30901699, -0.5), (0.30901699, -0.5, 0.80901699)885.5941, 337.83599, 129.04187

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Components

#1: Antibody Light chain of Fab 1D5


Mass: 11984.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Bal b/c
#2: Antibody Heavy chain of Fab 1D5


Mass: 13153.761 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Bal b/c
#3: Protein Genome polyprotein


Mass: 33467.273 Da / Num. of mol.: 1 / Fragment: UNP residues 566-870 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, human / Strain: TW-2007-00141 / Tissue: muscle / References: UniProt: A0A0K2BNC7
#4: Protein Genome polyprotein


Mass: 28095.559 Da / Num. of mol.: 1 / Fragment: UNP residues 70-325 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, human / Strain: TW-2007-00141 / Tissue: muscle / References: UniProt: A0A0K2BNC7
#5: Protein Genome polyprotein


Mass: 26274.836 Da / Num. of mol.: 1 / Fragment: UNP residues 326-565 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, human / Strain: TW-2007-00141 / Tissue: muscle / References: UniProt: A0A0K2BNC7
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: Structure of Coxsackievirus A6 (CVA6) virus A-particle in complex with the neutralizing antibody fragment 1D5
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus A6
Buffer solutionpH: 7.4
Details: NaCl 137mmol/L, KCl 2.7mmol/L, Na2HPO4 10mmol/L, KH2PO4 2mmol/L
Buffer componentName: PBS
SpecimenConc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 93000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 4100 nm / Cs: 2.3 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 2382
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2.1particle selection
2EPU1.4.3image acquisition
4CTFFIND4.1CTF correction
7Chimeramodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 17015
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12067 / Symmetry type: POINT
Atomic model buildingB value: 223.15 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0116922
ELECTRON MICROSCOPYf_angle_d0.8899444
ELECTRON MICROSCOPYf_dihedral_angle_d7.1215487
ELECTRON MICROSCOPYf_chiral_restr0.0561047
ELECTRON MICROSCOPYf_plane_restr0.0061207

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