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- PDB-7qw9: Cryo-EM structure of coxsackievirus A6 mature virion -

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Basic information

Entry
Database: PDB / ID: 7qw9
TitleCryo-EM structure of coxsackievirus A6 mature virion
Components(Capsid protein ...Capsid) x 4
KeywordsVIRUS / enterovirus / coxsackievirus A6 / virion / native / capsid / cryo-EM
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 / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 / 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) / 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 ...Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / STEARIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsButtner, C.R. / Spurny, R. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX-1925982X Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: Commun Biol / Year: 2022
Title: Cryo-electron microscopy and image classification reveal the existence and structure of the coxsackievirus A6 virion.
Authors: Carina R Büttner / Radovan Spurný / Tibor Füzik / Pavel Plevka /
Abstract: Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous ...Coxsackievirus A6 (CV-A6) has recently overtaken enterovirus A71 and CV-A16 as the primary causative agent of hand, foot, and mouth disease worldwide. Virions of CV-A6 were not identified in previous structural studies, and it was speculated that the virus is unique among enteroviruses in using altered particles with expanded capsids to infect cells. In contrast, the virions of other enteroviruses are required for infection. Here we used cryo-electron microscopy (cryo-EM) to determine the structures of the CV-A6 virion, altered particle, and empty capsid. We show that the CV-A6 virion has features characteristic of virions of other enteroviruses, including a compact capsid, VP4 attached to the inner capsid surface, and fatty acid-like molecules occupying the hydrophobic pockets in VP1 subunits. Furthermore, we found that in a purified sample of CV-A6, the ratio of infectious units to virions is 1 to 500. Therefore, it is likely that virions of CV-A6 initiate infection, like those of other enteroviruses. Our results provide evidence that future vaccines against CV-A6 should target its virions instead of the antigenically distinct altered particles. Furthermore, the structure of the virion provides the basis for the rational development of capsid-binding inhibitors that block the genome release of CV-A6.
History
DepositionJan 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7716
Polymers95,2594
Non-polymers5132
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,746,283360
Polymers5,715,512240
Non-polymers30,771120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(1), (1), (1)
2generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
3generate(1), (-1), (-1)
4generate(0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5)
5generate(0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017)
6generate(-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017)
7generate(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
8generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
9generate(-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017)
10generate(0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017)
11generate(-1), (-1), (1)
12generate(-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017)
13generate(-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017)
14generate(-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017)
15generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
16generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
17generate(-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017)
18generate(-1), (1), (-1)
19generate(-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017)
20generate(-1), (1), (-1)
21generate(-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5)
22generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
23generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
24generate(0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017)
25generate(-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5)
26generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017)
27generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
28generate(1), (-1), (-1)
29generate(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
30generate(0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017)
31generate(-1), (1), (-1)
32generate(0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5)
33generate(-1), (-1), (1)
34generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
35generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
36generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
37generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
38generate(0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5)
39generate(0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017)
40generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
41generate(1), (-1), (-1)
42generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
43generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
44generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
45generate(0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5)
46generate(-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017)
47generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
48generate(1), (1), (1)
49generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
50generate(1), (1), (1)
51generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
52generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
53generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
54generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
55generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
56generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)
57generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
58generate(-1), (-1), (1)
59generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
60generate(-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017)

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1 / / P1D / Virion protein 1


Mass: 33530.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The first amino-acid of VP1 in the corresponding section of the GenBank polyprotein entry (AAR38844) (Asn) is not the actual first residue as the proteolytic cleavage of the viral ...Details: The first amino-acid of VP1 in the corresponding section of the GenBank polyprotein entry (AAR38844) (Asn) is not the actual first residue as the proteolytic cleavage of the viral polyprotein occurs at an alternative location, leaving the following residue Asp-2 as the first residue (D-1), and the Asn as the additional C-term residue described for VP3 (N-241). Residues 301-303 are not modelled/visible in the virion structure but the very C-terminal residue F-304 (partially) is.
Source: (natural) Coxsackievirus A6 / References: UniProt: Q6JKS2
#2: Protein Capsid protein VP2 / / P1B / Virion protein 2


Mass: 28006.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / References: UniProt: Q6JKS2
#3: Protein Capsid protein VP3 / / P1C / Virion protein 3


Mass: 26489.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VP3 has an additional C-terminal residue (N-241) compared to GenBank entry AAR38844 due to alternative cleavage of the polyprotein (see compound details for molecule 1 VP1).
Source: (natural) Coxsackievirus A6 / References: UniProt: Q6JKS2
#4: Protein Capsid protein VP4 / / P1A / Virion protein 4


Mass: 7231.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / References: UniProt: Q6JKS2

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Coxsackievirus A6VIRUS#1-#40NATURAL
2CapsidCOMPLEX#1-#41NATURALnative CV-A6 virion
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
118 MDaNO
218 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Coxsackievirus A686107Gdula
32Coxsackievirus A686107Gdula
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: CV-A6 / Diameter: 322 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4 / Details: PBS, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.2 mg/mLpotassium dihydrogen phosphateKH2PO41
21.15 mg/mLdisodium hydrogen phosphateNa2HPO41
30.2 mg/mL2981001
48 mg/mLsodium chlorideNaClSodium chloride1
SpecimenConc.: 2.5 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 R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 620 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9862
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7

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Processing

SoftwareName: REFMAC / Version: 5.8.0258 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1crYOLOparticle selection
2EPU1.12image acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9Coot0.9.5model refinementmodel building
10PHENIX1.19.2model refinementREAL SPACE refinement
11REFMAC5model refinementRECIPROCAL SPACE refinement
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 211991
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1769 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 66 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: correlation coefficient
Details: iterative cycles of building - real space refinement - reciprocal space refinement
Atomic model buildingPDB-ID: 5XS4

5xs4

RefinementResolution: 2.7→340.16 Å / Cor.coef. Fo:Fc: 0.908 / SU B: 10.314 / SU ML: 0.187 / ESU R: 0.29
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.28217 --
obs0.28217 355386 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.182 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Total: 32650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.01333510
ELECTRON MICROSCOPYr_bond_other_d0.0020.01729815
ELECTRON MICROSCOPYr_angle_refined_deg1.5721.65545765
ELECTRON MICROSCOPYr_angle_other_deg1.2841.56369435
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.5854170
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.0122.8531630
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.134154975
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.26715160
ELECTRON MICROSCOPYr_chiral_restr0.0630.24530
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0237785
ELECTRON MICROSCOPYr_gen_planes_other0.0020.026955
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_it10.2586.12216755
ELECTRON MICROSCOPYr_mcbond_other10.2576.12116754
ELECTRON MICROSCOPYr_mcangle_it14.599.29520900
ELECTRON MICROSCOPYr_mcangle_other14.599.29520901
ELECTRON MICROSCOPYr_scbond_it9.0056.55116755
ELECTRON MICROSCOPYr_scbond_other9.0066.5516752
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.9549.60824864
ELECTRON MICROSCOPYr_long_range_B_refined20.9620.96125271
ELECTRON MICROSCOPYr_long_range_B_other20.9620.96125271
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.505 26131 -
obs--100 %

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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