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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 / homologyPeptidase C3A/C3B, picornaviral / picornavirus capsid protein / Protein of unknown function DUF3724, picornavirus / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein ...Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Protein of unknown function DUF3724, picornavirus / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / Picornavirus core protein 2A / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Protein of unknown function (DUF3724) / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / RNA helicase / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphatase / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / suppression by virus of host gene expression / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / structural molecule activity / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceMus musculus (house mouse)
Coxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsZheng, Q.B. / He, M.Z. / Xu, L.F. / Yu, H. / Li, S.W. / Cheng, T.
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 Hou / Wei Wang / Xiangzhong Ye / Jun Zhang / Timothy S Baker / Tong Cheng / Z Hong Zhou / Xiaodong Yan / Ningshao Xia
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 12, 2017 / Release: Sep 27, 2017

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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
  • EMDB-6757
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  • Superimposition on EM map
  • EMDB-6757
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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
Polyers112,9765
Non-polymers00
Water0
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
Polyers6,778,545300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)14380
ΔGint (kcal/M)-93
Surface area (Å2)37020
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers564,87925
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers677,85530
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
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
Polyers6,778,545300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide Light chain of Fab 1D5


Mass: 11984.327 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse) / Strain: Bal b/c
#2: Protein/peptide Heavy chain of Fab 1D5


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


Mass: 33467.273 Da / Num. of mol.: 1 / Fragment: UNP residues 566-870 / 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/peptide Genome polyprotein


Mass: 28095.559 Da / Num. of mol.: 1 / Fragment: UNP residues 70-325 / 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/peptide Genome polyprotein


Mass: 26274.836 Da / Num. of mol.: 1 / Fragment: UNP residues 326-565 / Source: (natural) Coxsackievirus A6 / Cell line: human rhabdomyosarcoma (RD) cell / Organ: Homo sapiens, human / Strain: TW-2007-00141 / Tissue: muscle / References: UniProt: A0A0K2BNC7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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: 1, 2, 3, 4, 5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus A6
Buffer solutionDetails: NaCl 137mmol/L, KCl 2.7mmol/L, Na2HPO4 10mmol/L, KH2PO4 2mmol/L
pH: 7.4
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 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000 / 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 mm / 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) / Number of grids imaged: 5 / Number 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 selectionNumber of particles selected: 17015
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12067 / Symmetry type: POINT
Atomic model buildingOverall b value: 223.15 / Ref protocol: AB INITIO MODEL / Ref 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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