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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
DescriptorLight chain of Fab 1D5
Heavy chain of Fab 1D5
Genome polyprotein
KeywordsVIRUS / Coxsackievirus A6 / Immune-complex / Icosahedral
Specimen sourceMus musculus / mammal / ハツカネズミ, はつかねずみ /
Coxsackievirus A6 / virus
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsZheng, Q.B. / He, M.Z. / Xu, L.F. / Yu, H. / Li, S.W. / Cheng, T.
CitationNat Commun, 2017, 8, 505-505

Nat Commun, 2017, 8, 505-505 Yorodumi Papers
Atomic structures of Coxsackievirus A6 and its complex with a neutralizing antibody.
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

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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
  • EMDB-6757
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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: Polypeptide(L)Light chain of Fab 1D5


Mass: 11984.327 Da / Num. of mol.: 1
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#2: Polypeptide(L)Heavy chain of Fab 1D5


Mass: 13153.761 Da / Num. of mol.: 1
Source: (natural) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
#3: Polypeptide(L)Genome polyprotein


Mass: 33467.273 Da / Num. of mol.: 1 / Fragment: UNP residues 566-870 / Source: (natural) Coxsackievirus A6 / virus / References: UniProt: A0A0K2BNC7

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)Genome polyprotein


Mass: 28095.559 Da / Num. of mol.: 1 / Fragment: UNP residues 70-325 / Source: (natural) Coxsackievirus A6 / virus / References: UniProt: A0A0K2BNC7

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)Genome polyprotein


Mass: 26274.836 Da / Num. of mol.: 1 / Fragment: UNP residues 326-565 / Source: (natural) Coxsackievirus A6 / virus / References: UniProt: A0A0K2BNC7

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 FIELD / 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 scansDimension width: 4096 / Dimension 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2.1PARTICLE SELECTION1
2EPU1.4.3IMAGE ACQUISITION1
4CTFFind4.1CTF CORRECTION1
7ChimeraMODEL FITTING1
9Relion1.4INITIAL EULER ASSIGNMENT1
10Relion1.4FINAL EULER ASSIGNMENT1
11Relion1.4CLASSIFICATION1
12Relion1.4RECONSTRUCTION1
13CootMODEL REFINEMENT1
14PhenixMODEL REFINEMENT1
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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