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- PDB-4n53: Human enterovirus 71 uncoating intermediate captured at atomic re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n53 | ||||||
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Title | Human enterovirus 71 uncoating intermediate captured at atomic resolution | ||||||
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![]() | VIRUS / hand-foot-and-mouth disease / human enterovirus 71 / virion / pocket factor / picornavirus / icosahedral virus | ||||||
Function / homology | ![]() RNA-protein covalent cross-linking / : / : / 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 ...RNA-protein covalent cross-linking / : / : / 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 / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, R. / Lyu, K. | ||||||
![]() | ![]() Title: Human enterovirus 71 uncoating captured at atomic resolution. Authors: Lyu, K. / Ding, J. / Han, J.F. / Zhang, Y. / Wu, X.Y. / He, Y.L. / Qin, C.F. / Chen, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | 139.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 585.7 KB | Display | ![]() |
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Full document | ![]() | 595.4 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n43C ![]() 1d4mS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | The asymmetric unit contains 20 copies of the protomer. Each protomer consists of one copy each of VP1, VP2, VP3 and VP4. The biological assembly contains 60 copies of the protomer. |
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Components
#1: Protein | Mass: 32699.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: isolated in Fuyang, Anhui in 2008, grow in RD cells Source: (natural) ![]() ![]() Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148 References: UniProt: S5QA87 |
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#2: Protein | Mass: 27726.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: isolated in Fuyang, Anhui in 2008, grow in RD cells Source: (natural) ![]() ![]() Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148 References: UniProt: S4VM80 |
#3: Protein | Mass: 26440.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: isolated in Fuyang, Anhui in 2008, grow in RD cells Source: (natural) ![]() ![]() Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148 References: UniProt: S5ZCI0 |
#4: Protein | Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: isolated in Fuyang, Anhui in 2008, grow in RD cells Source: (natural) ![]() ![]() Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148 References: UniProt: S6C3M9 |
#5: Chemical | ChemComp-SPH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 289 K / Method: hanging drop / pH: 4.5 Details: 0.1M Sodium Acetate containing 3.5M Sodium Formate, pH 4.5, hanging drop, temperature 289K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.306→48.286 Å / Num. all: 505463 / Num. obs: 314499 / % possible obs: 62.22 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 1.5 % / Rmerge(I) obs: 0.216 / Χ2: 2.289 / Net I/σ(I): 4.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1D4M Resolution: 3.3063→48.286 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 116.42 Å2 / Biso mean: 50.47 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3063→48.286 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3063→3.389 Å
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