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- PDB-3j9e: Atomic structure of a non-enveloped virus reveals pH sensors for ... -

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Basic information

Entry
Database: PDB / ID: 3j9e
TitleAtomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry
ComponentsVP5
KeywordsVIRAL PROTEIN / non-enveloped virus / cell entry / pH sensor
Function / homologyOuter capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5 / viral capsid / structural molecule activity / Outer capsid protein VP5
Function and homology information
Biological speciesBluetongue virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, X. / Patel, A. / Celma, C. / Roy, P. / Zhou, Z.H.
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry.
Authors: Xing Zhang / Avnish Patel / Cristina C Celma / Xuekui Yu / Polly Roy / Z Hong Zhou /
Abstract: Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- ...Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- and low-pH structures of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc finger that may function to maintain VP2 in a metastable state and a conserved His866, which senses early-endosomal pH. The membrane-penetration protein VP5 has three domains: dagger, unfurling and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that can sense late-endosomal pH and also possesses four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided-mutagenesis studies support these coordinated pH-sensing mechanisms.
History
DepositionJan 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

Deposited unit
D: VP5


Theoretical massNumber of molelcules
Total (without water)59,0701
Polymers59,0701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein VP5


Mass: 59070.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bluetongue virus 1 / References: UniProt: K7QP12

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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
IDNameTypeParent-ID
1Bluetongue Virus 1Bluetongue diseaseVIRUS0
2VP5 of Bluetongue Virus1
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Capra hircus
Buffer solutionpH: 8.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh grid with thin carbon support
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 29, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 14000 X / Calibrated magnification: 24140 X / Nominal defocus max: 3300 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 82 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 1630

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Processing

EM softwareName: FREALIGN / Category: 3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: reference match / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5008 / Nominal pixel size: 1.01 Å / Actual pixel size: 1.01 Å / Symmetry type: POINT
RefinementResolution: 3.3→3.3 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 15.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1416 456 0.06 %
Rwork0.1595 784867 -
obs0.1595 785323 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 569.48 Å2 / Biso mean: 66.0333 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: LAST / Resolution: 3.5→39.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 0 0 4098
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0193558
ELECTRON MICROSCOPYf_angle_d2.0294789
ELECTRON MICROSCOPYf_chiral_restr0.085535
ELECTRON MICROSCOPYf_plane_restr0.008620
ELECTRON MICROSCOPYf_dihedral_angle_d20.9331350
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5-4.00630.21231680.2468261913262081
4.0063-5.04590.11951200.1235261555261675
5.0459-39.92630.11711680.1416261399261567
Refinement TLS params.Method: refined / Origin x: -24.9305 Å / Origin y: 75.5041 Å / Origin z: 325.1532 Å
111213212223313233
T0.1911 Å2-0.1254 Å20.0028 Å2-0.25 Å20.2057 Å2--0.2419 Å2
L0.5346 °20.1312 °2-0.2021 °2-0.9542 °20.1479 °2--0.4702 °2
S0.1767 Å °-0.11 Å °0.1097 Å °0.166 Å °0.0029 Å °0.032 Å °-0.1197 Å °0.0463 Å °0.1641 Å °
Refinement TLS groupSelection details: all

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