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Yorodumi- PDB-5fki: Pseudorabies virus (PrV) nuclear egress complex proteins fitted a... -
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-Basic information
Entry | Database: PDB / ID: 5fki | ||||||
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Title | Pseudorabies virus (PrV) nuclear egress complex proteins fitted as a hexameric lattice into a sub-tomogram average derived from focused- ion beam milled lamellae electron cryo-microscopic data | ||||||
Components |
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Keywords | VIRAL PROTEIN / Alpha-Herpesvirinae / herpesvirus simplex / HSV-1 / Pseudorabies virus / PRV / Nuclear egress complex / nuclear envelope / nucleoplasmic reticulum / inner nuclear membrane / vesicle transport / nucleo-cytoplasmic transport / RYOFIB / Focused ion beam milling / FIB-SEM | ||||||
Function / homology | Function and homology information host cell nuclear inner membrane / viral budding from nuclear membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Suid herpesvirus 1 | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / Resolution: 35 Å | ||||||
Authors | Hagen, C. / Dent, K.C. / Zeev Ben Mordehai, T. / Vasishtan, D. / Antonin, W. / Mettenleiter, T.C. / Gruenewald, K. | ||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling. Authors: Tzviya Zeev-Ben-Mordehai / Marion Weberruß / Michael Lorenz / Juliana Cheleski / Teresa Hellberg / Cathy Whittle / Kamel El Omari / Daven Vasishtan / Kyle C Dent / Karl Harlos / Kati ...Authors: Tzviya Zeev-Ben-Mordehai / Marion Weberruß / Michael Lorenz / Juliana Cheleski / Teresa Hellberg / Cathy Whittle / Kamel El Omari / Daven Vasishtan / Kyle C Dent / Karl Harlos / Kati Franzke / Christoph Hagen / Barbara G Klupp / Wolfram Antonin / Thomas C Mettenleiter / Kay Grünewald / Abstract: Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus ...Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC), which, in turn, mediates the formation of tight-fitting membrane vesicles around capsids at the inner nuclear membrane. Here, we present the crystal structure of the pseudorabies virus NEC. The structure revealed that a zinc finger motif in pUL31 and an extensive interaction network between the two proteins stabilize the complex. Comprehensive mutational analyses, characterized both in situ and in vitro, indicated that the interaction network is not redundant but rather complementary. Fitting of the NEC crystal structure into the recently determined cryoEM-derived hexagonal lattice, formed in situ by pUL31 and pUL34, provided details on the molecular basis of NEC coat formation and inner nuclear membrane remodeling. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5fki.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fki.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5fki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fki_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5fki_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5fki_validation.xml.gz | 358.3 KB | Display | |
Data in CIF | 5fki_validation.cif.gz | 595.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/5fki ftp://data.pdbj.org/pub/pdb/validation_reports/fk/5fki | HTTPS FTP |
-Related structure data
Related structure data | 3197M 5e8cC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 28235.549 Da / Num. of mol.: 42 Source method: isolated from a genetically manipulated source Details: Two proteins (PUL31 AND PUL34) of pseudorabies virus (PRV) are co-expressed in the cells forming there the herpesviral nuclear egress complex lining as a coat perinuclear vesicles. Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL31 / Plasmid: pETDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: G3G955 #2: Protein | Mass: 20287.975 Da / Num. of mol.: 42 Source method: isolated from a genetically manipulated source Details: Two proteins (PUL31 AND PUL34) of pseudorabies virus (PRV) are co-expressed in the cells forming there the herpesviral nuclear egress complex lining as a coat perinuclear vesicles. Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL34 / Plasmid: pETDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: G3G8R3 #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: PORCINE EPITHELIAL-LIKE EMBRYONIC EFN-R KIDNEY CELLS STABLY CO- EXPRESSING PRV UL31 AND UL34, THE LATTER FUSED WITH GFP (CELL LINE DESIGNATED AS BK-EF-UL31- 34GFP CATALOGUE NO. RIE 1083 OF THE ...Name: PORCINE EPITHELIAL-LIKE EMBRYONIC EFN-R KIDNEY CELLS STABLY CO- EXPRESSING PRV UL31 AND UL34, THE LATTER FUSED WITH GFP (CELL LINE DESIGNATED AS BK-EF-UL31- 34GFP CATALOGUE NO. RIE 1083 OF THE COLLECTION OF CELL LINES IN VETERINARY MEDICINE AT THE FLI, GREIFSWALD-INSEL RIEMS, GERMANY) Type: CELL |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
Specimen support | Details: OTHER |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BLOTTED MANUALLY WITH A BENT STRIP OF WHATMAN NO. 1 FILTER PAPER FROM THE NON-COATED GRID SIDE FOR 2 ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BLOTTED MANUALLY WITH A BENT STRIP OF WHATMAN NO. 1 FILTER PAPER FROM THE NON-COATED GRID SIDE FOR 2 TO 3 S IMMEDIATELY BEFORE VITRIFICATION BY THE GRAVITY-DRIVEN PLUNGING APPARATUS IN A ETHANE-PROPANE MIXTURE COOLED BY LIQUID NITROGEN, TIMERESOLVEDSTATE- TWO DAYS OF INCUBATION (37 DEGREE C, 5 PERCENT CO2) IN PLASTIC MICROSCOPE SLIDE GROWTH CHAMBERS (MUE-SLIDE 2X9 WELL, IBIDI GMBH) BEFORE CRYO- IMMOBILIZATION, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Apr 26, 2013 / Details: 2048 X 2048 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 52650 X / Nominal defocus max: 6000 nm / Nominal defocus min: -6000 nm / Cs: 2 mm |
Specimen holder | Tilt angle max: 52 ° / Tilt angle min: -50 ° |
Image recording | Electron dose: 114 e/Å2 / Film or detector model: GATAN MULTISCAN |
Image scans | Num. digital images: 35 |
-Processing
EM software |
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Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Method: WEIGHTED BACK PROJECTION / Resolution: 35 Å / Num. of particles: 300 / Actual pixel size: 11.4 Å Details: FIT OF HEXAMERIC LATTICE OF NEC INTO SUBTOMOGRAM AVERAGE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3197. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: MINIMISATION OF ATOMIC CLASHES AND PROTRUSION FROM MAP Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 5E8C | ||||||||||||
Refinement | Highest resolution: 35 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 35 Å
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