+Open data
-Basic information
Entry | Database: PDB / ID: 5uot | ||||||||||||
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Title | CryoEM structure of the helical assembly of full length MxB | ||||||||||||
Components | Interferon-induced GTP-binding protein Mx2 | ||||||||||||
Keywords | ANTIVIRAL PROTEIN / cryoEM / mx2 / mxb / assembly / interferon / hiv-1 / dynamin / helical reconstruction / Molecular dynamic simulation | ||||||||||||
Function / homology | Function and homology information response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / protein transport / microtubule binding ...response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / ISG15 antiviral mechanism / defense response / Interferon alpha/beta signaling / protein transport / microtubule binding / defense response to virus / microtubule / regulation of cell cycle / innate immune response / GTPase activity / GTP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
Authors | Perilla, J.R. / Alvarez, F.J.D. / Zhang, P. / Schulten, K. | ||||||||||||
Funding support | United States, United Kingdom, 3items
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Citation | Journal: Sci Adv / Year: 2017 Title: CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. Authors: Frances J D Alvarez / Shaoda He / Juan R Perilla / Sooin Jang / Klaus Schulten / Alan N Engelman / Sjors H W Scheres / Peijun Zhang / Abstract: Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, ...Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation. Using cryo-electron microscopy (cryoEM), we determined the MxB assembly structure at 4.6 Å resolution, representing the first near-atomic resolution structure in the mammalian dynamin superfamily. The structure revealed previously described and novel MxB assembly interfaces. Mutational analyses demonstrated a critical role for one of the novel interfaces in HIV-1 restriction. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5uot.cif.gz | 6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5uot.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5uot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uot_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5uot_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 5uot_validation.xml.gz | 885.2 KB | Display | |
Data in CIF | 5uot_validation.cif.gz | 1.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/5uot ftp://data.pdbj.org/pub/pdb/validation_reports/uo/5uot | HTTPS FTP |
-Related structure data
Related structure data | 8577MC 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: 70979.758 Da / Num. of mol.: 62 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MX2 / Production host: Mammalia (mammals) / References: UniProt: P20592 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: helical assembly of MBP fusion of MxB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.1252 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Mammalia (mammals) | |||||||||||||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 93000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.2 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.6 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1123 |
Image scans | Movie frames/image: 7 / Used frames/image: 2-6 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 58.4 ° / Axial rise/subunit: 8.25 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 51553 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44955 / Num. of class averages: 64 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Accession code: 4WHJ / Initial refinement model-ID: 1 / Pdb chain residue range: 92-711 / PDB-ID: 4WHJ / Source name: PDB / Type: experimental model
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