+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8577 | ||||||||||||
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Title | CryoEM structure of the helical assembly of full length MxB | ||||||||||||
Map data | Structure of full-length wild type dynamin-like MxB | ||||||||||||
Sample |
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Keywords | cryoEM / mx2 / mxb / assembly / interferon / hiv-1 / dynamin / helical reconstruction / Molecular dynamic simulation / antiviral protein | ||||||||||||
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 | helical reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
Authors | Alvarez FJD / He S / Scheres SHW / Zhang P | ||||||||||||
Funding support | United States, United Kingdom, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8577.map.gz | 196.6 MB | EMDB map data format | |
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Header (meta data) | emd-8577-v30.xml emd-8577.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8577_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_8577.png | 251.2 KB | ||
Filedesc metadata | emd-8577.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8577 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8577 | HTTPS FTP |
-Validation report
Summary document | emd_8577_validation.pdf.gz | 258.3 KB | Display | EMDB validaton report |
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Full document | emd_8577_full_validation.pdf.gz | 257.4 KB | Display | |
Data in XML | emd_8577_validation.xml.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8577 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8577 | HTTPS FTP |
-Related structure data
Related structure data | 5uotMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8577.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of full-length wild type dynamin-like MxB | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.147 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : helical assembly of MBP fusion of MxB
Entire | Name: helical assembly of MBP fusion of MxB |
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Components |
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-Supramolecule #1: helical assembly of MBP fusion of MxB
Supramolecule | Name: helical assembly of MBP fusion of MxB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 125.2 KDa |
-Macromolecule #1: Interferon-induced GTP-binding protein Mx2
Macromolecule | Name: Interferon-induced GTP-binding protein Mx2 / type: protein_or_peptide / ID: 1 / Number of copies: 62 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 70.979758 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: YEQKVRPCID LIDSLRALGV EQDLALPAIA VIGDQSSGKS SVLEALSGVA LPRGSGIVTR CPLVLKLKKQ PCEAWAGRIS YRNTELELQ DPGQVEKEIH KAQNVMAGNG RGISHELISL EITSPEVPDL TIIDLPGITR VAVDNQPRDI GLQIKALIKK Y IQRQQTIN ...String: YEQKVRPCID LIDSLRALGV EQDLALPAIA VIGDQSSGKS SVLEALSGVA LPRGSGIVTR CPLVLKLKKQ PCEAWAGRIS YRNTELELQ DPGQVEKEIH KAQNVMAGNG RGISHELISL EITSPEVPDL TIIDLPGITR VAVDNQPRDI GLQIKALIKK Y IQRQQTIN LVVVPCNVDI ATTEALSMAH EVDPEGDRTI GILTKPDLMD RGTEKSVMNV VRNLTYPLKK GYMIVKCRGQ QE ITNRLSL AEATKKEITF FQTHPYFRVL LEEGSATVPR LAERLTTELI MHIQKSLPLL EGQIRESHQK ATEELRRCGA DIP SQEADK MFFLIEKIKM FNQDIEKLVE GEEVVRENET RLYNKIREDF KNWVGILATN TQKVKNIIHE EVEKYEKQYR GKEL LGFVN YKTFEIIVHQ YIQQLVEPAL SMLQKAMEII QQAFINVAKK HFGEFFNLNQ TVQSTIEDIK VKHTAKAENM IQLQF RMEQ MVFCQDQIYS VVLKKVREEI FNPLGTPSQN MKLNSHFPSN ESSVSSFTEI GIHLNAYFLE TSKRLANQIP FIIQYF MLR ENGDSLQKAM MQILQEKNRY SWLLQEQSET ATKRRILKER IYRLTQARHA LCQFSS UniProtKB: Interferon-induced GTP-binding protein Mx2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-6 / Number grids imaged: 1 / Number real images: 1123 / Average exposure time: 1.6 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 93000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 92-711 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-5uot: |