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- EMDB-8577: CryoEM structure of the helical assembly of full length MxB -

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Basic information

Entry
Database: EMDB / ID: EMD-8577
TitleCryoEM structure of the helical assembly of full length MxB
Map dataStructure of full-length wild type dynamin-like MxB
Sample
  • Complex: helical assembly of MBP fusion of MxB
    • Protein or peptide: Interferon-induced GTP-binding protein Mx2
Function / homology
Function and homology information


response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / defense response / ISG15 antiviral mechanism / Interferon alpha/beta signaling / protein transport / microtubule binding ...response to interferon-alpha / regulation of nucleocytoplasmic transport / mRNA transport / nuclear pore / response to virus / defense response / ISG15 antiviral mechanism / 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
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Interferon-induced GTP-binding protein Mx2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsAlvarez FJD / He S / Scheres SHW / Zhang P
CitationJournal: 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
DepositionFeb 1, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseFeb 21, 2018-
UpdateJan 23, 2019-
Current statusJan 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uot
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5uot
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8577.png

Downloads & links

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Map

FileDownload / File: emd_8577.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of full-length wild type dynamin-like MxB
Voxel sizeX=Y=Z: 1.147 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 0.045
Minimum - Maximum-0.09070253 - 0.19853778
Average (Standard dev.)0.0008830468 (±0.011216302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 516.14996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1471.1471.147
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z516.150516.150516.150
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-0.0910.1990.001

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Supplemental data

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Sample components

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Entire : helical assembly of MBP fusion of MxB

EntireName: helical assembly of MBP fusion of MxB
Components
  • Complex: helical assembly of MBP fusion of MxB
    • Protein or peptide: Interferon-induced GTP-binding protein Mx2

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Supramolecule #1: helical assembly of MBP fusion of MxB

SupramoleculeName: helical assembly of MBP fusion of MxB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mammalia (mammals)
Molecular weightTheoretical: 125.2 KDa

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Macromolecule #1: Interferon-induced GTP-binding protein Mx2

MacromoleculeName: Interferon-induced GTP-binding protein Mx2 / type: protein_or_peptide / ID: 1 / Number of copies: 62 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.979758 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
2.0 mMEGTA(ethylene glycol-bis(B-aminoethyl ether)-N,N,N',N'-tetraacetic acid)
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 93000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 51553 / Software - Name: EMAN (ver. 2.0)
CTF correctionSoftware - Name: Gctf (ver. 0.5)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 64
Applied symmetry - Helical parameters - Δz: 8.25 Å
Applied symmetry - Helical parameters - Δ&Phi: 58.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0 beta) / Number images used: 44955
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4whj


Chain - Chain ID: A / Chain - Residue range: 92-711
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5uot:
CryoEM structure of the helical assembly of full length MxB

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Atomic model buiding 2

Initial modelPDB ID:

4whj


Chain - Chain ID: B / Chain - Residue range: 92-711
Output model

PDB-5uot:
CryoEM structure of the helical assembly of full length MxB

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