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

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Basic information

Entry
Database: PDB / ID: 5uot
TitleCryoEM structure of the helical assembly of full length MxB
ComponentsInterferon-induced GTP-binding protein Mx2
KeywordsANTIVIRAL 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 / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsPerilla, J.R. / Alvarez, F.J.D. / Zhang, P. / Schulten, K.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of HealthGM082251, GM085043, GM104601, GM067887, AI039394 United States
Medical Research Council (United Kingdom)MC_UP_A025_1013 United Kingdom
National Science FoundationOCI 07-25070, ACI-1238993 United States
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, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_database_status.process_site
Revision 1.2Jan 23, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / em_3d_fitting_list

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Assembly

Deposited unit
0: Interferon-induced GTP-binding protein Mx2
1: Interferon-induced GTP-binding protein Mx2
2: Interferon-induced GTP-binding protein Mx2
3: Interferon-induced GTP-binding protein Mx2
4: Interferon-induced GTP-binding protein Mx2
5: Interferon-induced GTP-binding protein Mx2
6: Interferon-induced GTP-binding protein Mx2
7: Interferon-induced GTP-binding protein Mx2
8: Interferon-induced GTP-binding protein Mx2
9: Interferon-induced GTP-binding protein Mx2
a: Interferon-induced GTP-binding protein Mx2
b: Interferon-induced GTP-binding protein Mx2
c: Interferon-induced GTP-binding protein Mx2
d: Interferon-induced GTP-binding protein Mx2
e: Interferon-induced GTP-binding protein Mx2
f: Interferon-induced GTP-binding protein Mx2
g: Interferon-induced GTP-binding protein Mx2
h: Interferon-induced GTP-binding protein Mx2
i: Interferon-induced GTP-binding protein Mx2
j: Interferon-induced GTP-binding protein Mx2
k: Interferon-induced GTP-binding protein Mx2
l: Interferon-induced GTP-binding protein Mx2
m: Interferon-induced GTP-binding protein Mx2
n: Interferon-induced GTP-binding protein Mx2
o: Interferon-induced GTP-binding protein Mx2
p: Interferon-induced GTP-binding protein Mx2
q: Interferon-induced GTP-binding protein Mx2
r: Interferon-induced GTP-binding protein Mx2
s: Interferon-induced GTP-binding protein Mx2
t: Interferon-induced GTP-binding protein Mx2
u: Interferon-induced GTP-binding protein Mx2
v: Interferon-induced GTP-binding protein Mx2
w: Interferon-induced GTP-binding protein Mx2
x: Interferon-induced GTP-binding protein Mx2
y: Interferon-induced GTP-binding protein Mx2
z: Interferon-induced GTP-binding protein Mx2
A: Interferon-induced GTP-binding protein Mx2
B: Interferon-induced GTP-binding protein Mx2
C: Interferon-induced GTP-binding protein Mx2
D: Interferon-induced GTP-binding protein Mx2
E: Interferon-induced GTP-binding protein Mx2
F: Interferon-induced GTP-binding protein Mx2
G: Interferon-induced GTP-binding protein Mx2
H: Interferon-induced GTP-binding protein Mx2
I: Interferon-induced GTP-binding protein Mx2
J: Interferon-induced GTP-binding protein Mx2
K: Interferon-induced GTP-binding protein Mx2
L: Interferon-induced GTP-binding protein Mx2
M: Interferon-induced GTP-binding protein Mx2
N: Interferon-induced GTP-binding protein Mx2
O: Interferon-induced GTP-binding protein Mx2
P: Interferon-induced GTP-binding protein Mx2
Q: Interferon-induced GTP-binding protein Mx2
R: Interferon-induced GTP-binding protein Mx2
S: Interferon-induced GTP-binding protein Mx2
T: Interferon-induced GTP-binding protein Mx2
U: Interferon-induced GTP-binding protein Mx2
V: Interferon-induced GTP-binding protein Mx2
W: Interferon-induced GTP-binding protein Mx2
X: Interferon-induced GTP-binding protein Mx2
Y: Interferon-induced GTP-binding protein Mx2
Z: Interferon-induced GTP-binding protein Mx2


Theoretical massNumber of molelcules
Total (without water)4,400,74562
Polymers4,400,74562
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area285260 Å2
ΔGint-1258 kcal/mol
Surface area1754500 Å2
MethodPISA

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Components

#1: Protein ...
Interferon-induced GTP-binding protein Mx2 / Interferon-regulated resistance GTP-binding protein MxB / Myxovirus resistance protein 2 / p78-related 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: helical assembly of MBP fusion of MxB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1252 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalia (mammals)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaClSodium chloride1
220 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
32 mM(ethylene glycol-bis(B-aminoethyl ether)-N,N,N',N'-tetraacetic acid)EGTA1
41 mMDithiothreitolDTT1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.2 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage 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 scansMovie frames/image: 7 / Used frames/image: 2-6

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2SerialEMimage acquisition
4Gctf0.5CTF correction
7MDFF2.1model fitting
9MDFF3model refinement
12RELION2.0 betaclassification
13RELION2.0 beta3D reconstruction
14NAMDmodel fitting
15Rosettamodel fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 58.4 ° / Axial rise/subunit: 8.25 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 51553
3D reconstructionResolution: 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
IDProtocolSpace
1FLEXIBLE FITREAL
2
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
14WHJ

4whj

A192-711
24WHJ

4whj

B292-711

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