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- EMDB-20871: Combined map of the half-complex from tetradecameric assembly of ... -
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Basic information
Entry | Database: EMDB / ID: EMD-20871 | |||||||||
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Title | Combined map of the half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC | |||||||||
![]() | TgMcr-AAA_TgMcrC | |||||||||
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![]() | Endonuclease / AAA protein / GTPase / Methylation-dependent restriction / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
![]() | Niu Y / Suzuki H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes. Authors: Yiming Niu / Hiroshi Suzuki / Christopher J Hosford / Thomas Walz / Joshua S Chappie / ![]() ![]() Abstract: McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis ...McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9 KB | Display | ![]() |
Images | ![]() | 182.2 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 49.5 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ut8MC ![]() 6ut3C ![]() 6ut4C ![]() 6ut5C ![]() 6ut6C ![]() 6ut7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TgMcr-AAA_TgMcrC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_20871_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_20871_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Tetradecameric assembly of the McrB-AAA_McrC complex from T. gamm...
Entire | Name: Tetradecameric assembly of the McrB-AAA_McrC complex from T. gammatolerans |
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Components |
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-Supramolecule #1: Tetradecameric assembly of the McrB-AAA_McrC complex from T. gamm...
Supramolecule | Name: Tetradecameric assembly of the McrB-AAA_McrC complex from T. gammatolerans type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: GTPase subunit of restriction endonuclease
Macromolecule | Name: GTPase subunit of restriction endonuclease / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.137219 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNESAGHNIK EDYFRVDMLL NKKGQVILYG PPGTGKTWIA RKYVVEETNE KTPGNKWEFI TFHQSYSYEE FIEGFRPRTD NEEKIRYVV EDGIFKKIAL RALVKGLFEL EDATIGKDKI HRLYILLTKK EPLSPTEYEE YLRLKRYLWE LVGGLPKDKL K NLTPKFYL ...String: MNESAGHNIK EDYFRVDMLL NKKGQVILYG PPGTGKTWIA RKYVVEETNE KTPGNKWEFI TFHQSYSYEE FIEGFRPRTD NEEKIRYVV EDGIFKKIAL RALVKGLFEL EDATIGKDKI HRLYILLTKK EPLSPTEYEE YLRLKRYLWE LVGGLPKDKL K NLTPKFYL IIDEINRGNI SKIFGELITL LEKDKRLGGE NQLIVRLPYS GEPFAVPPNL YIIGTMNTAD RSIALLDVAL RR RFAFIEV EPRPEFLEKE NLKKIREKKL KTEDRKRLNE KLNELFSKLG NDNYFLKTLL EKINVRITVV KDRDHRIGHS YFL NVETVE DLHHVWYYEV LPLLMEYFYN DWETIKWVLN EKGKEHGNVF FEKLRLTGPN GEEAYQLKVL EGDAFIGALK RIIS KNTPS QEGGATTNEE NSPENTQSQT EGD UniProtKB: GTPase subunit of restriction endonuclease |
-Macromolecule #2: McrBC 5-methylcytosine restriction system component
Macromolecule | Name: McrBC 5-methylcytosine restriction system component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 54.339406 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPRLTTITLY EHDEKRYRDI AGDKKAIQDA LIKLNKQFKK DFKKLDRSED NSDTEDTIDE SKGVVEVYAN KIKARHYVGF AAVDNVFLQ ILPKVFKPKK EQTQETQEDT WEPILAFIRM LDMAYGLKIK DHDLAYLQGR NLRPNLYEVF IYLFAKSLWS E VQRGYHRE ...String: MPRLTTITLY EHDEKRYRDI AGDKKAIQDA LIKLNKQFKK DFKKLDRSED NSDTEDTIDE SKGVVEVYAN KIKARHYVGF AAVDNVFLQ ILPKVFKPKK EQTQETQEDT WEPILAFIRM LDMAYGLKIK DHDLAYLQGR NLRPNLYEVF IYLFAKSLWS E VQRGYHRE YVEVHREEKF LRGKLLMSRQ IRKLPHQLNT FSVEVHELIE DNLLNRIFYA SVREALRRTT WGLNRKLLGE LM LAFDGIT PIHLRTEHFE RVHFTRLNER FRRPFELAKL LFMPASGKGR SREVSGFFVD MNKLFERFIE RVLVRNLPPE YKL FYQESY PFLKNQNGSS QKPDYVVRKG NTPVVVLDAK YRELKERIPS SDMLRQLYVY SRIWGYKTSH ENDSKPPAVI VIPS SSTYN QGLPDKPLEF EFFDERKLFI VAYNMDYVKT GAIFKADKNF RRSLNNIIGK LNT UniProtKB: McrBC 5-methylcytosine restriction system component |
-Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
Macromolecule | Name: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: GSP |
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Molecular weight | Theoretical: 539.246 Da |
Chemical component information | ![]() ChemComp-GSP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 14.0 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 4271 / Average exposure time: 10.0 sec. / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |