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Yorodumi- EMDB-10134: CryoEM structure of murine perforin-2 ectodomain in a pre-pore form -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10134 | |||||||||
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Title | CryoEM structure of murine perforin-2 ectodomain in a pre-pore form | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane ...dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane / cytoplasmic vesicle / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ni T / Yu X / Gilbert RJC | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Sci Adv / Year: 2020 Title: Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity. Authors: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor ...Authors: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor Anderluh / Simon Scheuring / Robert J C Gilbert / Abstract: Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual ...Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins. | |||||||||
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_10134.map.gz | 14.9 MB | EMDB map data format | |
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Header (meta data) | emd-10134-v30.xml emd-10134.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10134_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_10134.png | 80.3 KB | ||
Masks | emd_10134_msk_1.map | 178 MB | Mask map | |
Others | emd_10134_half_map_1.map.gz emd_10134_half_map_2.map.gz | 135.6 MB 135.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10134 | HTTPS FTP |
-Related structure data
Related structure data | 6sb3MC 6sb1C 6sb4C 6sb5C 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_10134.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10134_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10134_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10134_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Murine perforin-2 ecto domain
Entire | Name: Murine perforin-2 ecto domain |
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Components |
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-Supramolecule #1: Murine perforin-2 ecto domain
Supramolecule | Name: Murine perforin-2 ecto domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pHLsec-1D4 |
-Macromolecule #1: Macrophage-expressed gene 1 protein
Macromolecule | Name: Macrophage-expressed gene 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 71.129531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ETGDKPLGET GTTGFQICKN ALKLPVLEVL PGGGWDNLRN VDMGRVMDLT YTNCKTTEDG QYIIPDEVYT IPQKESNLEM NSEVLESWM NYQSTTSLSI NTELALFSRV NGKFSTEFQR MKTLQVKDQA VTTRVQVRNR IYTVKTTPTS ELSLGFTKAL M DICDQLEK ...String: ETGDKPLGET GTTGFQICKN ALKLPVLEVL PGGGWDNLRN VDMGRVMDLT YTNCKTTEDG QYIIPDEVYT IPQKESNLEM NSEVLESWM NYQSTTSLSI NTELALFSRV NGKFSTEFQR MKTLQVKDQA VTTRVQVRNR IYTVKTTPTS ELSLGFTKAL M DICDQLEK NQTKMATYLA ELLILNYGTH VITSVDAGAA LVQEDHVRSS FLLDNQNSQN TVTASAGIAF LNIVNFKVET DY ISQTSLT KDYLSNRTNS RVQSFGGVPF YPGITLETWQ KGITNHLVAI DRAGLPLHFF IKPDKLPGLP GPLVKKLSKT VET AVRHYY TFNTHPGCTN VDSPNFNFQA NMDDDSCDAK VTNFTFGGVY QECTELSGDV LCQNLEQKNL LTGDFSCPPG YSPV HLLSQ THEEGYSRLE CKKKCTLKIF CKTVCEDVFR VAKAEFRAYW CVAAGQVPDN SGLLFGGVFT DKTINPMTNA QSCPA GYIP LNLFESLKVC VSLDYELGFK FSVPFGGFFS CIMGNPLVNS DTAKDVRAPS LKKCPGGFSQ HLAVISDGCQ VSYCVK AGI FTGGSLLPVR LPPYTKPPLM SQVATNTVIV TNSETARSWI KDPQTNQWKL GEPLELRRAM TVIHGDSNGM SGGGTET SQ VAPA |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 32 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 |
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Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |