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- EMDB-20620: EM structure of MPEG-1 (L425K, alpha conformation) soluble pre-po... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20620 | |||||||||
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Title | EM structure of MPEG-1 (L425K, alpha conformation) soluble pre-pore complex | |||||||||
![]() | MPEG-1 (L425K, alpha conformation) soluble pre-pore complex | |||||||||
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Function / homology | ![]() dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / 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 ...dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / 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 / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.37 Å | |||||||||
![]() | Pang SS / Bayly-Jones C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of the acid activatable pore-forming immune effector Macrophage-expressed gene 1. Authors: Siew Siew Pang / Charles Bayly-Jones / Mazdak Radjainia / Bradley A Spicer / Ruby H P Law / Adrian W Hodel / Edward S Parsons / Susan M Ekkel / Paul J Conroy / Georg Ramm / Hariprasad ...Authors: Siew Siew Pang / Charles Bayly-Jones / Mazdak Radjainia / Bradley A Spicer / Ruby H P Law / Adrian W Hodel / Edward S Parsons / Susan M Ekkel / Paul J Conroy / Georg Ramm / Hariprasad Venugopal / Phillip I Bird / Bart W Hoogenboom / Ilia Voskoboinik / Yann Gambin / Emma Sierecki / Michelle A Dunstone / James C Whisstock / ![]() ![]() ![]() Abstract: Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, ...Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, however, its mode of action remains unknown. We use cryo-Electron Microscopy (cryo-EM) to determine the 2.4 Å structure of a hexadecameric assembly of MPEG1 that displays the expected features of a soluble prepore complex. We further discover that MPEG1 prepore-like assemblies can be induced to perforate membranes through acidification, such as would occur within maturing phagolysosomes. We next solve the 3.6 Å cryo-EM structure of MPEG1 in complex with liposomes. These data reveal that a multi-vesicular body of 12 kDa (MVB12)-associated β-prism (MABP) domain binds membranes such that the pore-forming machinery of MPEG1 is oriented away from the bound membrane. This unexpected mechanism of membrane interaction suggests that MPEG1 remains bound to the phagolysosome membrane while simultaneously forming pores in engulfed bacterial targets. | |||||||||
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 | ![]() | 141.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14 KB | Display | ![]() |
Images | ![]() | 177.8 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() | 122.1 MB 226.2 MB 226.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 687.8 KB | Display | ![]() |
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Full document | ![]() | 687.3 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u2jMC ![]() 6u23C ![]() 6u2kC ![]() 6u2lC ![]() 6u2wC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | MPEG-1 (L425K, alpha conformation) soluble pre-pore complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 |
-Additional map: MPEG-1 (L425K, alpha conformation) soluble pre-pore complex unsharpened...
File | emd_20620_additional.map | ||||||||||||
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Annotation | MPEG-1 (L425K, alpha conformation) soluble pre-pore complex unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: MPEG-1 (L425K, alpha conformation) soluble pre-pore complex, half...
File | emd_20620_half_map_1.map | ||||||||||||
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Annotation | MPEG-1 (L425K, alpha conformation) soluble pre-pore complex, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: MPEG-1 (L425K, alpha conformation) soluble pre-pore complex, half...
File | emd_20620_half_map_2.map | ||||||||||||
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Annotation | MPEG-1 (L425K, alpha conformation) soluble pre-pore complex, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MPEG-1 (L425K, alpha conformation) soluble pre-pore
Entire | Name: MPEG-1 (L425K, alpha conformation) soluble pre-pore |
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Components |
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-Supramolecule #1: MPEG-1 (L425K, alpha conformation) soluble pre-pore
Supramolecule | Name: MPEG-1 (L425K, alpha conformation) soluble pre-pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.3 MDa |
-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: ![]() |
Molecular weight | Theoretical: 71.126148 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KSGKPSGEMD EVGVQKCKNA LKLPVLEVLP GGGWDNLRNV DMGRVMELTY SNCRTTEDGQ YIIPDEIFTI PQKQSNLEMN SEILESWAN YQSSTSYSIN TELSLFSKVN GKFSTEFQRM KTLQVKDQAI TTRVQVRNLV YTVKINPTLE LSSGFRKELL D ISDRLENN ...String: KSGKPSGEMD EVGVQKCKNA LKLPVLEVLP GGGWDNLRNV DMGRVMELTY SNCRTTEDGQ YIIPDEIFTI PQKQSNLEMN SEILESWAN YQSSTSYSIN TELSLFSKVN GKFSTEFQRM KTLQVKDQAI TTRVQVRNLV YTVKINPTLE LSSGFRKELL D ISDRLENN QTRMATYLAE LLVLNYGTHV TTSVDAGAAL IQEDHLRASF LQDSQSSRSA VTASAGLAFQ NTVNFKFEEN YT SQNVLTK SYLSNRTNSR VQSIGGVPFY PGITLQAWQQ GITNHLVAID RSGLPLHFFI NPNMLPDLPG PLVKKVSKTV ETA VKRYYT FNTYPGCTDL NSPNFNFQAN TDDGSCEGKM TNFSFGGVYQ ECTQLSGNRD VLLCQKLEQK NPLTGDFSCP SGYS PVHLL SQIHEEGYNH LECHRKCTLK VFCKTVCEDV FQVAKAEFRA FWCVASSQVP ENSGLLFGGL FSSKSINPMT NAQSC PAGY FPLRLFENLK VCVSQDYELG SRFAVPFGGF FSCTVGNPLV DPAISRDLGA PSLKKCPGGF SQHPALISDG CQVSYC VKS GLFTGGSLPP ARLPPFTRPP LMSQAATNTV IVTNSENARS WIKDSQTHQW RLGEPIELRR AMNVIHGDGG GLSHHHH HH |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 16 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.2 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 44.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |