+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20622 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | EM map of MPEG-1(w.t.) pre-pore complex bound to liposome | |||||||||
Map data | MPEG-1(w.t.) pre-pore complex bound to liposome | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.94 Å | |||||||||
Authors | Pang SS / Bayly-Jones C | |||||||||
Funding support | Australia, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2019 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20622.map.gz | 20.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20622-v30.xml emd-20622.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20622_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_20622.png | 139.8 KB | ||
Masks | emd_20622_msk_1.map | 103 MB | Mask map | |
Others | emd_20622_additional.map.gz emd_20622_additional_1.map.gz emd_20622_half_map_1.map.gz emd_20622_half_map_2.map.gz | 74.9 MB 74.9 MB 75.9 MB 75.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20622 | HTTPS FTP |
-Validation report
Summary document | emd_20622_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20622_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_20622_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20622 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_20622.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MPEG-1(w.t.) pre-pore complex bound to liposome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20622_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: MPEG-1(w.t.) pre-pore complex bound to liposome, additional map
File | emd_20622_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MPEG-1(w.t.) pre-pore complex bound to liposome, additional map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: MPEG-1(w.t.) pre-pore complex bound to liposome, additional map
File | emd_20622_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MPEG-1(w.t.) pre-pore complex bound to liposome, additional map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: MPEG-1(w.t.) pre-pore complex bound to liposome, half map 1
File | emd_20622_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MPEG-1(w.t.) pre-pore complex bound to liposome, half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: MPEG-1(w.t.) pre-pore complex bound to liposome, half map 2
File | emd_20622_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MPEG-1(w.t.) pre-pore complex bound to liposome, half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : MPEG-1 (w.t.) pre-pore complex bound to liposome
Entire | Name: MPEG-1 (w.t.) pre-pore complex bound to liposome |
---|---|
Components |
|
-Supramolecule #1: MPEG-1 (w.t.) pre-pore complex bound to liposome
Supramolecule | Name: MPEG-1 (w.t.) pre-pore complex bound to liposome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Macrophage-Expressed Gene 1 protein
Macromolecule | Name: Macrophage-Expressed Gene 1 protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: KSGKPSGEMD EVGVQKCKNA LKLPVLEVLP GGGWDNLRNV DMGRVMELTY SNCRTTEDGQ YIIPDEIFTI PQKQSNLEMN SEILESWANY QSSTSYSINT ELSLFSKVNG KFSTEFQRMK TLQVKDQAIT TRVQVRNLVY TVKINPTLEL SSGFRKELLD ISDRLENNQT ...String: KSGKPSGEMD EVGVQKCKNA LKLPVLEVLP GGGWDNLRNV DMGRVMELTY SNCRTTEDGQ YIIPDEIFTI PQKQSNLEMN SEILESWANY QSSTSYSINT ELSLFSKVNG KFSTEFQRMK TLQVKDQAIT TRVQVRNLVY TVKINPTLEL SSGFRKELLD ISDRLENNQT RMATYLAELL VLNYGTHVTT SVDAGAALIQ EDHLRASFLQ DSQSSRSAVT ASAGLAFQNT VNFKFEENYT SQNVLTKSYL SNRTNSRVQS IGGVPFYPGI TLQAWQQGIT NHLVAIDRSG LPLHFFINPN MLPDLPGPLV KKVSKTVETA VKRYYTFNTY PGCTDLNSPN FNFQANTDDG SCEGKMTNFS FGGVYQECTQ LSGNRDVLLC QKLEQKNPLT GDFSCPSGYS PVHLLSQIHE EGYNHLECHR KCTLLVFCKT VCEDVFQVAK AEFRAFWCVA SSQVPENSGL LFGGLFSSKS INPMTNAQSC PAGYFPLRLF ENLKVCVSQD YELGSRFAVP FGGFFSCTVG NPLVDPAISR DLGAPSLKKC PGGFSQHPAL ISDGCQVSYC VKSGLFTGGS LPPARLPPFT RPPLMSQAAT NTVIVTNSEN ARSWIKDSQT HQWRLGEPIE LRRAMNVIHG DGGGLSHHHH HH |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.7 mg/mL |
---|---|
Buffer | pH: 7.2 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
Details | MPEG-1 protein mixed with POPC:POPS liposomes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |