[English] 日本語
Yorodumi
- EMDB-20617: EM map of MPEG-1 (w.t.) soluble pre-pore complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20617
TitleEM map of MPEG-1 (w.t.) soluble pre-pore complex
Map dataMPEG-1 (w.t.) soluble pre-pore complex, sharpened map
Sample
  • Complex: Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore
    • Protein or peptide: Macrophage-Expressed Gene 1 protein (MPEG-1)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPang SS / Bayly-Jones C
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council Australia
CitationJournal: 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
DepositionAug 19, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20617.png

Downloads & links

-
Map

FileDownload / File: emd_20617.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMPEG-1 (w.t.) soluble pre-pore complex, sharpened map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.16101511 - 0.27217007
Average (Standard dev.)0.0009211707 (±0.010345885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z374.000374.000374.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ172172172
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.1610.2720.001

-
Supplemental data

-
Mask #1

Fileemd_20617_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: MPEG-1 (w.t.) soluble pre-pore complex, unsharpened map

Fileemd_20617_additional.map
AnnotationMPEG-1 (w.t.) soluble pre-pore complex, unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: MPEG-1 (w.t.) soluble pre-pore complex, unsharpened map

Fileemd_20617_additional_1.map
AnnotationMPEG-1 (w.t.) soluble pre-pore complex, unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: MPEG-1 (w.t.) soluble pre-pore complex, half map #1

Fileemd_20617_half_map_1.map
AnnotationMPEG-1 (w.t.) soluble pre-pore complex, half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: MPEG-1 (w.t.) soluble pre-pore complex, half map #2

Fileemd_20617_half_map_2.map
AnnotationMPEG-1 (w.t.) soluble pre-pore complex, half map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore

EntireName: Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore
Components
  • Complex: Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore
    • Protein or peptide: Macrophage-Expressed Gene 1 protein (MPEG-1)

-
Supramolecule #1: Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore

SupramoleculeName: Head-to-head assembly of MPEG-1 (w.t.) soluble pre-pore
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 2.3 MDa

-
Macromolecule #1: Macrophage-Expressed Gene 1 protein (MPEG-1)

MacromoleculeName: Macrophage-Expressed Gene 1 protein (MPEG-1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.2
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: D16 (2x16 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 25359
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more