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- EMDB-15086: Structure of murine perforin-2 (Mpeg1) pore in twisted form -

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Basic information

Entry
Database: EMDB / ID: EMD-15086
TitleStructure of murine perforin-2 (Mpeg1) pore in twisted form
Map datafinal map, local resolution filtered
Sample
  • Complex: murine perforin-2 ectodomain in twisted pore form
    • Protein or peptide: Macrophage-expressed gene 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspore forming protein / MACPF / beta-barrel / immunity / IMMUNE SYSTEM
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
Macrophage-expressed gene 1 protein / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
Macrophage-expressed gene 1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsYu X / Ni T / Zhang P / Gilbert R
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: EMBO J / Year: 2022
Title: Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.
Authors: Xiulian Yu / Tao Ni / George Munson / Peijun Zhang / Robert J C Gilbert /
Abstract: Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a ...Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a pore-forming structure upon acidification; but its mechanism of conformational transition has been debated. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures of PFN2 in pre-pore and pore conformations in isolation and bound to liposomes. In isolation and upon acidification, the pre-assembled complete pre-pore rings convert to pores in both flat ring and twisted conformations. On membranes, in situ assembled PFN2 pre-pores display various degrees of completeness; whereas PFN2 pores are mainly incomplete arc structures that follow the same subunit packing arrangements as found in isolation. Both assemblies on membranes use their P2 β-hairpin for binding to the lipid membrane surface. Overall, these structural snapshots suggest a molecular mechanism for PFN2 pre-pore to pore transition on a targeted membrane, potentially using the twisted pore as an intermediate or alternative state to the flat conformation, with the capacity to cause bilayer distortion during membrane insertion.
History
DepositionJun 2, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15086.png

Downloads & links

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Map

FileDownload / File: emd_15086.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal map, local resolution filtered
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 376.92 Å		1.05 Å/pix.
x 360 pix.
= 376.92 Å		1.05 Å/pix.
x 360 pix.
= 376.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.13998666 - 0.2161142
Average (Standard dev.)0.00018464375 (±0.004717589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 376.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15086_msk_1.map
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Half map: #2

Fileemd_15086_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_15086_half_map_2.map
Projections & Slices
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Sample components

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Entire : murine perforin-2 ectodomain in twisted pore form

EntireName: murine perforin-2 ectodomain in twisted pore form
Components
  • Complex: murine perforin-2 ectodomain in twisted pore form
    • Protein or peptide: Macrophage-expressed gene 1 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: murine perforin-2 ectodomain in twisted pore form

SupramoleculeName: murine perforin-2 ectodomain in twisted pore form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Macrophage-expressed gene 1 protein

MacromoleculeName: Macrophage-expressed gene 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 71.359812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 SGGGTKT ET SQVAPA

UniProtKB: Macrophage-expressed gene 1 protein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 3.8
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10135

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116274
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8a1s:
Structure of murine perforin-2 (Mpeg1) pore in twisted form

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