6SB5 | pdb_00006sb5

CryoEM structure of murine perforin-2 ectodomain in a pore form

PDB DOI: https://doi.org/10.2210/pdb6SB5/pdb
EM Map EMD-10135: EMDB EMDataResource

Classification: TOXIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2019-07-18 Released: 2020-02-05
Deposition Author(s): Ni, T., Yu, X., Gilbert, R.J.C.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity.

Ni, T., Jiao, F., Yu, X., Aden, S., Ginger, L., Williams, S.I., Bai, F., Prazak, V., Karia, D., Stansfeld, P., Zhang, P., Munson, G., Anderluh, G., Scheuring, S., Gilbert, R.J.C.

(2020) Sci Adv 6: eaax8286-eaax8286

PubMed: 32064340 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aax8286
Primary Citation Related Structures:
6SB1, 6SB3, 6SB4, 6SB5

PubMed 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 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.

Organizational Affiliation

Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content

Total Structure Weight: 1,145.15 kDa
Atom Count: 67,760
Modeled Residue Count: 8,688
Deposited Residue Count: 10,336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage-expressed gene 1 protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	646	Mus musculus	Mutation(s): 0 Gene Names: Mpeg1 Membrane Entity: Yes
UniProt
Find proteins for A1L314 (Mus musculus) Explore A1L314 Go to UniProtKB: A1L314
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1L314
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P	Go to GlyGen: A1L314-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain IA [auth J] SDF format, chain JA [auth J] SDF format, chain KA [auth K] SDF format, chain LA [auth K] SDF format, chain MA [auth L] SDF format, chain NA [auth L] SDF format, chain OA [auth M] SDF format, chain PA [auth M] SDF format, chain Q [auth A] SDF format, chain QA [auth N] SDF format, chain R [auth A] SDF format, chain RA [auth N] SDF format, chain S [auth B] SDF format, chain SA [auth O] SDF format, chain T [auth B] SDF format, chain TA [auth O] SDF format, chain U [auth C] SDF format, chain UA [auth P] SDF format, chain V [auth C] SDF format, chain VA [auth P] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth K] MOL2 format, chain MA [auth L] MOL2 format, chain NA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth M] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth N] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth O] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth O] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth P] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth P] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth K] mmCIF format, chain MA [auth L] mmCIF format, chain NA [auth L] mmCIF format, chain OA [auth M] mmCIF format, chain PA [auth M] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth N] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth N] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth O] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth O] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth P] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth P] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth F] BA [auth F] CA [auth G] DA [auth G] EA [auth H] AA [auth F], BA [auth F], CA [auth G], DA [auth G], EA [auth H], FA [auth H], GA [auth I], HA [auth I], IA [auth J], JA [auth J], KA [auth K], LA [auth K], MA [auth L], NA [auth L], OA [auth M], PA [auth M], Q [auth A], QA [auth N], R [auth A], RA [auth N], S [auth B], SA [auth O], T [auth B], TA [auth O], U [auth C], UA [auth P], V [auth C], VA [auth P], W [auth D], X [auth D], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain R [auth A] Focus chain RA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain T [auth B] Focus chain TA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain V [auth C] Focus chain VA [auth P] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain MA [auth L] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain Q [auth A] Focus chain QA [auth N] Focus chain R [auth A] Focus chain RA [auth N] Focus chain S [auth B] Focus chain SA [auth O] Focus chain T [auth B] Focus chain TA [auth O] Focus chain U [auth C] Focus chain UA [auth P] Focus chain V [auth C] Focus chain VA [auth P] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Ni, T.

Yu, X.

Gilbert, R.J.C.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N000331/1

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2020-02-26
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Structure summary
Version 1.4: 2025-07-09
Changes: Data collection