6SB3

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

PDB DOI: https://doi.org/10.2210/pdb6SB3/pdb
EM Map EMD-10134: EMDB EMDataResource

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

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 (United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 1,145.15 kDa
Atom Count: 75,712
Modelled Residue Count: 9,664
Deposited Residue Count: 10,336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1L314
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) 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]	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: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

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 (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