6U2J

EM structure of MPEG-1 (L425K, alpha conformation) soluble pre-pore complex

PDB DOI: https://doi.org/10.2210/pdb6U2J/pdb
EM Map EMD-20620: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPMmpstruc

Deposited: 2019-08-20 Released: 2019-09-25
Deposition Author(s): Pang, S.S., Bayly-Jones, C.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 1,148.35 kDa
Atom Count: 71,744
Modelled Residue Count: 9,200
Deposited Residue Count: 10,272
Unique protein chains: 1

Macromolecules

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(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	642	Homo sapiens	Mutation(s): 1 Gene Names: MPEG1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q2M385 (Homo sapiens) Explore Q2M385 Go to UniProtKB: Q2M385
PHAROS: Q2M385 GTEx: ENSG00000197629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2M385
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 GA [auth A] SDF format, chain HA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth E] SDF format, chain LA [auth F] SDF format, chain MA [auth G] SDF format, chain NA [auth H] SDF format, chain OA [auth I] SDF format, chain PA [auth J] SDF format, chain QA [auth K] SDF format, chain RA [auth L] SDF format, chain SA [auth M] SDF format, chain TA [auth N] SDF format, chain UA [auth O] SDF format, chain VA [auth P] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth H] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain SA [auth M] MOL2 format, chain TA [auth N] MOL2 format, chain UA [auth O] MOL2 format, chain VA [auth P]	GA [auth A] HA [auth B] IA [auth C] JA [auth D] KA [auth E] GA [auth A], HA [auth B], IA [auth C], JA [auth D], KA [auth E], LA [auth F], MA [auth G], NA [auth H], OA [auth I], PA [auth J], QA [auth K], RA [auth L], SA [auth M], TA [auth N], UA [auth O], VA [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain SA [auth M] Focus chain TA [auth N] Focus chain UA [auth O] Focus chain VA [auth P]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-25

Deposition Author(s):

Pang, S.S.

Bayly-Jones, C.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2019-09-25
Type: Initial release
Version 1.1: 2019-10-02
Changes: Data collection, Database references
Version 1.2: 2020-01-15
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary