8WQT

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM1 complex

PDB DOI: https://doi.org/10.2210/pdb8WQT/pdb
EM Map EMD-37753: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-10-12 Released: 2024-10-16
Deposition Author(s): Fu, Y., Kim, H., Zamyatina, A., Kim, H.M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural insight on tailored modulation of TLR4-mediated pro-inflammatory response by disaccharide Lipid A mimetics

Fu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 179.89 kDa
Atom Count: 12,332
Modelled Residue Count: 1,462
Deposited Residue Count: 1,492
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	A [auth C], B [auth D]	142	Mus musculus	Mutation(s): 0 Gene Names: Ly96
UniProt
Find proteins for Q9JHF9 (Mus musculus) Explore Q9JHF9 Go to UniProtKB: Q9JHF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9JHF9
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth C] Focus chain B [auth D]	Go to GlyGen: Q9JHF9-1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	C [auth A], D [auth B]	604	Mus musculus	Mutation(s): 0 Gene Names: Tlr4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QUK6 (Mus musculus) Explore Q9QUK6 Go to UniProtKB: Q9QUK6
IMPC: MGI:96824
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9QUK6
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain C [auth A] Focus chain D [auth B]	Go to GlyGen: Q9QUK6-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth E]	2		N-Glycosylation	Interactions Focus chain E [auth F] Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth E] Interactions & Density Focus chain E [auth F] Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Focus chain J [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0IL (Subject of Investigation/LOI) Query on 0IL Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain T [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain T [auth A]	DA [auth B], T [auth A]	(3R)-3-(tetradecanoyloxy)tetradecanoic acid C₂₈ H₅₄ O₄ IYESSKQVAKTOQB-AREMUKBSSA-N		Interactions Focus chain DA [auth B] Focus chain T [auth A] Interactions & Density Focus chain DA [auth B] Focus chain T [auth A]
2IL (Subject of Investigation/LOI) Query on 2IL Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	K [auth C], L [auth C], O [auth D], P [auth D]	(3R)-3-(dodecanoyloxy)tetradecanoic acid C₂₆ H₅₀ O₄ IKRFTYQBIVDIMM-XMMPIXPASA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]
X6Z (Subject of Investigation/LOI) Query on X6Z Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain U [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain U [auth A]	BA [auth B], U [auth A]	[(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate C₇ H₁₅ O₉ P KJZYYYMWKHTJAM-VEIUFWFVSA-N		Interactions Focus chain BA [auth B] Focus chain U [auth A] Interactions & Density Focus chain BA [auth B] Focus chain U [auth A]
GP4 (Subject of Investigation/LOI) Query on GP4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain S [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain S [auth A]	CA [auth B], S [auth A]	2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose C₆ H₁₄ N O₈ P QWDBGVNDGYUIAC-UKFBFLRUSA-N		Interactions Focus chain CA [auth B] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain S [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] EA [auth B] FA [auth B] GA [auth B] HA [auth B] AA [auth A], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], M [auth C], N [auth C], Q [auth D], R [auth D], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	Institute for Basic Science, IBS

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection
Version 2.0: 2025-02-12
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary