8WO1

Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex

PDB DOI: https://doi.org/10.2210/pdb8WO1/pdb
EM Map EMD-37677: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2023-10-06 Released: 2024-10-09
Deposition Author(s): Fu, Y., Kim, H., Zamyatina, A., Kim, H.M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.24 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., Kim, H.

To be published.

Macromolecule Content

Total Structure Weight: 178.6 kDa
Atom Count: 12,406
Modelled Residue Count: 1,482
Deposited Residue Count: 1,494
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	A, B	605	Homo sapiens	Mutation(s): 0 Gene Names: TLR4
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens) Explore O00206 Go to UniProtKB: O00206
PHAROS: O00206 GTEx: ENSG00000136869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00206
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B	Go to GlyGen: O00206-1
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
Lymphocyte antigen 96	C, D	142	Homo sapiens	Mutation(s): 0 Gene Names: LY96
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9 Go to UniProtKB: Q9Y6Y9
PHAROS: Q9Y6Y9 GTEx: ENSG00000154589
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6Y9
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C Focus chain D	Go to GlyGen: Q9Y6Y9-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I	3		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Small Molecules

Ligands 6 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 S [auth C] SDF format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	S [auth C], X [auth D]	(3R)-3-(tetradecanoyloxy)tetradecanoic acid C₂₈ H₅₄ O₄ IYESSKQVAKTOQB-AREMUKBSSA-N		Interactions Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain S [auth C] Focus chain X [auth D]
2IL (Subject of Investigation/LOI) Query on 2IL Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	R [auth C], W [auth D]	(3R)-3-(dodecanoyloxy)tetradecanoic acid C₂₆ H₅₀ O₄ IKRFTYQBIVDIMM-XMMPIXPASA-N		Interactions Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain R [auth C] Focus chain W [auth D]
A1L01 (Subject of Investigation/LOI) Query on A1L01 Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	U [auth C], Z [auth D]	(3~{S})-3-decanoyloxytetradecanoic acid C₂₄ H₄₆ O₄ WLNJGOIHOQOCJP-QFIPXVFZSA-N		Interactions Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain U [auth C] Focus chain Z [auth D]
X6N (Subject of Investigation/LOI) Query on X6N Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	T [auth C], Y [auth D]	[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate C₇ H₁₅ O₉ P NLMCYSYQBJOKBW-MSPRSRQBSA-N		Interactions Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain T [auth C] Focus chain Y [auth D]
GP4 (Subject of Investigation/LOI) Query on GP4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	K [auth A], N [auth B]	2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose C₆ H₁₄ N O₈ P QWDBGVNDGYUIAC-UKFBFLRUSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	L [auth A] M [auth A] O [auth B] P [auth B] Q [auth C] L [auth A], M [auth A], O [auth B], P [auth B], Q [auth C], V [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	PHENIX	1.16_3549:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

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: 2024-10-09
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection
Version 2.0: 2025-02-05
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary