8WSA

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lymphocyte antigen 96A [auth C],
C [auth D]
142Mus musculusMutation(s): 0 
Gene Names: Ly96
UniProt
Find proteins for Q9JHF9 (Mus musculus)
Explore Q9JHF9 
Go to UniProtKB:  Q9JHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JHF9
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9JHF9-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 4B [auth A],
D [auth B]
604Mus musculusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QUK6
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q9QUK6-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0IL (Subject of Investigation/LOI)
Query on 0IL

Download Ideal Coordinates CCD File 
H [auth C],
U [auth D]
(3R)-3-(tetradecanoyloxy)tetradecanoic acid
C28 H54 O4
IYESSKQVAKTOQB-AREMUKBSSA-N
2IL (Subject of Investigation/LOI)
Query on 2IL

Download Ideal Coordinates CCD File 
G [auth C],
T [auth D]
(3R)-3-(dodecanoyloxy)tetradecanoic acid
C26 H50 O4
IKRFTYQBIVDIMM-XMMPIXPASA-N
A1L01 (Subject of Investigation/LOI)
Query on A1L01

Download Ideal Coordinates CCD File 
J [auth C],
Q [auth A]
(3~{S})-3-decanoyloxytetradecanoic acid
C24 H46 O4
WLNJGOIHOQOCJP-QFIPXVFZSA-N
X6N (Subject of Investigation/LOI)
Query on X6N

Download Ideal Coordinates CCD File 
I [auth C],
V [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
GP4 (Subject of Investigation/LOI)
Query on GP4

Download Ideal Coordinates CCD File 
BA [auth B],
P [auth A]
2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-UKFBFLRUSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
E [auth C]
F [auth C]
K [auth A]
L [auth A]
AA [auth B],
E [auth C],
F [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
R [auth D],
S [auth D],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.16_3549:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic OfInstitute for Basic Science, IBS

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection