3RG1

Crystal structure of the RP105/MD-1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


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

Literature

An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1.

Yoon, S.I., Hong, M., Wilson, I.A.

(2011) Nat.Struct.Mol.Biol. 18: 1028-1035

  • DOI: 10.1038/nsmb.2106

  • PubMed Abstract: 

    • RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 Å resolution shares a similar overa ...

    RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 Å resolution shares a similar overall architecture to its homolog TLR4-MD-2 but assembles into an unusual 2:2 homodimer that differs from any other known TLR-ligand assembly. The homodimer is assembled in a head-to-head orientation that juxtaposes the N-terminal leucine-rich repeats (LRRs) of the two RP105 chains, rather than the usual tail-to-tail configuration of C-terminal LRRs in ligand-activated TLR dimers, such as TLR1-TRL2, TLR2-TLR6, TLR3-TLR3 and TLR4-TLR4. Another unusual interaction is mediated by an RP105-specific asparagine-linked glycan, which wedges MD-1 into the co-receptor binding concavity on RP105. This unique mode of assembly represents a new paradigm for TLR complexes and suggests a molecular mechanism for regulating LPS responses.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD180 molecule
A, E, I, M, B, F, J, N
612Bos taurusMutation(s): 0 
Gene Names: CD180
Find proteins for A6QNK7 (Bos taurus)
Go to Gene View: CD180
Go to UniProtKB:  A6QNK7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LY86 protein
C, D, G, H, K, L, O, P
147Bos taurusMutation(s): 0 
Gene Names: LY86
Find proteins for A4IFT3 (Bos taurus)
Go to Gene View: LY86
Go to UniProtKB:  A4IFT3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGT
Query on PGT
Download SDF File 
Download CCD File 
D, H, L, P
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
PHOSPHATIDYLGLYCEROL; 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
A, B, E, F, I, J, M, N
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
A, B, E, F, I, J, M, N
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, E, F, I, J, M, N
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 101.509α = 94.00
b = 141.577β = 91.66
c = 141.953γ = 91.37
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASESphasing
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Database references
  • Version 1.2: 2011-09-21
    Type: Database references