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 
  • R-Value Observed: 0.240 

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This is version 2.0 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
  • Primary Citation of Related Structures:  
    3RG1

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CD180 molecule612Bos taurusMutation(s): 0 
Gene Names: CD180
UniProt
Find proteins for A6QNK7 (Bos taurus)
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Go to UniProtKB:  A6QNK7
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UniProt GroupA6QNK7
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LY86 protein147Bos taurusMutation(s): 0 
Gene Names: LY86
UniProt
Find proteins for A4IFT3 (Bos taurus)
Explore A4IFT3 
Go to UniProtKB:  A4IFT3
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UniProt GroupA4IFT3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
CA [auth c],
EA [auth e],
Q,
S,
AA [auth a],
CA [auth c],
EA [auth e],
Q,
S,
U,
W,
Y
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DA [auth d],
FA [auth f],
R,
T,
BA [auth b],
DA [auth d],
FA [auth f],
R,
T,
V,
X,
Z
8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G61846BY
GlyCosmos:  G61846BY
GlyGen:  G61846BY
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGT
Query on PGT

Download Ideal Coordinates CCD File 
GA [auth D],
HA [auth H],
IA [auth L],
JA [auth P]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-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 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.509α = 94
b = 141.577β = 91.66
c = 141.953γ = 91.37
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary