Immunological Recognition of Microbial Pathogens

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Title
Immunological Recognition of Microbial
Pathogens Structure and Function of Large
Macromolecular Assemblies 38th Course
International School of Crystallography Erice,
Sicily Ian A. Wilson, June 11, 2006.
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Pathogen Detection by the Innate and Adaptive
Immune Systems
TLR Choe 2005
Hard-wired, Pattern recognition
TREM-1 Kelker 2004
NKG2D Wolan 2001
Innate immunity (immediate 0-4 hours)
CD1 Zeng 1997
Early induced response (early 4-96 hours)
Adaptive immunity (late gt96 hours)
MHC Bjorkman, Wiley 1987
Gene rearrangements, Clonal expansion, All
antigens
TCR Garcia 1996
Ab Davies, Poljak 1971
Adapted from Nature Immunology  5, 971 - 974
(2004) The interface between innate and adaptive
immunity Kasper Hoebe, Edith Janssen  Bruce
Beutler
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Rudd PM et al., J Mol Biol 293351-66, 1999
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Rudolph M et al., Ann. Rev. Biophys. Biomol.
Struc. 31121-49, 2002
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Figure 3-25
Adaptive immunity- polymorphic MHC class I and
class II
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Innate immunity non-polymorphic CD1a-d
MHC-like, but hydrophobic binding groove
a1
a2
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CD1-presented Antigens
phosphatidylinosi- tol dimannoside
phosphatidyl- inositol
phosphatidyl- choline
didehydroxy- mycobactin
CD1d
glucose- monomycolate
CD1d
?-galacturonosyl ceramide
sulfatide
?-galactosyl ceramide
adapted from Brigl M Brenner MB (2004) Ann.
Rev. Immunol. 22817-890
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CD1d-C8-aGalCer complex
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CD1 lipid antigen complexes
CD1d
CD1a
2.2 Å
2.1 Å
2.6 Å
CD1a-sulfatide (C18) Zajonc et al. (2003) Nat.
Immunol. 4808-815
CD1d-aGC (C8) Zajonc et al. (2005) Nat. Immunol.
810-818
CD1d-PIM-2 (C16) Zajonc et al.
unpublished
2.8 Å
1.8 Å
1.9 Å
CD1a-lipopeptide (C16) Zajonc et al. (2005)
Immunity. 22209-219
CD1d-aGSL (C14) Wu D. and Zajonc et al.
unpublished
CD1d-sulfatide (C24) Zajonc et al. (2005) JEM
2021517-26-815
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TCR view of CD1d ligands
(iNKT)
iNKT Kd0.35 µM
CD1d-PIM-2 (C16) Zajonc et al. unpublished
iNKT Kd0.035-0.35 mM
NKT
CD1d-aGSL (C14) Wu D. and Zajonc et al.
unpublished
CD1d-sulfatide (C24) Zajonc et al. (2005) JEM
2021517-26-815
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CD1b-GMM
2200 Å3 C80
90
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TLRs as interface between innate and adaptive
immunity
Int Immunol. 17 1-14 (2005) Takeda K, Akira S.
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TLRs recognize wide range of pathogen-associated
molecules

Bacteria
Fungi
Viruses Parasites
Host Gram- Myco-
All
All RSV
MCMV, VSV and Trypanosoma Negative
bacteria

reovirus Influenza
cruzi LPS Diacyl-
Triacyl- CpG Flagellin
Zymosan F protein dsRNA ssRNA
GPI anchors HSP60,
Lipoproteins Lipoproteins



fibrinogen TLR4- TLR2-
TLR2- TLR9 TLR5
TLR2- TLR4- TLR3
TLR7, TLR2 TLR4-
TLR4 TLR6 TLR1
TLR6
TLR4 TLR8
TLR4
Nature Reviews Immunology 5, 446-458
(2005) Foo Y. Liew et al
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Overall structure
Science 309, 581-585 (2005) Choe J, Kelker MS,
Wilson IA
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Glycosylation-free face contains all the
functional sites
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Putative dsRNA binding site
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Predicted Modes of Signaling
Ligand induced dimerization Pre-existin
g dimer
RNA binding
TIR domain
Signaling
RNA binding
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Why study antibodies from sharks? Cartilaginous
fish (sharks, skates and rays) are the most
primitive vertebrates with the typical
components of an adaptive immune system
(antibodies, TCRs, MHCs, RAG1/RAG2, etc).
Currently, crystal structures exist only for
antibodies from mice, rats, hamsters, humans, and
camels.
Molecular timescale for vertebrate evolution From
an analysis of 658 nuclear genes- agrees well
with fossil record All times indicate Millions of
year (Myr) separating humans and the group shown.
From Kumar and Hedges, Nature, 392 917, 1998.
?sharks
?lamprey
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Ig diversity
From Flajnik, M.F. Nat. Rev. Immunol. 2688-698,
2002.
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Some different Ig tertiary arrangements
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Shark IgNAR Ab single domain, only 2 CDRs
Non-canonical disulfides from C97(CDR3) to C104
(FR4), and C92 (CDR3) to C35 (FR2)
Long CDR3 folds over to partially cover what
would be the VL-VH interface in normal
antibodies.
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IgNAR
HV2
CDR3
CDR1
Lysozyme
Stanfield RL, Dooley H, Flajnik MF, Wilson IA
Science( 2004)3051770-3
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Annu. Rev. Immunol. 2006. 24497518
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Acknowledgements
TLR-3 Jungwoo Choe,TSRI Matthew S. Kelker,
TSRI Shark Antibodies Robyn Stanfield,
TSRI Helen Dooley, U. Maryland Martin Flajnik,
U.Maryland
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wilson_at_scripps.edu
CD1-lipid complexes

• Dirk Zajonc (TSRI)
• Thomas Bowden (St. Andrews)
• Max Crispin (Oxford)
• Marc Elsliger (TSRI)
• Luc Teyton (TSRI)
• Chi-Huey Wong (TSRI)
• Doug Wu
• Branch Moody (Harvard)
• D. Young, T.-Y. Cheng, I. Van Rhijn
• Michael Brenner (Harvard)
• C. Dascher, M. Vincent, J. Gumperz
• Mitch Kronenberg (LIAI)
• Y. Kinjo, B. Sullivan, S. Sidobre
• Vipin Kumar (TPIMS)
• I. Maricic, R. Halder, K. Roy