|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
125 a.a.
|
|
|
|
|
|
|
|
|
|
|
146 a.a.
|
|
|
|
|
|
|
|
|
|
|
150 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Immune system
|
|
|
Title:
|
|
Crystal structure of murine nk cell ligand rae-1 beta in complex with nkg2d
|
|
Structure:
|
|
Nkg2-d type ii integral membrane protein. Chain: a, b. Fragment: rae-1beta, unp residues 109-232. Synonym: killer cell lectin-like receptor subfamily k member 1, nk cell receptor d, nkg2-d-activating nk receptor. Engineered: yes. Retinoic acid early-inducible protein 1-beta. Chain: c, d. Fragment: immunoreceptor nkg2d, unp residues 31-204.
|
|
Source:
|
|
Mus musculus. Mouse. Organism_taxid: 10090. Gene: klrk1, nkg2d, rae-1 beta. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: nkg2d, raet1b.
|
|
Resolution:
|
|
|
1.95Å
|
R-factor:
|
0.192
|
R-free:
|
0.217
|
|
|
Authors:
|
|
P.Li,R.K.Strong
|
Key ref:
|
|
P.Li
et al.
(2002).
Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D.
Immunity,
16,
77-86.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
26-Feb-14
|
Release date:
|
09-Apr-14
|
|
|
Supersedes:
|
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
O54709
(NKG2D_MOUSE) -
NKG2-D type II integral membrane protein from Mus musculus
|
|
|
|
Seq:
Struc:
|
|
|
|
232 a.a.
125 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Immunity
16:77-86
(2002)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D.
|
|
P.Li,
G.McDermott,
R.K.Strong.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Induced by retinoic acid and implicated in playing a role in development, rodent
RAE-1 proteins are ligands for the activating immunoreceptor NKG2D, widely
expressed on natural killer cells, T cells, and macrophages. RAE-1 proteins
(alpha, beta, gamma, and delta) are distant major histocompatibility complex
(MHC) class I homologs, comprising isolated alpha1alpha2 platform domains. The
crystal structure of RAE-1beta was distorted from other MHC homologs and
displayed noncanonical disulfide bonds. The loss of any remnant of a peptide
binding groove was facilitated by the close approach of the groove-defining
helices through a hydrophobic, leucine-rich interface. The RAE-1beta-murine
NKG2D complex structure resembled the human NKG2D-MICA receptor-ligand complex
and further demonstrated the promiscuity of the NKG2D ligand binding site.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 3.
Figure 3. Structures of Murine NKD NK Cell Receptor-Ligand
ComplexesRibbon representations (top) and GRASP (Nicholls et
al., 1991) molecular surfaces (bottom) are shown for the
structures of (A) the muNKG2D–RAE-1β, (B) huNKG2D–MICA, and
(C) Ly49A-H-2D^d complexes. Ribbons of the ligands are colored
by domain: α1, yellow; α2, red; α3 (when present), green; and
β[2]-m (when present), cyan; ribbons of the receptors are
colored by chain: blue or purple. Molecular surfaces of the
platform domains are oriented such that the view is looking down
onto the NKG2D binding surface of RAE-1 and MICA. In (A), the
molecular surface of muNKG2D was included in an orientation
looking down onto the RAE-1 binding surface, as if the receptor
had been peeled away from the complex. Molecular surfaces are
colored by electrostatic potential, with positively charged
areas in blue and negatively charged areas in red. In (C), the
bound peptide in H-2D^d is shown in ball-and-stick
representation.
|
|
Figure 4.
Figure 4. Interactions of RAE-1β-muNKG2D Complexes in the
CrystalTwo views of the reciprocal, crystallographic interaction
between muNKG2D homodimers are shown, a view perpendicular to a
hypothetical cell-cell interface (top) and a view down onto the
complexes (bottom). Molecules are shown as ribbon
representations colored by domain (muNKG2D-A, blue; muNKG2D-B,
purple; RAE-1β α1, yellow; and RAE-1β α2, orange). The
approximate position of the crystallographic 6[1] screw axis is
indicated, as are hypothetical cell surfaces and the paths of
membrane anchor elements (black arrows). The position of Asn179
is indicated in red on the ribbons and by red arrows.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Cell Press:
Immunity
(2002,
16,
77-86)
copyright 2002.
|
|
| |
Figures were
selected
by the author.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
Y.Li,
Q.Wang,
and
R.A.Mariuzza
(2011).
Structure of the human activating natural cytotoxicity receptor NKp30 bound to its tumor cell ligand B7-H6.
|
| |
J Exp Med,
208,
703-714.
|
|
|
|
|
|
|
H.P.Su,
K.Singh,
A.G.Gittis,
and
D.N.Garboczi
(2010).
The structure of the poxvirus A33 protein reveals a dimer of unique C-type lectin-like domains.
|
| |
J Virol,
84,
2502-2510.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Zhi,
J.Mans,
M.J.Paskow,
P.H.Brown,
P.Schuck,
S.Jonjić,
K.Natarajan,
and
D.H.Margulies
(2010).
Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms.
|
| |
Biochemistry,
49,
2443-2453.
|
|
|
|
|
|
|
O.Cédile,
N.Popa,
F.Pollet-Villard,
N.Garmy,
e.l. .C.Ibrahim,
and
J.Boucraut
(2010).
The NKG2D ligands RAE-1δ and RAE-1ε differ with respect to their receptor affinity, expression profiles and transcriptional regulation.
|
| |
PLoS One,
5,
e13466.
|
|
|
|
|
|
|
A.V.Romphruk,
A.Romphruk,
T.K.Naruse,
S.Raroengjai,
C.Puapairoj,
H.Inoko,
and
C.Leelayuwat
(2009).
Polymorphisms of NKG2D ligands: diverse RAET1/ULBP genes in northeastern Thais.
|
| |
Immunogenetics,
61,
611-617.
|
|
|
|
|
|
|
J.Arapovic,
T.Lenac,
R.Antulov,
B.Polic,
Z.Ruzsics,
L.N.Carayannopoulos,
U.H.Koszinowski,
A.Krmpotic,
and
S.Jonjic
(2009).
Differential susceptibility of RAE-1 isoforms to mouse cytomegalovirus.
|
| |
J Virol,
83,
8198-8207.
|
|
|
|
|
|
|
J.Mans,
L.Zhi,
M.J.Revilleza,
L.Smith,
A.Redwood,
K.Natarajan,
and
D.H.Margulies
(2009).
Structure and function of murine cytomegalovirus MHC-I-like molecules: how the virus turned the host defense to its advantage.
|
| |
Immunol Res,
43,
264-279.
|
|
|
|
|
|
|
M.Wittenbrink,
J.Spreu,
and
A.Steinle
(2009).
Differential NKG2D binding to highly related human NKG2D ligands ULBP2 and RAET1G is determined by a single amino acid in the alpha2 domain.
|
| |
Eur J Immunol,
39,
1642-1651.
|
|
|
|
|
|
|
E.J.Petrie,
C.S.Clements,
J.Lin,
L.C.Sullivan,
D.Johnson,
T.Huyton,
A.Heroux,
H.L.Hoare,
T.Beddoe,
H.H.Reid,
M.C.Wilce,
A.G.Brooks,
and
J.Rossjohn
(2008).
CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence.
|
| |
J Exp Med,
205,
725-735.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Y.Kwong,
S.Baskar,
H.Zhang,
C.L.Mackall,
and
C.Rader
(2008).
Generation, affinity maturation, and characterization of a human anti-human NKG2D monoclonal antibody with dual antagonistic and agonistic activity.
|
| |
J Mol Biol,
384,
1143-1156.
|
|
|
|
|
|
|
S.L.Rogers,
and
J.Kaufman
(2008).
High allelic polymorphism, moderate sequence diversity and diversifying selection for B-NK but not B-lec, the pair of lectin-like receptor genes in the chicken MHC.
|
| |
Immunogenetics,
60,
461-475.
|
|
|
|
|
|
|
J.M.Dijkstra,
T.Katagiri,
K.Hosomichi,
K.Yanagiya,
H.Inoko,
M.Ototake,
T.Aoki,
K.Hashimoto,
and
T.Shiina
(2007).
A third broad lineage of major histocompatibility complex (MHC) class I in teleost fish; MHC class II linkage and processed genes.
|
| |
Immunogenetics,
59,
305-321.
|
|
|
|
|
|
|
J.Mans,
K.Natarajan,
A.Balbo,
P.Schuck,
D.Eikel,
S.Hess,
H.Robinson,
H.Simic,
S.Jonjic,
C.T.Tiemessen,
and
D.H.Margulies
(2007).
Cellular expression and crystal structure of the murine cytomegalovirus major histocompatibility complex class I-like glycoprotein, m153.
|
| |
J Biol Chem,
282,
35247-35258.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.C.Sullivan,
C.S.Clements,
T.Beddoe,
D.Johnson,
H.L.Hoare,
J.Lin,
T.Huyton,
E.J.Hopkins,
H.H.Reid,
M.C.Wilce,
J.Kabat,
F.Borrego,
J.E.Coligan,
J.Rossjohn,
and
A.G.Brooks
(2007).
The heterodimeric assembly of the CD94-NKG2 receptor family and implications for human leukocyte antigen-E recognition.
|
| |
Immunity,
27,
900-911.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Duprat,
M.P.Lefranc,
and
O.Gascuel
(2006).
A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin.
|
| |
Bioinformatics,
22,
453-459.
|
|
|
|
|
|
|
L.Deng,
and
R.A.Mariuzza
(2006).
Structural basis for recognition of MHC and MHC-like ligands by natural killer cell receptors.
|
| |
Semin Immunol,
18,
159-166.
|
|
|
|
|
|
|
M.G.Rudolph,
R.L.Stanfield,
and
I.A.Wilson
(2006).
How TCRs bind MHCs, peptides, and coreceptors.
|
| |
Annu Rev Immunol,
24,
419-466.
|
|
|
|
|
|
|
A.N.Zelensky,
and
J.E.Gready
(2005).
The C-type lectin-like domain superfamily.
|
| |
FEBS J,
272,
6179-6217.
|
|
|
|
|
|
|
D.Garrity,
M.E.Call,
J.Feng,
and
K.W.Wucherpfennig
(2005).
The activating NKG2D receptor assembles in the membrane with two signaling dimers into a hexameric structure.
|
| |
Proc Natl Acad Sci U S A,
102,
7641-7646.
|
|
|
|
|
|
|
I.Ohki,
T.Ishigaki,
T.Oyama,
S.Matsunaga,
Q.Xie,
M.Ohnishi-Kameyama,
T.Murata,
D.Tsuchiya,
S.Machida,
K.Morikawa,
and
S.Tate
(2005).
Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL.
|
| |
Structure,
13,
905-917.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.L.Lanier
(2005).
NK cell recognition.
|
| |
Annu Rev Immunol,
23,
225-274.
|
|
|
|
|
|
|
R.Biassoni,
and
N.Dimasi
(2005).
Human natural killer cell receptor functions and their implication in diseases.
|
| |
Expert Rev Clin Immunol,
1,
405-417.
|
|
|
|
|
|
|
R.Olson,
K.E.Huey-Tubman,
C.Dulac,
and
P.J.Bjorkman
(2005).
Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.
|
| |
PLoS Biol,
3,
e257.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Huang,
S.Gilfillan,
M.Cella,
M.J.Miley,
O.Lantz,
L.Lybarger,
D.H.Fremont,
and
T.H.Hansen
(2005).
Evidence for MR1 antigen presentation to mucosal-associated invariant T cells.
|
| |
J Biol Chem,
280,
21183-21193.
|
|
|
|
|
|
|
B.J.McFarland,
and
R.K.Strong
(2003).
Thermodynamic analysis of degenerate recognition by the NKG2D immunoreceptor: not induced fit but rigid adaptation.
|
| |
Immunity,
19,
803-812.
|
|
|
|
|
|
|
D.H.Margulies
(2003).
Molecular interactions: stiff or floppy (or somewhere in between?).
|
| |
Immunity,
19,
772-774.
|
|
|
|
|
|
|
D.H.Raulet
(2003).
Roles of the NKG2D immunoreceptor and its ligands.
|
| |
Nat Rev Immunol,
3,
781-790.
|
|
|
|
|
|
|
G.Das,
and
C.A.Janeway
(2003).
MHC specificity of iIELs.
|
| |
Trends Immunol,
24,
88-93.
|
|
|
|
|
|
|
J.Jameson,
D.Witherden,
and
W.L.Havran
(2003).
T-cell effector mechanisms: gammadelta and CD1d-restricted subsets.
|
| |
Curr Opin Immunol,
15,
349-353.
|
|
|
|
|
|
|
M.Gleimer,
and
P.Parham
(2003).
Stress management: MHC class I and class I-like molecules as reporters of cellular stress.
|
| |
Immunity,
19,
469-477.
|
|
|
|
|
|
|
S.Radaev,
and
P.D.Sun
(2003).
Structure and function of natural killer cell surface receptors.
|
| |
Annu Rev Biophys Biomol Struct,
32,
93.
|
|
|
|
|
|
|
W.M.Yokoyama,
and
B.F.Plougastel
(2003).
Immune functions encoded by the natural killer gene complex.
|
| |
Nat Rev Immunol,
3,
304-316.
|
|
|
|
|
|
|
E.Vivier,
E.Tomasello,
and
P.Paul
(2002).
Lymphocyte activation via NKG2D: towards a new paradigm in immune recognition?
|
| |
Curr Opin Immunol,
14,
306-311.
|
|
|
|
|
|
|
K.L.McQueen,
and
P.Parham
(2002).
Variable receptors controlling activation and inhibition of NK cells.
|
| |
Curr Opin Immunol,
14,
615-621.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
 |
|
Links
