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2WY3
Biol. Unit 2
Info
Asym.Unit (248 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (118 KB)
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(1)
Title
:
STRUCTURE OF THE HCMV UL16-MICB COMPLEX ELUCIDATES SELECT BINDING OF A VIRAL IMMUNOEVASIN TO DIVERSE NKG2D LIGANDS
Authors
:
S. Mueller, G. Zocher, A. Steinle, T. Stehle
Date
:
11 Nov 09 (Deposition) - 02 Feb 10 (Release) - 18 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Immune System-Viral Protein Complex, Immune Response, Innate Immunity, Structural Mimicry, Immunoglobulin Domain, Membrane, Cytolysis, Ulbp, Nkg2D, Nk Cell, Cell Membrane, Transmembrane, Viral Immune Evasion, Natural Killer Cell, Convergent Evolution
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Muller, G. Zocher, A. Steinle, T. Stehle
Structure Of The Hcmv Ul16-Micb Complex Elucidates Select Binding Of A Viral Immunoevasin To Diverse Nkg2D Ligands.
Plos Pathog. V. 6 723 2010
[
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3a: 2,5,8,11,14,17,20,23,26,29,32,35,3... (PEUa)
3b: 2,5,8,11,14,17,20,23,26,29,32,35,3... (PEUb)
3c: 2,5,8,11,14,17,20,23,26,29,32,35,3... (PEUc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
PEU
2
Ligand/Ion
2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
[
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]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:52 , ASN B:84 , SER B:86 , HOH B:2162 , HOH B:2163 , HOH B:2164 , GLN D:82 , HIS D:83 , HOH D:2072
BINDING SITE FOR RESIDUE NAG B1203
02
AC4
SOFTWARE
ASN B:132 , HOH B:2169 , HOH B:2170 , HOH B:2171 , HOH B:2172 , HOH B:2173 , TRP D:81 , VAL D:87 , ASP D:104 , PEU D:1160 , HOH D:2104
BINDING SITE FOR RESIDUE NAG B1206
03
AC5
SOFTWARE
GLN B:82 , HIS B:83 , ASN D:84 , SER D:86 , VAL D:87 , HOH D:2077 , HOH D:2159 , HOH D:2160 , HOH D:2161 , HOH D:2162
BINDING SITE FOR RESIDUE NAG D1203
04
AC6
SOFTWARE
ASN A:113 , GLU A:115 , ARG A:134 , GLU D:71 , ASN D:95 , HOH D:2093 , HOH D:2163 , HOH D:2164 , HOH D:2165
BINDING SITE FOR RESIDUE NAG D1204
05
AC7
SOFTWARE
SER A:133 , GLN A:136 , HOH A:2145 , VAL D:98 , ASN D:101 , ILE D:105 , HOH D:2166 , HOH D:2167 , HOH D:2168 , HOH D:2169 , HOH D:2170
BINDING SITE FOR RESIDUE NAG D1205
06
AC8
SOFTWARE
TRP B:81 , VAL B:87 , ASP B:104 , HOH B:2140 , ASN D:132 , HOH D:2134 , HOH D:2171 , HOH D:2173 , HOH D:2174 , HOH D:2175
BINDING SITE FOR RESIDUE NAG D1206
07
BC1
SOFTWARE
ASN C:8 , MET C:10 , LEU C:23 , GLN C:91 , TYR C:111 , GLY C:114
BINDING SITE FOR RESIDUE PEU C1176
08
BC2
SOFTWARE
ARG A:35 , LYS A:44 , LYS C:40
BINDING SITE FOR RESIDUE ACT A1177
09
BC3
SOFTWARE
LYS C:154 , ARG C:158 , HOH D:2113
BINDING SITE FOR RESIDUE ACT C1177
10
BC4
SOFTWARE
MET A:0 , GLU A:1 , HIS A:3 , GLU A:68 , ARG A:75 , ILE A:98 , HIS A:99 , GLU A:100 , SER A:102 , LYS A:152 , THR A:155 , ARG A:158 , ALA A:159 , ASP A:163 , GLN A:169 , HOH A:2076 , HOH A:2158 , HOH A:2160 , VAL B:27 , LEU B:29 , GLY B:30 , SER B:31 , LYS B:32 , SER B:33 , SER B:34 , SER B:36 , THR B:37 , CYS B:38 , ASN B:41 , GLU B:44 , LEU B:45 , ALA B:46 , ILE B:48 , PRO B:50 , GLY B:51 , GLU B:52 , THR B:53 , TRP B:54 , THR B:55 , LEU B:56 , HIS B:57 , GLY B:58 , MET B:59 , CYS B:60 , ILE B:61 , SER B:62 , ILE B:63 , CYS B:64 , TYR B:65 , TYR B:66 , GLU B:67 , NAG B:1203 , NAG B:1204 , NAG B:1205 , NAG B:1206 , HOH B:2007 , HOH B:2013 , HOH B:2032 , HOH B:2041 , HOH B:2043 , HOH B:2057 , HOH B:2058 , HOH B:2066 , HOH B:2067 , HOH B:2068 , HOH B:2069 , HOH B:2070 , HOH B:2071 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075 , HOH B:2076 , HOH B:2077 , HOH B:2078 , HOH B:2079 , HOH B:2080 , HOH B:2081 , HOH B:2082 , HOH B:2083 , HOH B:2084 , HOH B:2085 , HOH B:2088 , HOH B:2089 , HOH B:2090 , HOH B:2091 , HOH B:2092 , HOH B:2093 , HOH B:2094 , HOH B:2096 , HOH B:2097 , HOH B:2098 , HOH B:2099 , HOH B:2101 , HOH B:2102 , HOH B:2103 , HOH B:2104 , HOH B:2105 , HOH B:2106 , HOH B:2107 , HOH B:2108 , HOH B:2109 , HOH B:2110 , HOH B:2111 , HOH B:2112 , HOH B:2113 , HOH B:2116 , HOH B:2117 , HOH B:2119 , HOH B:2120 , HOH B:2121 , HOH B:2124 , HOH B:2125 , HOH B:2126 , HOH B:2129 , HOH B:2131 , HOH B:2133 , HOH B:2134 , HOH B:2135 , HOH B:2136 , HOH B:2137 , HOH B:2138 , HOH B:2140 , HOH B:2141 , HOH B:2142 , HOH B:2143 , HOH B:2144 , HOH B:2145 , HOH B:2146 , HOH B:2147 , HOH B:2148 , HOH B:2149 , HOH B:2150 , HOH B:2152 , HOH B:2153 , HOH B:2154 , HOH B:2155 , HOH B:2157 , HOH B:2158 , HOH B:2159 , HOH B:2160 , HOH B:2168 , HOH B:2169 , HOH B:2170 , ALA C:56 , ASP C:60 , TRP D:81 , HIS D:83 , ASN D:132 , LEU D:133 , ASN D:145 , THR D:147 , NAG D:1202 , NAG D:1203 , NAG D:1206 , HOH D:2078 , HOH D:2162
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 68 RESIDUES 68 TO 1202
11
BC5
SOFTWARE
ALA A:56 , ASP A:60 , GLN A:131 , SER A:132 , SER A:133 , ARG A:134 , HOH A:2118 , GLU B:67 , TRP B:81 , HIS B:83 , ASN B:132 , LEU B:133 , ASN B:145 , THR B:147 , LYS B:149 , NAG B:1202 , NAG B:1203 , NAG B:1206 , HOH B:2065 , HOH B:2083 , GLU C:68 , ARG C:75 , LYS C:152 , THR C:155 , HIS C:156 , ARG C:158 , ALA C:159 , ASP C:163 , HOH C:2110 , VAL D:27 , ASP D:28 , LEU D:29 , GLY D:30 , SER D:31 , LYS D:32 , SER D:33 , SER D:34 , SER D:36 , THR D:37 , CYS D:38 , ASN D:41 , GLU D:44 , LEU D:45 , ALA D:46 , ILE D:48 , PRO D:50 , GLY D:51 , GLU D:52 , THR D:53 , TRP D:54 , THR D:55 , LEU D:56 , HIS D:57 , GLY D:58 , MET D:59 , CYS D:60 , ILE D:61 , SER D:62 , ILE D:63 , CYS D:64 , TYR D:65 , TYR D:66 , GLU D:67 , NAG D:1203 , NAG D:1204 , NAG D:1205 , NAG D:1206 , HOH D:2027 , HOH D:2039 , HOH D:2048 , HOH D:2057 , HOH D:2058 , HOH D:2059 , HOH D:2060 , HOH D:2061 , HOH D:2062 , HOH D:2063 , HOH D:2064 , HOH D:2065 , HOH D:2066 , HOH D:2067 , HOH D:2068 , HOH D:2069 , HOH D:2070 , HOH D:2071 , HOH D:2072 , HOH D:2073 , HOH D:2074 , HOH D:2075 , HOH D:2077 , HOH D:2078 , HOH D:2079 , HOH D:2082 , HOH D:2083 , HOH D:2084 , HOH D:2085 , HOH D:2086 , HOH D:2089 , HOH D:2091 , HOH D:2092 , HOH D:2093 , HOH D:2094 , HOH D:2095 , HOH D:2096 , HOH D:2097 , HOH D:2098 , HOH D:2099 , HOH D:2100 , HOH D:2101 , HOH D:2102 , HOH D:2103 , HOH D:2104 , HOH D:2105 , HOH D:2106 , HOH D:2107 , HOH D:2108 , HOH D:2110 , HOH D:2111 , HOH D:2112 , HOH D:2113 , HOH D:2116 , HOH D:2117 , HOH D:2118 , HOH D:2120 , HOH D:2122 , HOH D:2123 , HOH D:2124 , HOH D:2125 , HOH D:2126 , HOH D:2127 , HOH D:2128 , HOH D:2129 , HOH D:2130 , HOH D:2131 , HOH D:2132 , HOH D:2133 , HOH D:2134 , HOH D:2136 , HOH D:2137 , HOH D:2138 , HOH D:2139 , HOH D:2140 , HOH D:2141 , HOH D:2142 , HOH D:2143 , HOH D:2144 , HOH D:2145 , HOH D:2146 , HOH D:2148 , HOH D:2149 , HOH D:2150 , HOH D:2151 , HOH D:2153 , HOH D:2154 , HOH D:2156 , HOH D:2158 , HOH D:2166 , HOH D:2171 , HOH D:2176 , HOH D:2177
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 68 RESIDUES 68 TO 1202
[
close Site info
]
SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_044068 (E16G, chain C, )
2: VAR_044069 (P45H, chain C, )
3: VAR_044070 (D52N, chain C, )
4: VAR_044071 (E57E, chain C, )
5: VAR_044072 (D65G, chain C, )
6: VAR_044074 (I98M, chain C, )
7: VAR_059527 (N113H, chain C, )
8: VAR_044075 (N113N, chain C, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_044068
E
39
G
MICB_HUMAN
Polymorphism
45578846
C
E
16
G
2
UniProt
VAR_044069
P
68
H
MICB_HUMAN
Polymorphism
45583740
C
P
45
H
3
UniProt
VAR_044070
D
75
N
MICB_HUMAN
Polymorphism
3131639
C
D
52
N
4
UniProt
VAR_044071
K
80
E
MICB_HUMAN
Polymorphism
1065075
C
E
57
E
5
UniProt
VAR_044072
D
88
G
MICB_HUMAN
Polymorphism
45486091
C
D
65
G
7
UniProt
VAR_044074
I
121
M
MICB_HUMAN
Polymorphism
3134900
C
I
98
M
8
UniProt
VAR_059527
D
136
H
MICB_HUMAN
Polymorphism
1051788
C
N
113
H
9
UniProt
VAR_044075
D
136
N
MICB_HUMAN
Polymorphism
1051788
C
N
113
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2wy3a_ (A:)
1b: SCOP_d2wy3c_ (C:)
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Protein Domains
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Organisms
(
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(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
automated matches
(52)
Protein domain
:
automated matches
(52)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d2wy3a_
A:
1b
d2wy3c_
C:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2wy3A00 (A:0-175)
1b: CATH_2wy3C00 (C:1-175)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Human herpesvirus 5 strain ad169. Organism_taxid: 10360.
(1)
1a
2wy3A00
A:0-175
1b
2wy3C00
C:1-175
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain D
Asymmetric Unit 1
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Asym.Unit (248 KB)
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Biol.Unit 1 (122 KB)
Header - Biol.Unit 1
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