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3C2I
Asym. Unit
Info
Asym.Unit (67 KB)
Biol.Unit 1 (62 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF METHYL-CPG BINDING DOMAIN OF HUMAN MECP2 IN COMPLEX WITH A METHYLATED DNA SEQUENCE FROM BDNF
Authors
:
K. L. Ho, I. W. Mcnae, L. Schmiedeberg, R. J. Klose, A. P. Bird, M. D. Walkinshaw
Date
:
25 Jan 08 (Deposition) - 13 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Water Mediated Recognition, Protein-Methylated Dna Complex, Asx-St-Motif, Alternative Splicing, Chromosomal Rearrangement, Disease Mutation, Dna-Binding, Nucleus, Phosphoprotein, Polymorphism, Repressor, Transcription Regulator
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Ho, I. W. Mcnae, L. Schmiedeberg, R. J. Klose, A. P. Bird, M. D. Walkinshaw
Mecp2 Binding To Dna Depends Upon Hydration At Methyl-Cpg
Mol. Cell V. 29 525 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONO... (5CMa)
1b: 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONO... (5CMb)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5CM
2
Mod. Nucleotide
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
[
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]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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]
SAPs(SNPs)/Variants
(28, 28)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_023552 (D97E, chain A, )
02: VAR_018182 (D97Y, chain A, )
03: VAR_023553 (L100R, chain A, )
04: VAR_017462 (L100V, chain A, )
05: VAR_018183 (P101H, chain A, )
06: VAR_018184 (P101L, chain A, )
07: VAR_010276 (P101R, chain A, )
08: VAR_023554 (P101S, chain A, )
09: VAR_018185 (P101T, chain A, )
10: VAR_018186 (R106Q, chain A, )
11: VAR_010272 (R106W, chain A, )
12: VAR_018187 (R111G, chain A, )
13: VAR_023555 (Y120D, chain A, )
14: VAR_010277 (L124F, chain A, )
15: VAR_018188 (Q128P, chain A, )
16: VAR_010273 (R133C, chain A, )
17: VAR_018189 (R133H, chain A, )
18: VAR_010278 (S134C, chain A, )
19: VAR_018190 (K135E, chain A, )
20: VAR_017581 (E137G, chain A, )
21: VAR_010279 (M140V, chain A, )
22: VAR_010280 (P152R, chain A, )
23: VAR_023556 (F155I, chain A, )
24: VAR_010274 (F155S, chain A, )
25: VAR_018191 (D156G, chain A, )
26: VAR_023557 (T158A, chain A, )
27: VAR_010275 (T158M, chain A, )
28: VAR_023558 (G161V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_023552
D
97
E
MECP2_HUMAN
Disease (RTT)
---
A
D
97
E
02
UniProt
VAR_018182
D
97
Y
MECP2_HUMAN
Disease (RTT)
---
A
D
97
Y
03
UniProt
VAR_023553
L
100
R
MECP2_HUMAN
Disease (RTT)
---
A
L
100
R
04
UniProt
VAR_017462
L
100
V
MECP2_HUMAN
Disease (RTT)
28935168
A
L
100
V
05
UniProt
VAR_018183
P
101
H
MECP2_HUMAN
Disease (RTT)
---
A
P
101
H
06
UniProt
VAR_018184
P
101
L
MECP2_HUMAN
Disease (RTT)
---
A
P
101
L
07
UniProt
VAR_010276
P
101
R
MECP2_HUMAN
Disease (RTT)
---
A
P
101
R
08
UniProt
VAR_023554
P
101
S
MECP2_HUMAN
Disease (RTT)
---
A
P
101
S
09
UniProt
VAR_018185
P
101
T
MECP2_HUMAN
Disease (RTT)
---
A
P
101
T
10
UniProt
VAR_018186
R
106
Q
MECP2_HUMAN
Disease (RTT)
---
A
R
106
Q
11
UniProt
VAR_010272
R
106
W
MECP2_HUMAN
Disease (RTT)
28934907
A
R
106
W
12
UniProt
VAR_018187
R
111
G
MECP2_HUMAN
Disease (RTT)
---
A
R
111
G
13
UniProt
VAR_023555
Y
120
D
MECP2_HUMAN
Disease (RTT)
---
A
Y
120
D
14
UniProt
VAR_010277
L
124
F
MECP2_HUMAN
Disease (RTT)
---
A
L
124
F
15
UniProt
VAR_018188
Q
128
P
MECP2_HUMAN
Disease (RTT)
---
A
Q
128
P
16
UniProt
VAR_010273
R
133
C
MECP2_HUMAN
Disease (RTT)
28934904
A
R
133
C
17
UniProt
VAR_018189
R
133
H
MECP2_HUMAN
Disease (RTT)
---
A
R
133
H
18
UniProt
VAR_010278
S
134
C
MECP2_HUMAN
Disease (RTT)
---
A
S
134
C
19
UniProt
VAR_018190
K
135
E
MECP2_HUMAN
Disease (RTT)
---
A
K
135
E
20
UniProt
VAR_017581
E
137
G
MECP2_HUMAN
Disease (MRXS13)
---
A
E
137
G
21
UniProt
VAR_010279
A
140
V
MECP2_HUMAN
Disease (MRXS13)
28934908
A
M
140
V
22
UniProt
VAR_010280
P
152
R
MECP2_HUMAN
Disease (RTT)
---
A
P
152
R
23
UniProt
VAR_023556
F
155
I
MECP2_HUMAN
Disease (RTT)
---
A
F
155
I
24
UniProt
VAR_010274
F
155
S
MECP2_HUMAN
Disease (RTT)
28934905
A
F
155
S
25
UniProt
VAR_018191
D
156
G
MECP2_HUMAN
Disease (RTT)
---
A
D
156
G
26
UniProt
VAR_023557
T
158
A
MECP2_HUMAN
Disease (RTT)
---
A
T
158
A
27
UniProt
VAR_010275
T
158
M
MECP2_HUMAN
Disease (RTT)
28934906
A
T
158
M
28
UniProt
VAR_023558
G
161
V
MECP2_HUMAN
Disease (RTT)
---
A
G
161
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(2, 2)
Info
All Exons
Exon 1.13d (A:91-126)
Exon 1.14e (A:126-162)
View:
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All Exon Boundaries
1: Boundary 1.5/1.13d
2: Boundary 1.13d/1.14e
3: Boundary 1.14e/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3a
ENST00000303391
3a
ENSE00001869751
X:153363212-153363061
152
MECP2_HUMAN
-
0
0
-
-
1.5
ENST00000303391
5
ENSE00001790905
X:153357765-153357642
124
MECP2_HUMAN
1-9
9
0
-
-
1.13d
ENST00000303391
13d
ENSE00001621260
X:153298008-153297658
351
MECP2_HUMAN
9-126
118
1
A:91-126
36
1.14e
ENST00000303391
14e
ENSE00001252086
X:153296901-153287024
9878
MECP2_HUMAN
126-486
361
1
A:126-162
37
[
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SCOP Domains
(0, 0)
Info
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3c2iA01 (A:93-156)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Methyl-cpg-binding Protein 2; Chain A
(5)
Homologous Superfamily
:
Methyl-cpg-binding Protein 2; Chain A
(5)
Human (Homo sapiens)
(4)
1a
3c2iA01
A:93-156
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Pfam Domains
(0, 0)
Info
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