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Asym. Unit
Info
Asym.Unit (310 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (152 KB)
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(1)
Title
:
STRUCTURE OF DNMT3A-DNMT3L C-TERMINAL DOMAIN COMPLEX
Authors
:
D. Jia, X. Cheng
Date
:
29 Jul 07 (Deposition) - 04 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.89
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Dna Methyltransferase 3A (Dnmt3A) And Its Regulatory Factor, Dna Methyltransferase 3-Like Protein (Dnmt3L), Nucleus, S- Adenosyl-L-Methionine, Transferase/Transferase Regulator Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Jia, R. Z. Jurkowska, X. Zhang, A. Jeltsch, X. Cheng
Structure Of Dnmt3A Bound To Dnmt3L Suggests A Model For De Novo Dna Methylation.
Nature V. 449 248 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
1b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
1c: S-ADENOSYL-L-HOMOCYSTEINE (SAHc)
1d: S-ADENOSYL-L-HOMOCYSTEINE (SAHd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SAH
4
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:636 , ASP A:637 , GLY A:638 , ILE A:639 , THR A:641 , SER A:659 , GLU A:660 , VAL A:661 , CYS A:662 , ASP A:682 , VAL A:683 , ARG A:684 , GLY A:703 , PRO A:705 , LEU A:726 , ARG A:887 , SER A:888 , TRP A:889
BINDING SITE FOR RESIDUE SAH A 1
2
AC2
SOFTWARE
PHE D:636 , ASP D:637 , GLY D:638 , ILE D:639 , THR D:641 , SER D:659 , GLU D:660 , VAL D:661 , CYS D:662 , ASP D:682 , VAL D:683 , ARG D:684 , GLY D:703 , PRO D:705 , LEU D:726 , ARG D:887 , SER D:888 , TRP D:889
BINDING SITE FOR RESIDUE SAH D 4
3
AC3
SOFTWARE
PHE E:636 , GLY E:638 , ILE E:639 , THR E:641 , SER E:659 , GLU E:660 , VAL E:661 , CYS E:662 , ASP E:682 , VAL E:683 , ARG E:684 , GLY E:703 , PRO E:705 , LEU E:726 , ARG E:887 , SER E:888 , TRP E:889
BINDING SITE FOR RESIDUE SAH E 5
4
AC4
SOFTWARE
PHE H:636 , GLY H:638 , ILE H:639 , THR H:641 , GLU H:660 , VAL H:661 , CYS H:662 , ASP H:682 , VAL H:683 , GLY H:703 , ARG H:887 , SER H:888 , TRP H:889
BINDING SITE FOR RESIDUE SAH H 8
[
close Site info
]
SAPs(SNPs)/Variants
(10, 40)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_051962 (R278G, chain B/C/F/G, )
02: VAR_071467 (L644P, chain A/D/E/H, )
03: VAR_067234 (G695D, chain A/D/E/H, )
04: VAR_071468 (P696L, chain A/D/E/H, )
05: VAR_071469 (R745C, chain A/D/E/H, )
06: VAR_067236 (R878C, chain A/D/E/H, )
07: VAR_067237 (R878H, chain A/D/E/H, )
08: VAR_067238 (R878P, chain A/D/E/H, )
09: VAR_071471 (F898S, chain A/D/E/H, )
10: VAR_071472 (P900L, chain A/D/E/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_051962
R
278
G
DNM3L_HUMAN
Polymorphism
7354779
B/C/F/G
R
278
G
02
UniProt
VAR_071467
L
648
P
DNM3A_HUMAN
Disease (TBRS)
---
A/D/E/H
L
644
P
03
UniProt
VAR_067234
G
699
D
DNM3A_HUMAN
Unclassified
---
A/D/E/H
G
695
D
04
UniProt
VAR_071468
P
700
L
DNM3A_HUMAN
Disease (TBRS)
---
A/D/E/H
P
696
L
05
UniProt
VAR_071469
R
749
C
DNM3A_HUMAN
Disease (TBRS)
---
A/D/E/H
R
745
C
06
UniProt
VAR_067236
R
882
C
DNM3A_HUMAN
Unclassified
---
A/D/E/H
R
878
C
07
UniProt
VAR_067237
R
882
H
DNM3A_HUMAN
Unclassified
---
A/D/E/H
R
878
H
08
UniProt
VAR_067238
R
882
P
DNM3A_HUMAN
Unclassified
---
A/D/E/H
R
878
P
09
UniProt
VAR_071471
F
902
S
DNM3A_HUMAN
Disease (TBRS)
---
A/D/E/H
F
898
S
10
UniProt
VAR_071472
P
904
L
DNM3A_HUMAN
Disease (TBRS)
---
A/D/E/H
P
900
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: SAM_MT_C5 (A:630-908,D:630-908,E:630-908,H:63...)
2: C5_MTASE_1 (A:698-710,D:698-710,E:698-710,H:69...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SAM_MT_C5
PS51679
C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
DNM3A_HUMAN
634-912
4
A:630-908
D:630-908
E:630-908
H:630-908
2
C5_MTASE_1
PS00094
C-5 cytosine-specific DNA methylases active site.
DNM3A_HUMAN
702-714
4
A:698-710
D:698-710
E:698-710
H:698-710
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.20a (A:623-642 | D:626-642 | E:623-642 ...)
Exon 1.21c (A:642-690 | D:642-690 | E:642-690 ...)
Exon 1.22 (A:691-721 | D:691-721 | E:691-721 ...)
Exon 1.23 (A:721-770 | D:721-770 | E:721-770 ...)
Exon 1.25b (A:771-799 | D:771-799 | E:771-799 ...)
Exon 1.26b (A:799-822 | D:799-822 | E:799-822 ...)
Exon 1.27b (A:823-862 (gaps) | D:823-862 (gaps...)
Exon 1.28c (A:862-908 | D:862-908 | E:862-908 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.19b/1.20a
2: Boundary 1.20a/1.21c
3: Boundary 1.21c/1.22
4: Boundary 1.22/1.23
5: Boundary 1.23/1.25b
6: Boundary 1.25b/1.26b
7: Boundary 1.26b/1.27b
8: Boundary 1.27b/1.28c
9: Boundary 1.28c/-
View:
Label:
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
1.2
ENST00000321117
2
ENSE00001522911
chr2:
25564754-25564695
60
DNM3A_HUMAN
-
0
0
-
-
1.3
ENST00000321117
3
ENSE00001408175
chr2:
25537030-25536782
249
DNM3A_HUMAN
1-24
24
0
-
-
1.4
ENST00000321117
4
ENSE00000808934
chr2:
25523112-25523008
105
DNM3A_HUMAN
25-59
35
0
-
-
1.5a
ENST00000321117
5a
ENSE00001326003
chr2:
25505580-25505310
271
DNM3A_HUMAN
60-150
91
0
-
-
1.6
ENST00000321117
6
ENSE00001486208
chr2:
25498412-25498369
44
DNM3A_HUMAN
150-164
15
0
-
-
1.7
ENST00000321117
7
ENSE00000808931
chr2:
25497956-25497810
147
DNM3A_HUMAN
165-213
49
0
-
-
1.11
ENST00000321117
11
ENSE00001739049
chr2:
25471121-25470906
216
DNM3A_HUMAN
214-285
72
0
-
-
1.12b
ENST00000321117
12b
ENSE00001281470
chr2:
25470618-25470460
159
DNM3A_HUMAN
286-338
53
0
-
-
1.13b
ENST00000321117
13b
ENSE00001071033
chr2:
25470027-25469920
108
DNM3A_HUMAN
339-374
36
0
-
-
1.14c
ENST00000321117
14c
ENSE00001281455
chr2:
25469645-25469489
157
DNM3A_HUMAN
375-427
53
0
-
-
1.15a
ENST00000321117
15a
ENSE00001071035
chr2:
25469178-25469029
150
DNM3A_HUMAN
427-477
51
0
-
-
1.16
ENST00000321117
16
ENSE00001281442
chr2:
25468933-25468889
45
DNM3A_HUMAN
477-492
16
0
-
-
1.17b
ENST00000321117
17b
ENSE00001071029
chr2:
25468201-25468122
80
DNM3A_HUMAN
492-518
27
0
-
-
1.18
ENST00000321117
18
ENSE00001071031
chr2:
25467521-25467409
113
DNM3A_HUMAN
519-556
38
0
-
-
1.19b
ENST00000321117
19b
ENSE00001281418
chr2:
25467207-25467024
184
DNM3A_HUMAN
556-617
62
0
-
-
1.20a
ENST00000321117
20a
ENSE00001281558
chr2:
25466851-25466767
85
DNM3A_HUMAN
618-646
29
4
A:623-642
D:626-642
E:623-642
H:626-642
20
17
20
17
1.21c
ENST00000321117
21c
ENSE00001071020
chr2:
25464576-25464431
146
DNM3A_HUMAN
646-694
49
4
A:642-690
D:642-690
E:642-690
H:642-690
49
49
49
49
1.22
ENST00000321117
22
ENSE00001071021
chr2:
25463599-25463509
91
DNM3A_HUMAN
695-725
31
4
A:691-721
D:691-721
E:691-721
H:691-721
31
31
31
31
1.23
ENST00000321117
23
ENSE00001726066
chr2:
25463319-25463171
149
DNM3A_HUMAN
725-774
50
4
A:721-770
D:721-770
E:721-770
H:721-770
50
50
50
50
1.25b
ENST00000321117
25b
ENSE00001622127
chr2:
25462084-25461999
86
DNM3A_HUMAN
775-803
29
4
A:771-799
D:771-799
E:771-799
H:771-799
29
29
29
29
1.26b
ENST00000321117
26b
ENSE00001679782
chr2:
25459874-25459805
70
DNM3A_HUMAN
803-826
24
4
A:799-822
D:799-822
E:799-822
H:799-822
24
24
24
24
1.27b
ENST00000321117
27b
ENSE00001765738
chr2:
25458694-25458576
119
DNM3A_HUMAN
827-866
40
4
A:823-862 (gaps)
D:823-862 (gaps)
E:823-862 (gaps)
H:823-862 (gaps)
40
40
40
40
1.28c
ENST00000321117
28c
ENSE00001761921
chr2:
25457289-25455845
1445
DNM3A_HUMAN
866-912
47
4
A:862-908
D:862-908
E:862-908
H:862-908
47
47
47
47
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DNA_methylase_2qrvH01 (H:630-772)
1b: PFAM_DNA_methylase_2qrvH02 (H:630-772)
1c: PFAM_DNA_methylase_2qrvH03 (H:630-772)
1d: PFAM_DNA_methylase_2qrvH04 (H:630-772)
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Clan
:
NADP_Rossmann
(1239)
Family
:
DNA_methylase
(15)
Homo sapiens (Human)
(2)
1a
DNA_methylase-2qrvH01
H:630-772
1b
DNA_methylase-2qrvH02
H:630-772
1c
DNA_methylase-2qrvH03
H:630-772
1d
DNA_methylase-2qrvH04
H:630-772
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