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Asym. Unit
Info
Asym.Unit (242 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 10 (33 KB)
Biol.Unit 11 (33 KB)
Biol.Unit 12 (33 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (33 KB)
Biol.Unit 6 (33 KB)
Biol.Unit 7 (33 KB)
Biol.Unit 8 (33 KB)
Biol.Unit 9 (34 KB)
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(1)
Title
:
STRUCTURE OF THE HEPARIN-INDUCED E1-DIMER OF THE AMYLOID PRECURSOR PROTEIN (APP)
Authors
:
S. O. Dahms, S. Hoefgen, D. Roeser, B. Schlott, K. H. Guhrs, M. E. Than
Date
:
25 Nov 09 (Deposition) - 23 Feb 10 (Release) - 05 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: F,H (1x)
Biol. Unit 4: E,G (1x)
Biol. Unit 5: A (1x)
Biol. Unit 6: B (1x)
Biol. Unit 7: C (1x)
Biol. Unit 8: D (1x)
Biol. Unit 9: E (1x)
Biol. Unit 10: F (1x)
Biol. Unit 11: G (1x)
Biol. Unit 12: H (1x)
Keywords
:
Protein Structure, Alzheimer Disease, Amyloid, Amyloidosis, Apoptosis, Cell Adhesion, Copper, Disease Mutation, Disulfide Bond, Endocytosis, Heparin-Binding, Metal-Binding, Neurodegeneration, Notch Signaling Pathway, Proteoglycan, Zinc, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. O. Dahms, S. Hoefgen, D. Roeser, B. Schlott, K. H. Guhrs, M. E. Than
Structure And Biochemical Analysis Of The Heparin-Induced E1 Dimer Of The Amyloid Precursor Protein.
Proc. Natl. Acad. Sci. Usa V. 107 5381 2010
[
close entry info
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: (3R)-BUTANE-1,3-DIOL (BU4a)
2b: (3R)-BUTANE-1,3-DIOL (BU4b)
2c: (3R)-BUTANE-1,3-DIOL (BU4c)
2d: (3R)-BUTANE-1,3-DIOL (BU4d)
2e: (3R)-BUTANE-1,3-DIOL (BU4e)
2f: (3R)-BUTANE-1,3-DIOL (BU4f)
2g: (3R)-BUTANE-1,3-DIOL (BU4g)
2h: (3R)-BUTANE-1,3-DIOL (BU4h)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
BU4
8
Ligand/Ion
(3R)-BUTANE-1,3-DIOL
3
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:83 , ASN A:84 , PRO A:173 , CYS A:174 , GLY A:175 , ILE A:176
BINDING SITE FOR RESIDUE BU4 A 1
02
AC2
SOFTWARE
PRO B:188 , LEU B:189 , ALA B:190 , ARG G:194
BINDING SITE FOR RESIDUE BU4 B 7
03
AC3
SOFTWARE
ALA B:88 , ASN B:89 , ARG B:116 , HOH B:209 , HOH B:221 , HOH B:226 , ARG H:194
BINDING SITE FOR RESIDUE SO4 B 2
04
AC4
SOFTWARE
GLN B:90 , HIS B:151 , LYS B:155 , ACT H:6
BINDING SITE FOR RESIDUE ACT B 208
05
AC5
SOFTWARE
ARG A:194 , LEU C:189 , ALA C:190
BINDING SITE FOR RESIDUE BU4 C 5
06
AC6
SOFTWARE
ASN C:89 , ARG C:116 , HOH C:210 , HOH C:216 , ARG E:194
BINDING SITE FOR RESIDUE SO4 C 3
07
AC7
SOFTWARE
GLN C:90 , HIS C:151 , ACT E:9 , LYS E:155
BINDING SITE FOR RESIDUE ACT C 8
08
AC8
SOFTWARE
THR D:83 , ASN D:84 , PRO D:173 , CYS D:174 , GLY D:175
BINDING SITE FOR RESIDUE BU4 D 2
09
AC9
SOFTWARE
ARG A:180 , ARG D:140 , HOH F:5
BINDING SITE FOR RESIDUE SO4 D 5
10
BC1
SOFTWARE
LEU E:189 , ALA E:190 , ARG F:194
BINDING SITE FOR RESIDUE BU4 E 6
11
BC2
SOFTWARE
ARG C:194 , ALA E:88 , ASN E:89 , ARG E:116 , HOH E:210 , HOH E:231
BINDING SITE FOR RESIDUE SO4 E 4
12
BC3
SOFTWARE
ACT C:8 , GLN E:90 , HIS E:151 , LYS E:155
BINDING SITE FOR RESIDUE ACT E 9
13
BC4
SOFTWARE
GLY F:175 , ILE F:176
BINDING SITE FOR RESIDUE BU4 F 4
14
BC5
SOFTWARE
PRO G:173 , CYS G:174 , GLY G:175 , ILE G:176
BINDING SITE FOR RESIDUE BU4 G 3
15
BC6
SOFTWARE
ARG D:194 , LEU H:189 , ALA H:190
BINDING SITE FOR RESIDUE BU4 H 8
16
BC7
SOFTWARE
ARG B:194 , ALA H:88 , ASN H:89 , ARG H:116 , HOH H:227 , HOH H:228 , HOH H:230 , HOH H:246
BINDING SITE FOR RESIDUE SO4 H 1
17
BC8
SOFTWARE
ACT B:208 , GLN H:90 , HIS H:151 , LYS H:155
BINDING SITE FOR RESIDUE ACT H 6
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: A4_EXTRA (A:181-188,B:181-188,C:181-188,D:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
A4_EXTRA
PS00319
Amyloidogenic glycoprotein extracellular domain signature.
A4_HUMAN
181-188
8
A:181-188
B:181-188
C:181-188
D:181-188
E:181-188
F:181-188
G:181-188
H:181-188
[
close PROSITE info
]
Exons
(4, 32)
Info
All Exons
Exon 1.5b (A:28-75 | B:26-75 | C:26-75 | D:28...)
Exon 1.6b (A:76-119 | B:76-119 | C:76-119 | D...)
Exon 1.7b (A:119-156 | B:119-156 | C:119-156 ...)
Exon 1.8a (A:157-202 | B:157-198 | C:157-199 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2f/1.5b
2: Boundary 1.5b/1.6b
3: Boundary 1.6b/1.7b
4: Boundary 1.7b/1.8a
5: Boundary 1.8a/1.9b
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
1.2f
ENST00000346798
2f
ENSE00001909719
chr21:
27542972-27542882
91
A4_HUMAN
1-19
19
0
-
-
1.5b
ENST00000346798
5b
ENSE00001612324
chr21:
27484463-27484296
168
A4_HUMAN
20-75
56
8
A:28-75
B:26-75
C:26-75
D:28-75
E:26-75
F:28-75
G:28-75
H:26-75
48
50
50
48
50
48
48
50
1.6b
ENST00000346798
6b
ENSE00001017345
chr21:
27462388-27462259
130
A4_HUMAN
76-119
44
8
A:76-119
B:76-119
C:76-119
D:76-119
E:76-119
F:76-119
G:76-119
H:76-119
44
44
44
44
44
44
44
44
1.7b
ENST00000346798
7b
ENSE00001726854
chr21:
27425664-27425552
113
A4_HUMAN
119-156
38
8
A:119-156
B:119-156
C:119-156
D:119-156
E:119-156
F:119-156
G:119-156
H:119-156
38
38
38
38
38
38
38
38
1.8a
ENST00000346798
8a
ENSE00001017348
chr21:
27423509-27423316
194
A4_HUMAN
157-221
65
8
A:157-202
B:157-198
C:157-199
D:157-200
E:157-202
F:157-202
G:157-201
H:157-200
46
42
43
44
46
46
45
44
1.9b
ENST00000346798
9b
ENSE00001303241
chr21:
27394358-27394156
203
A4_HUMAN
221-289
69
0
-
-
1.11
ENST00000346798
11
ENSE00001327560
chr21:
27372497-27372330
168
A4_HUMAN
289-345
57
0
-
-
1.12a
ENST00000346798
12a
ENSE00001309322
chr21:
27369731-27369675
57
A4_HUMAN
345-364
20
0
-
-
1.13
ENST00000346798
13
ENSE00001017338
chr21:
27354790-27354657
134
A4_HUMAN
364-408
45
0
-
-
1.14a
ENST00000346798
14a
ENSE00001608815
chr21:
27348341-27348267
75
A4_HUMAN
409-433
25
0
-
-
1.15b
ENST00000346798
15b
ENSE00001017350
chr21:
27347541-27347383
159
A4_HUMAN
434-486
53
0
-
-
1.16
ENST00000346798
16
ENSE00001299537
chr21:
27328069-27327941
129
A4_HUMAN
487-529
43
0
-
-
1.17
ENST00000346798
17
ENSE00001299406
chr21:
27327003-27326904
100
A4_HUMAN
530-563
34
0
-
-
1.19
ENST00000346798
19
ENSE00001299617
chr21:
27284274-27284053
222
A4_HUMAN
563-637
75
0
-
-
1.20
ENST00000346798
20
ENSE00001324614
chr21:
27277389-27277336
54
A4_HUMAN
637-655
19
0
-
-
1.21b
ENST00000346798
21b
ENSE00001318724
chr21:
27269985-27269885
101
A4_HUMAN
655-688
34
0
-
-
1.22a
ENST00000346798
22a
ENSE00001290140
chr21:
27264180-27264034
147
A4_HUMAN
689-737
49
0
-
-
1.23f
ENST00000346798
23f
ENSE00001725664
chr21:
27254082-27252861
1222
A4_HUMAN
738-770
33
0
-
-
[
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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
(2, 16)
Info
all PFAM domains
1a: PFAM_APP_Cu_bd_3ktmH01 (H:132-189)
1b: PFAM_APP_Cu_bd_3ktmH02 (H:132-189)
1c: PFAM_APP_Cu_bd_3ktmH03 (H:132-189)
1d: PFAM_APP_Cu_bd_3ktmH04 (H:132-189)
1e: PFAM_APP_Cu_bd_3ktmH05 (H:132-189)
1f: PFAM_APP_Cu_bd_3ktmH06 (H:132-189)
1g: PFAM_APP_Cu_bd_3ktmH07 (H:132-189)
1h: PFAM_APP_Cu_bd_3ktmH08 (H:132-189)
2a: PFAM_APP_N_3ktmH09 (H:30-131)
2b: PFAM_APP_N_3ktmH10 (H:30-131)
2c: PFAM_APP_N_3ktmH11 (H:30-131)
2d: PFAM_APP_N_3ktmH12 (H:30-131)
2e: PFAM_APP_N_3ktmH13 (H:30-131)
2f: PFAM_APP_N_3ktmH14 (H:30-131)
2g: PFAM_APP_N_3ktmH15 (H:30-131)
2h: PFAM_APP_N_3ktmH16 (H:30-131)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: APP_Cu_bd]
(2)
Family
:
APP_Cu_bd
(2)
Homo sapiens (Human)
(2)
1a
APP_Cu_bd-3ktmH01
H:132-189
1b
APP_Cu_bd-3ktmH02
H:132-189
1c
APP_Cu_bd-3ktmH03
H:132-189
1d
APP_Cu_bd-3ktmH04
H:132-189
1e
APP_Cu_bd-3ktmH05
H:132-189
1f
APP_Cu_bd-3ktmH06
H:132-189
1g
APP_Cu_bd-3ktmH07
H:132-189
1h
APP_Cu_bd-3ktmH08
H:132-189
Clan
:
no clan defined [family: APP_N]
(3)
Family
:
APP_N
(3)
Homo sapiens (Human)
(3)
2a
APP_N-3ktmH09
H:30-131
2b
APP_N-3ktmH10
H:30-131
2c
APP_N-3ktmH11
H:30-131
2d
APP_N-3ktmH12
H:30-131
2e
APP_N-3ktmH13
H:30-131
2f
APP_N-3ktmH14
H:30-131
2g
APP_N-3ktmH15
H:30-131
2h
APP_N-3ktmH16
H:30-131
[
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