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2YOA
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (56 KB)
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(1)
Title
:
SYNAPTOTAGMIN-1 C2B DOMAIN WITH PHOSPHOSERINE
Authors
:
A. Honigmann, G. Van Den Bogaart, E. Iraheta, H. J. Risselada, D. Milo V. Mueller, S. Muellar, U. Diederichsen, D. Fasshauer, H. Grubmuller S. W. Hell, C. Eggeling, K. Kuhnel, R. Jahn
Date
:
22 Oct 12 (Deposition) - 20 Mar 13 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Honigmann, G. Van Den Bogaart, E. Iraheta, H. J. Risselada, D. Milovanovic, V. Mueller, S. Muellar, U. Diederichsen, D. Fasshauer, H. Grubmuller, S. W. Hell, C. Eggeling, K. Kuhnel, R. Jah
Phosphatidylinositol 4, 5-Bisphosphate Clusters Act As Molecular Beacons For Vesicle Recruitment
Nat. Struct. Mol. Biol. V. 20 679 2013
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
2a: THIOCYANATE ION (SCNa)
2b: THIOCYANATE ION (SCNb)
2c: THIOCYANATE ION (SCNc)
2d: THIOCYANATE ION (SCNd)
2e: THIOCYANATE ION (SCNe)
3a: PHOSPHOSERINE (SEPa)
3b: PHOSPHOSERINE (SEPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
7
Ligand/Ion
CALCIUM ION
2
SCN
5
Ligand/Ion
THIOCYANATE ION
3
SEP
2
Mod. Residue
PHOSPHOSERINE
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:303 , ASP A:309 , ASP A:363 , TYR A:364 , ASP A:365 , SEP A:1004
BINDING SITE FOR RESIDUE CA A1001
02
AC2
SOFTWARE
MET A:302 , ASP A:303 , ASP A:363 , ASP A:365 , ASP A:371 , HOH A:2023
BINDING SITE FOR RESIDUE CA A1002
03
AC3
SOFTWARE
ASP A:365 , LYS A:369 , ASP A:371 , HOH A:2070 , HOH A:2071 , HOH A:2076
BINDING SITE FOR RESIDUE CA A1003
04
AC4
SOFTWARE
ASP A:303 , ASP A:309 , TYR A:364 , ASP A:365 , LYS A:366 , CA A:1001 , HOH A:2025 , HOH A:2072 , HOH A:2130 , ASN B:319 , HOH B:2038 , HOH B:2068
BINDING SITE FOR RESIDUE SEP A1004
05
AC5
SOFTWARE
ASP A:309 , TYR A:364 , HOH A:2027
BINDING SITE FOR RESIDUE CA A1005
06
AC6
SOFTWARE
LYS A:272 , TYR A:311 , LYS A:327 , HOH A:2131
BINDING SITE FOR RESIDUE SCN A1006
07
AC7
SOFTWARE
THR A:334 , ASN A:336 , TYR A:338 , ARG A:398
BINDING SITE FOR RESIDUE SCN A1007
08
AC8
SOFTWARE
ASP B:303 , ASP B:309 , ASP B:363 , TYR B:364 , ASP B:365 , SEP B:1004
BINDING SITE FOR RESIDUE CA B1001
09
AC9
SOFTWARE
MET B:302 , ASP B:303 , ASP B:363 , ASP B:365 , ASP B:371 , HOH B:2027
BINDING SITE FOR RESIDUE CA B1002
10
BC1
SOFTWARE
ASP B:365 , LYS B:369 , ASP B:371 , HOH B:2075 , HOH B:2076 , HOH B:2082
BINDING SITE FOR RESIDUE CA B1003
11
BC2
SOFTWARE
ASN A:319 , LYS A:321 , ASP B:303 , ASP B:309 , TYR B:364 , ASP B:365 , LYS B:366 , CA B:1001 , HOH B:2029 , HOH B:2047 , HOH B:2077 , HOH B:2123 , HOH B:2124
BINDING SITE FOR RESIDUE SEP B1004
12
BC3
SOFTWARE
PRO A:284 , VAL B:283 , PRO B:397 , ARG B:398 , HOH B:2017
BINDING SITE FOR RESIDUE SCN B1007
13
BC4
SOFTWARE
THR B:334 , ASN B:336 , TYR B:338 , ARG B:398 , HOH B:2048
BINDING SITE FOR RESIDUE SCN B1008
14
BC5
SOFTWARE
LYS B:272 , TYR B:311 , LYS B:327
BINDING SITE FOR RESIDUE SCN B1009
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: C2 (-|A:286-377,B:286-377)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C2
PS50004
C2 domain profile.
SYT1_RAT
156-244
286-377
2
-
A:286-377
B:286-377
[
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Exons
(3, 6)
Info
All Exons
Exon 1.9 (A:270-309 | B:271-309)
Exon 1.10 (A:309-353 | B:309-353)
Exon 1.11 (A:354-418 | B:354-419)
View:
Select:
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All Exon Boundaries
1: Boundary 1.8/1.9
2: Boundary 1.9/1.10
3: Boundary 1.10/1.11
4: Boundary 1.11/-
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
1.1
ENSRNOT00000048880
1
ENSRNOE00000351650
chr7:
47795496-47795335
162
SYT1_RAT
-
0
0
-
-
1.2
ENSRNOT00000048880
2
ENSRNOE00000347204
chr7:
47676650-47676550
101
SYT1_RAT
-
0
0
-
-
1.3
ENSRNOT00000048880
3
ENSRNOE00000362852
chr7:
47593840-47593779
62
SYT1_RAT
-
0
0
-
-
1.4
ENSRNOT00000048880
4
ENSRNOE00000059145
chr7:
47436218-47436039
180
SYT1_RAT
1-55
55
0
-
-
1.5
ENSRNOT00000048880
5
ENSRNOE00000059311
chr7:
47390137-47389953
185
SYT1_RAT
55-116
62
0
-
-
1.6
ENSRNOT00000048880
6
ENSRNOE00000059473
chr7:
47384355-47384233
123
SYT1_RAT
117-157
41
0
-
-
1.7
ENSRNOT00000048880
7
ENSRNOE00000059587
chr7:
47379588-47379421
168
SYT1_RAT
158-213
56
0
-
-
1.8
ENSRNOT00000048880
8
ENSRNOE00000364413
chr7:
47376456-47376289
168
SYT1_RAT
214-269
56
0
-
-
1.9
ENSRNOT00000048880
9
ENSRNOE00000306315
chr7:
47330574-47330457
118
SYT1_RAT
270-309
40
2
A:270-309
B:271-309
40
39
1.10
ENSRNOT00000048880
10
ENSRNOE00000059906
chr7:
47247255-47247122
134
SYT1_RAT
309-353
45
2
A:309-353
B:309-353
45
45
1.11
ENSRNOT00000048880
11
ENSRNOE00000317890
chr7:
47243869-47243375
495
SYT1_RAT
354-421
68
2
A:354-418
B:354-419
65
66
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2yoaa_ (A:)
1b: SCOP_d2yoab_ (B:)
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Classes
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(
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
C2 domain-like
(198)
Superfamily
:
C2 domain (Calcium/lipid-binding domain, CaLB)
(148)
Family
:
Synaptotagmin-like (S variant)
(38)
Protein domain
:
automated matches
(6)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(4)
1a
d2yoaa_
A:
1b
d2yoab_
B:
[
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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
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Protein & NOT Site
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (114 KB)
Header - Asym.Unit
Biol.Unit 1 (56 KB)
Header - Biol.Unit 1
Biol.Unit 2 (56 KB)
Header - Biol.Unit 2
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