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1D3B
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (32 KB)
Biol.Unit 3 (33 KB)
Biol.Unit 4 (33 KB)
Biol.Unit 5 (32 KB)
Biol.Unit 6 (33 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION
Authors
:
C. Kambach, S. Walke, J. M. Avis, E. De La Fortelle, J. Li, K. Nagai
Date
:
22 Dec 98 (Deposition) - 22 Dec 99 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Snrnp, Splicing, Sm, Core Snrnp Domain, Systemic Lupus Erythematosus, Sle, Rna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Kambach, S. Walke, R. Young, J. M. Avis, E. De La Fortelle, V. A. Raker, R. Luhrmann, J. Li, K. Nagai
Crystal Structures Of Two Sm Protein Complexes And Their Implications For The Assembly Of The Spliceosomal Snrnps.
Cell(Cambridge, Mass. ) V. 96 375 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 17)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
1c: CITRIC ACID (CITc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
3
Ligand/Ion
CITRIC ACID
2
GOL
14
Ligand/Ion
GLYCEROL
[
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
ASN G:23 , THR G:24 , GLY G:25 , ARG G:51 , ARG G:69 , HOH G:713 , HOH G:714 , ARG H:25 , ARG H:49
BINDING SITE FOR RESIDUE CIT G 701
02
AC2
SOFTWARE
SER B:7 , MET B:9 , MET B:38 , LEU B:77 , VAL B:78 , SER B:79 , MET B:80 , HOH B:714 , HOH B:715 , HOH B:718 , GLN C:42 , GLN C:60
BINDING SITE FOR RESIDUE CIT B 702
03
AC3
SOFTWARE
GLU I:21 , ASN I:23 , THR I:24 , GLY I:25 , ARG I:69 , HOH I:724 , HOH I:732 , HOH I:733 , ARG J:25 , ARG J:49
BINDING SITE FOR RESIDUE CIT I 703
04
AC4
SOFTWARE
ASP H:23 , ARG H:49 , HOH H:604 , HOH H:605 , HOH H:622 , HOH H:645
BINDING SITE FOR RESIDUE GOL H 601
05
AC5
SOFTWARE
ILE I:17 , VAL I:18 , THR I:19 , ARG I:29 , ILE I:72 , LEU I:73 , PRO I:74
BINDING SITE FOR RESIDUE GOL I 602
06
AC6
SOFTWARE
ASN G:23 , ARG G:69 , HOH G:743 , LEU H:21 , GLN H:22 , ASP H:23 , ASN H:76
BINDING SITE FOR RESIDUE GOL G 603
07
AC7
SOFTWARE
THR D:2 , HIS D:12 , MET D:17 , MET D:80 , HOH D:624 , HOH D:638
BINDING SITE FOR RESIDUE GOL D 604
08
AC8
SOFTWARE
ARG L:18 , ILE L:28 , GLU L:62
BINDING SITE FOR RESIDUE GOL L 605
09
AC9
SOFTWARE
GOL B:611 , ARG C:51 , ASP C:52
BINDING SITE FOR RESIDUE GOL C 606
10
BC1
SOFTWARE
THR A:47 , THR A:49 , VAL A:55 , ARG L:16 , HOH L:611 , HOH L:653
BINDING SITE FOR RESIDUE GOL A 607
11
BC2
SOFTWARE
ASN A:23 , ARG A:69 , GLN B:22 , ASP B:23 , ASN B:76 , HOH C:614
BINDING SITE FOR RESIDUE GOL B 608
12
BC3
SOFTWARE
ARG F:18 , ILE F:26 , PHE F:48 , GLU F:62 , GOL F:613 , HOH F:658
BINDING SITE FOR RESIDUE GOL F 609
13
BC4
SOFTWARE
ASN E:23 , ARG E:69 , GLN F:22 , ASP F:23 , ASN F:76
BINDING SITE FOR RESIDUE GOL F 610
14
BC5
SOFTWARE
ASP B:23 , ARG B:25 , ARG B:49 , ILE B:51 , HOH B:727 , ASP C:52 , GOL C:606
BINDING SITE FOR RESIDUE GOL B 611
15
BC6
SOFTWARE
GLU E:21 , GLY E:25 , ARG E:69 , HOH E:613 , ARG F:25 , ARG F:49 , HOH F:624 , HOH F:654 , HOH F:664
BINDING SITE FOR RESIDUE GOL E 612
16
BC7
SOFTWARE
PHE F:48 , GLU F:62 , LYS F:64 , GOL F:609 , ARG J:61 , GLU J:63
BINDING SITE FOR RESIDUE GOL F 613
17
BC8
SOFTWARE
ILE A:17 , THR A:19 , ILE A:72 , PRO A:74
BINDING SITE FOR RESIDUE GOL A 614
[
close Site info
]
SAPs(SNPs)/Variants
(5, 30)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_073380 (N55S, chain B/D/F/H/J/L, )
2: VAR_073381 (N55T, chain B/D/F/H/J/L, )
3: VAR_073382 (S56R, chain B/D/F/H/J/L, )
4: VAR_073383 (S56W, chain B/D/F/H/J/L, )
5: VAR_052274 (S79P, chain B/D/F/H/J/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073380
N
55
S
RSMB_HUMAN
Disease (CCMS)
---
B/D/F/H/J/L
N
55
S
2
UniProt
VAR_073381
N
55
T
RSMB_HUMAN
Disease (CCMS)
---
B/D/F/H/J/L
N
55
T
3
UniProt
VAR_073382
S
56
R
RSMB_HUMAN
Disease (CCMS)
---
B/D/F/H/J/L
S
56
R
4
UniProt
VAR_073383
S
56
W
RSMB_HUMAN
Disease (CCMS)
---
B/D/F/H/J/L
S
56
W
5
UniProt
VAR_052274
S
79
P
RSMB_HUMAN
Polymorphism
11545672
B/D/F/H/J/L
S
79
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(2, 12)
Info
All Exons
Exon 1.2a (A:4-42 | C:5-42 | E:2-42 | G:3-42 ...)
Exon 1.3b (A:43-75 | C:43-75 | E:43-75 | G:43...)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.2a
2: Boundary 1.2a/1.3b
3: Boundary 1.3b/1.4c
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
1.1a
ENST00000215829
1a
ENSE00001948969
chr22:
24951471-24952039
569
SMD3_HUMAN
-
0
0
-
-
1.2a
ENST00000215829
2a
ENSE00000879568
chr22:
24953625-24953768
144
SMD3_HUMAN
1-42
42
6
A:4-42
C:5-42
E:2-42
G:3-42
I:3-42
K:5-42
39
38
41
40
40
38
1.3b
ENST00000215829
3b
ENSE00000651723
chr22:
24963952-24964144
193
SMD3_HUMAN
43-107
65
6
A:43-75
C:43-75
E:43-75
G:43-75
I:43-75
K:43-75
33
33
33
33
33
33
1.4c
ENST00000215829
4c
ENSE00001402429
chr22:
24967884-24968740
857
SMD3_HUMAN
107-126
20
0
-
-
[
close EXON info
]
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1d3bb_ (B:)
1b: SCOP_d1d3bd_ (D:)
1c: SCOP_d1d3bf_ (F:)
1d: SCOP_d1d3bh_ (H:)
1e: SCOP_d1d3bj_ (J:)
1f: SCOP_d1d3bl_ (L:)
2a: SCOP_d1d3ba_ (A:)
2b: SCOP_d1d3bc_ (C:)
2c: SCOP_d1d3be_ (E:)
2d: SCOP_d1d3bg_ (G:)
2e: SCOP_d1d3bi_ (I:)
2f: SCOP_d1d3bk_ (K:)
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)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Sm-like fold
(103)
Superfamily
:
Sm-like ribonucleoproteins
(95)
Family
:
Sm motif of small nuclear ribonucleoproteins, SNRNP
(31)
Protein domain
:
B core SNRNP protein
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1d3bb_
B:
1b
d1d3bd_
D:
1c
d1d3bf_
F:
1d
d1d3bh_
H:
1e
d1d3bj_
J:
1f
d1d3bl_
L:
Protein domain
:
D3 core SNRNP protein
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1d3ba_
A:
2b
d1d3bc_
C:
2c
d1d3be_
E:
2d
d1d3bg_
G:
2e
d1d3bi_
I:
2f
d1d3bk_
K:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1d3bC00 (C:5-75)
1b: CATH_1d3bK00 (K:5-75)
1c: CATH_1d3bJ00 (J:2-87)
1d: CATH_1d3bL00 (L:2-91)
1e: CATH_1d3bA00 (A:4-75)
1f: CATH_1d3bG00 (G:3-75)
1g: CATH_1d3bI00 (I:3-75)
1h: CATH_1d3bE00 (E:2-75)
1i: CATH_1d3bB00 (B:7-87)
1j: CATH_1d3bF00 (F:5-87)
1k: CATH_1d3bD00 (D:2-87)
1l: CATH_1d3bH00 (H:3-88)
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.100, no name defined]
(40)
Human (Homo sapiens)
(2)
1a
1d3bC00
C:5-75
1b
1d3bK00
K:5-75
1c
1d3bJ00
J:2-87
1d
1d3bL00
L:2-91
1e
1d3bA00
A:4-75
1f
1d3bG00
G:3-75
1g
1d3bI00
I:3-75
1h
1d3bE00
E:2-75
1i
1d3bB00
B:7-87
1j
1d3bF00
F:5-87
1k
1d3bD00
D:2-87
1l
1d3bH00
H:3-88
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Chain H
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Chain J
Chain K
Chain L
Asymmetric Unit 1
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