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1M2O
Biol. Unit 1
Info
Asym.Unit (292 KB)
Biol.Unit 1 (285 KB)
Biol.Unit 2 (144 KB)
Biol.Unit 3 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SEC23-SAR1 COMPLEX
Authors
:
X. Bi, R. A. Corpina, J. Goldberg
Date
:
24 Jun 02 (Deposition) - 20 Sep 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Zinc-Finger, Beta Barrel, Vwa Domain, Gelsolin Domain, , Protein Transport-Signaling Protein Complex
(Keyword Search:
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Reference
:
X. Bi, R. A. Corpina, J. Goldberg
Structure Of The Sec23/24-Sar1 Pre-Budding Complex Of The Copii Vesicle Coat
Nature V. 419 271 2002
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:56 , CYS A:61 , CYS A:80 , CYS A:83
BINDING SITE FOR RESIDUE ZN A 800
2
AC2
SOFTWARE
CYS C:56 , CYS C:61 , CYS C:80 , CYS C:83
BINDING SITE FOR RESIDUE ZN C 800
3
AC3
SOFTWARE
THR B:37 , THR B:54 , GNP B:5200 , HOH B:5203 , HOH B:5211
BINDING SITE FOR RESIDUE MG B 210
4
AC4
SOFTWARE
THR D:37 , THR D:54 , GNP D:7200
BINDING SITE FOR RESIDUE MG D 210
5
AC5
SOFTWARE
ARG A:722 , LEU A:746 , LEU B:31 , ASP B:32 , ASN B:33 , ALA B:34 , GLY B:35 , LYS B:36 , THR B:37 , THR B:38 , PRO B:53 , THR B:54 , GLY B:76 , ASN B:132 , LYS B:133 , ASP B:135 , SER B:172 , VAL B:173 , VAL B:174 , MG B:210 , HOH B:5203 , HOH B:5211 , HOH B:5213 , HOH B:5217 , HOH B:5221
BINDING SITE FOR RESIDUE GNP B 5200
6
AC6
SOFTWARE
ARG C:722 , LEU C:746 , LEU D:31 , ASP D:32 , ASN D:33 , ALA D:34 , GLY D:35 , LYS D:36 , THR D:37 , THR D:38 , THR D:50 , PRO D:53 , THR D:54 , GLY D:76 , ASN D:132 , LYS D:133 , ASP D:135 , SER D:172 , VAL D:173 , VAL D:174 , MG D:210
BINDING SITE FOR RESIDUE GNP D 7200
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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Sorry, no Info available
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Exons
(0, 0)
Info
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1m2oa1 (A:524-626)
1b: SCOP_d1m2oc1 (C:524-626)
2a: SCOP_d1m2oa2 (A:2-44,A:391-523)
2b: SCOP_d1m2oc2 (C:2-44,C:391-523)
3a: SCOP_d1m2oa4 (A:627-765)
3b: SCOP_d1m2oc4 (C:627-765)
4a: SCOP_d1m2ob_ (B:)
4b: SCOP_d1m2od_ (D:)
5a: SCOP_d1m2oa3 (A:120-390)
5b: SCOP_d1m2oc3 (C:120-390)
6a: SCOP_d1m2oa5 (A:45-119)
6b: SCOP_d1m2oc5 (C:45-119)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
ERP29 C domain-like
(13)
Superfamily
:
Helical domain of Sec23/24
(7)
Family
:
Helical domain of Sec23/24
(7)
Protein domain
:
Sec23
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
1a
d1m2oa1
A:524-626
1b
d1m2oc1
C:524-626
Class
:
All beta proteins
(24004)
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
beta-sandwich domain of Sec23/24
(7)
Family
:
beta-sandwich domain of Sec23/24
(7)
Protein domain
:
Sec23
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
2a
d1m2oa2
A:2-44,A:391-523
2b
d1m2oc2
C:2-44,C:391-523
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Gelsolin-like
(96)
Superfamily
:
C-terminal, gelsolin-like domain of Sec23/24
(7)
Family
:
C-terminal, gelsolin-like domain of Sec23/24
(7)
Protein domain
:
Sec23
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
3a
d1m2oa4
A:627-765
3b
d1m2oc4
C:627-765
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
SAR1
(4)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
4a
d1m2ob_
B:
4b
d1m2od_
D:
Fold
:
vWA-like
(111)
Superfamily
:
vWA-like
(111)
Family
:
Trunk domain of Sec23/24
(7)
Protein domain
:
Sec23
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
5a
d1m2oa3
A:120-390
5b
d1m2oc3
C:120-390
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Zn-finger domain of Sec23/24
(7)
Family
:
Zn-finger domain of Sec23/24
(7)
Protein domain
:
Sec23
(3)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
6a
d1m2oa5
A:45-119
6b
d1m2oc5
C:45-119
[
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1m2oA03 (A:120-397)
1b: CATH_1m2oC03 (C:120-397)
2a: CATH_1m2oB00 (B:24-190)
2b: CATH_1m2oD00 (D:24-188)
3a: CATH_1m2oA05 (A:626-730)
3b: CATH_1m2oC05 (C:626-730)
4a: CATH_1m2oA01 (A:2-49,A:109-119,A:398-512)
4b: CATH_1m2oC01 (C:2-49,C:109-119,C:398-512)
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)
(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.410, no name defined]
(87)
Baker's yeast (Saccharomyces cerevisiae)
(6)
1a
1m2oA03
A:120-397
1b
1m2oC03
C:120-397
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Baker's yeast (Saccharomyces cerevisiae)
(61)
2a
1m2oB00
B:24-190
2b
1m2oD00
D:24-188
Topology
:
Severin
(74)
Homologous Superfamily
:
Severin
(74)
Baker's yeast (Saccharomyces cerevisiae)
(9)
3a
1m2oA05
A:626-730
3b
1m2oC05
C:626-730
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
beta-sandwich domain of Sec23/24
(9)
Baker's yeast (Saccharomyces cerevisiae)
(3)
4a
1m2oA01
A:2-49,A:109-119,A:398-512
4b
1m2oC01
C:2-49,C:109-119,C:398-512
[
close CATH info
]
Pfam Domains
(6, 12)
Info
all PFAM domains
1a: PFAM_Gelsolin_1m2oC01 (C:635-724)
1b: PFAM_Gelsolin_1m2oC02 (C:635-724)
2a: PFAM_Arf_1m2oD01 (D:24-188)
2b: PFAM_Arf_1m2oD02 (D:24-188)
3a: PFAM_Sec23_BS_1m2oC03 (C:399-512)
3b: PFAM_Sec23_BS_1m2oC04 (C:399-512)
4a: PFAM_Sec23_helical_1m2oC05 (C:525-625)
4b: PFAM_Sec23_helical_1m2oC06 (C:525-625)
5a: PFAM_zf_Sec23_Sec24_1m2oC07 (C:52-93)
5b: PFAM_zf_Sec23_Sec24_1m2oC08 (C:52-93)
6a: PFAM_Sec23_trunk_1m2oC09 (C:119-388)
6b: PFAM_Sec23_trunk_1m2oC10 (C:119-388)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ADF
(44)
Family
:
Gelsolin
(23)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
1a
Gelsolin-1m2oC01
C:635-724
1b
Gelsolin-1m2oC02
C:635-724
Clan
:
P-loop_NTPase
(1112)
Family
:
Arf
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
2a
Arf-1m2oD01
D:24-188
2b
Arf-1m2oD02
D:24-188
Clan
:
no clan defined [family: Sec23_BS]
(6)
Family
:
Sec23_BS
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
3a
Sec23_BS-1m2oC03
C:399-512
3b
Sec23_BS-1m2oC04
C:399-512
Clan
:
no clan defined [family: Sec23_helical]
(6)
Family
:
Sec23_helical
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
4a
Sec23_helical-1m2oC05
C:525-625
4b
Sec23_helical-1m2oC06
C:525-625
Clan
:
no clan defined [family: zf-Sec23_Sec24]
(8)
Family
:
zf-Sec23_Sec24
(8)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
5a
zf-Sec23_Sec24-1m2oC07
C:52-93
5b
zf-Sec23_Sec24-1m2oC08
C:52-93
Clan
:
vWA-like
(60)
Family
:
Sec23_trunk
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
6a
Sec23_trunk-1m2oC09
C:119-388
6b
Sec23_trunk-1m2oC10
C:119-388
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