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2QTV
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (155 KB)
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(1)
Title
:
STRUCTURE OF SEC23-SAR1 COMPLEXED WITH THE ACTIVE FRAGMENT OF SEC31
Authors
:
J. Goldberg, X. Bi, J. D. Mancias
Date
:
02 Aug 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,D
Biol. Unit 1: A,B,D (1x)
Keywords
:
Copii Coat, Vesicular Transport, Cytoplasm, Cytoplasmic Vesicle, Endoplasmic Reticulum, Er-Golgi Transport, Golgi Apparatus, Membrane, Metal-Binding, Protein Transport, Ubl Conjugation, Zinc, Gtp-Binding, Hydrolase, Nucleotide- Binding, Phosphorylation, Wd Repeat
(Keyword Search:
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Reference
:
X. Bi, J. D. Mancias, J. Goldberg
Insights Into Copii Coat Nucleation From The Structure Of Sec23. Sar1 Complexed With The Active Fragment Of Sec31.
Dev. Cell V. 13 635 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
2a: MAGNESIUM ION (MGa)
3a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
1
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
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (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
THR B:37 , THR B:54 , GNP B:200 , HOH B:213 , HOH B:219
BINDING SITE FOR RESIDUE MG B 210
3
AC3
SOFTWARE
ARG A:722 , 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:213 , HOH B:219 , HOH B:222 , HOH B:227 , HOH B:238
BINDING SITE FOR RESIDUE GNP B 200
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(3, 3)
Info
All Exons
Exon 1.1 (D:907-942)
Exon 2.2 (B:23-189 (gaps))
Exon 3.1 (A:2-768 (gaps))
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary 2.1/2.2
4: Boundary 2.2/-
5: Boundary -/3.1
6: Boundary 3.1/-
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
YDL195W
1
YDL195W.1
IV:107209-111030
3822
SEC31_YEAST
1-1273
1273
1
D:907-942
36
2.1
YPL218W
1
YPL218W.1
XVI:138697-138724
28
SAR1_YEAST
1-10
10
0
-
-
2.2
YPL218W
2
YPL218W.2
XVI:138864-139408
545
SAR1_YEAST
10-190
181
1
B:23-189 (gaps)
167
3.1
YPR181C
1
YPR181C.1
XVI:899663-897357
2307
SEC23_YEAST
1-768
768
1
A:2-768 (gaps)
767
[
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SCOP Domains
(6, 6)
Info
All SCOP Domains
1a: SCOP_d2qtva1 (A:524-626)
2a: SCOP_d2qtva2 (A:2-44,A:391-523)
3a: SCOP_d2qtva4 (A:627-768)
4a: SCOP_d2qtvb_ (B:)
5a: SCOP_d2qtva3 (A:120-390)
6a: SCOP_d2qtva5 (A: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
d2qtva1
A: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
d2qtva2
A:2-44,A: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
d2qtva4
A:627-768
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
d2qtvb_
B:
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
d2qtva3
A: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
d2qtva5
A:45-119
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2qtvA03 (A:120-397)
2a: CATH_2qtvB00 (B:23-189)
3a: CATH_2qtvA05 (A:626-730)
4a: CATH_2qtvA01 (A:2-49,A:109-119,A:398-512)
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Topologies
(
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(
)
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
2qtvA03
A:120-397
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Baker's yeast (Saccharomyces cerevisiae)
(61)
2a
2qtvB00
B:23-189
Topology
:
Severin
(74)
Homologous Superfamily
:
Severin
(74)
Baker's yeast (Saccharomyces cerevisiae)
(9)
3a
2qtvA05
A: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
2qtvA01
A:2-49,A:109-119,A:398-512
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Pfam Domains
(7, 7)
Info
all PFAM domains
1a: PFAM_Gelsolin_2qtvA01 (A:635-724)
2a: PFAM_Arf_2qtvB01 (B:23-189)
3a: PFAM_Sec23_BS_2qtvA02 (A:399-512)
4a: PFAM_Sec23_helical_2qtvA03 (A:525-625)
5a: PFAM_Sec31_2qtvD01 (D:907-942)
6a: PFAM_zf_Sec23_Sec24_2qtvA04 (A:52-93)
7a: PFAM_Sec23_trunk_2qtvA05 (A: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-2qtvA01
A:635-724
Clan
:
P-loop_NTPase
(1112)
Family
:
Arf
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
2a
Arf-2qtvB01
B:23-189
Clan
:
no clan defined [family: Sec23_BS]
(6)
Family
:
Sec23_BS
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
3a
Sec23_BS-2qtvA02
A: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-2qtvA03
A:525-625
Clan
:
no clan defined [family: Sec31]
(1)
Family
:
Sec31
(1)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
5a
Sec31-2qtvD01
D:907-942
Clan
:
no clan defined [family: zf-Sec23_Sec24]
(8)
Family
:
zf-Sec23_Sec24
(8)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
6a
zf-Sec23_Sec24-2qtvA04
A:52-93
Clan
:
vWA-like
(60)
Family
:
Sec23_trunk
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
7a
Sec23_trunk-2qtvA05
A:119-388
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