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3ZIA
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (528 KB)
Biol.Unit 2 (527 KB)
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(1)
Title
:
THE STRUCTURE OF F1-ATPASE FROM SACCHAROMYCES CEREVISIAE INHIBITED BY ITS REGULATORY PROTEIN IF1
Authors
:
G. C. Robinson, J. V. Bason, M. G. Montgomery, I. M. Fearnley, D. M. Muell A. G. W. Leslie, J. E. Walker
Date
:
07 Jan 13 (Deposition) - 13 Feb 13 (Release) - 06 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1: K,L,M,N,O,P,Q,R,S,T (1x)
Biol. Unit 2: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Hydrolase, Natural Inhibitor, Catalysis, Intermediate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. C. Robinson, J. V. Bason, M. G. Montgomery, I. M. Fearnley, D. M. Mueller, A. G. W. Leslie, J. E. Walker
The Structure Of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein If1.
Open Biol. V. 3 164 2013
[
close entry info
]
Hetero Components
(4, 28)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
1i: ADENOSINE-5'-DIPHOSPHATE (ADPi)
1j: ADENOSINE-5'-DIPHOSPHATE (ADPj)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
10
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
4
MG
10
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR K:178 , ATP K:600 , HOH K:2013 , HOH K:2014 , HOH K:2015
BINDING SITE FOR RESIDUE MG K 601
02
AC2
SOFTWARE
GLN C:174 , THR C:175 , GLY C:176 , LYS C:177 , THR C:178 , ALA C:179 , PHE C:359 , ARG C:364 , GLN C:432 , GLN C:434 , MG C:601 , HOH C:2044 , HOH C:2093 , ARG F:356
BINDING SITE FOR RESIDUE ADP C 600
03
AC3
SOFTWARE
GLN L:174 , THR L:175 , GLY L:176 , LYS L:177 , THR L:178 , ALA L:179 , PHE L:359 , ARG L:364 , GLN L:432 , GLN L:434 , MG L:601 , HOH L:2075 , HOH L:2156 , ASP O:359
BINDING SITE FOR RESIDUE ADP L 600
04
AC4
SOFTWARE
ILE L:363 , ILE L:367 , THR L:427
BINDING SITE FOR RESIDUE EDO L 604
05
AC5
SOFTWARE
GLY O:160 , VAL O:161 , GLY O:162 , LYS O:163 , THR O:164 , VAL O:165 , TYR O:345 , PHE O:418 , ALA O:421 , PHE O:424 , THR O:425 , HOH O:2052
BINDING SITE FOR RESIDUE ADP O 600
06
AC6
SOFTWARE
ARG O:231
BINDING SITE FOR RESIDUE EDO O 602
07
AC7
SOFTWARE
ARG L:375 , HOH L:2139 , GLY P:160 , VAL P:161 , GLY P:162 , LYS P:163 , THR P:164 , VAL P:165 , TYR P:345 , PHE P:418 , PHE P:424 , MG P:601 , HOH P:2030 , HOH P:2031 , HOH P:2032 , HOH P:2035
BINDING SITE FOR RESIDUE ADP P 600
08
AC8
SOFTWARE
THR P:164 , ADP P:600 , HOH P:2032 , HOH P:2033 , HOH P:2034 , HOH P:2035
BINDING SITE FOR RESIDUE MG P 601
09
AC9
SOFTWARE
LYS P:45 , VAL P:47 , MET P:64 , ASP P:65
BINDING SITE FOR RESIDUE EDO P 603
10
BC1
SOFTWARE
ARG A:173 , GLN A:174 , THR A:175 , GLY A:176 , LYS A:177 , THR A:178 , ALA A:179 , PHE A:359 , GLN A:432 , GLN A:434 , MG A:601 , HOH A:2005 , HOH A:2006 , TYR D:368
BINDING SITE FOR RESIDUE ATP A 600
11
BC2
SOFTWARE
THR A:178 , ATP A:600 , HOH A:2005 , HOH A:2006 , HOH A:2007
BINDING SITE FOR RESIDUE MG A 601
12
BC3
SOFTWARE
GLN B:174 , THR B:175 , GLY B:176 , LYS B:177 , THR B:178 , ALA B:179 , PHE B:359 , ARG B:364 , GLN B:432 , GLN B:434 , MG B:601 , HOH B:2046 , HOH B:2089 , HOH B:2090 , ASP E:359
BINDING SITE FOR RESIDUE ADP B 600
13
BC4
SOFTWARE
THR B:178 , ADP B:600 , HOH B:2045 , HOH B:2046 , HOH B:2047 , HOH B:2090
BINDING SITE FOR RESIDUE MG B 601
14
BC5
SOFTWARE
THR C:178 , ADP C:600 , HOH C:2044 , HOH C:2045 , HOH C:2046 , HOH C:2093
BINDING SITE FOR RESIDUE MG C 601
15
BC6
SOFTWARE
TYR C:246 , TYR C:280 , ASP C:299 , TYR C:302 , LEU C:303 , ARG C:306
BINDING SITE FOR RESIDUE EDO C 603
16
BC7
SOFTWARE
ARG C:375 , HOH C:2088 , HOH C:2090 , GLY D:158 , GLY D:160 , VAL D:161 , GLY D:162 , LYS D:163 , THR D:164 , VAL D:165 , TYR D:345 , ALA D:421 , PHE D:424 , MG D:601 , HOH D:2021
BINDING SITE FOR RESIDUE ADP D 600
17
BC8
SOFTWARE
HOH C:2090 , THR D:164 , ADP D:600 , HOH D:2018 , HOH D:2019 , HOH D:2021
BINDING SITE FOR RESIDUE MG D 601
18
BC9
SOFTWARE
GLY E:160 , VAL E:161 , GLY E:162 , LYS E:163 , THR E:164 , VAL E:165 , TYR E:345 , PHE E:418 , ALA E:421 , PHE E:424 , THR E:425 , HOH E:2008
BINDING SITE FOR RESIDUE ADP E 600
19
CC1
SOFTWARE
ARG B:375 , HOH B:2084 , GLY F:160 , VAL F:161 , GLY F:162 , LYS F:163 , THR F:164 , VAL F:165 , TYR F:345 , PHE F:418 , PHE F:424 , MG F:601 , HOH F:2041 , HOH F:2042 , HOH F:2044 , HOH F:2047
BINDING SITE FOR RESIDUE ADP F 600
20
CC2
SOFTWARE
THR F:164 , ADP F:600 , HOH F:2043 , HOH F:2044 , HOH F:2045 , HOH F:2047
BINDING SITE FOR RESIDUE MG F 601
21
CC3
SOFTWARE
ARG K:173 , GLN K:174 , THR K:175 , GLY K:176 , LYS K:177 , THR K:178 , ALA K:179 , PHE K:359 , GLN K:432 , GLN K:434 , MG K:601 , HOH K:2011 , HOH K:2012 , HOH K:2013 , HOH K:2015 , TYR N:368
BINDING SITE FOR RESIDUE ATP K 600
22
CC4
SOFTWARE
THR L:178 , ADP L:600 , HOH L:2075 , HOH L:2076 , HOH L:2077 , HOH L:2156
BINDING SITE FOR RESIDUE MG L 601
23
CC5
SOFTWARE
ARG L:293 , HOH L:2121 , VAL P:279 , HOH P:2053
BINDING SITE FOR RESIDUE EDO L 602
24
CC6
SOFTWARE
GLN M:174 , THR M:175 , GLY M:176 , LYS M:177 , THR M:178 , ALA M:179 , PHE M:359 , ARG M:364 , GLN M:432 , GLN M:434 , MG M:601 , HOH M:2031 , HOH M:2076 , ARG P:356
BINDING SITE FOR RESIDUE ADP M 600
25
CC7
SOFTWARE
THR M:178 , ADP M:600 , HOH M:2031 , HOH M:2032 , HOH M:2033 , HOH M:2076
BINDING SITE FOR RESIDUE MG M 601
26
CC8
SOFTWARE
TYR M:246 , TYR M:280 , ASP M:299 , TYR M:302 , LEU M:303 , ARG M:306
BINDING SITE FOR RESIDUE EDO M 602
27
CC9
SOFTWARE
ARG M:375 , HOH M:2070 , GLY N:158 , GLY N:160 , VAL N:161 , GLY N:162 , LYS N:163 , THR N:164 , VAL N:165 , TYR N:345 , ALA N:421 , PHE N:424 , MG N:601 , HOH N:2019
BINDING SITE FOR RESIDUE ADP N 600
28
DC1
SOFTWARE
HOH M:2070 , THR N:164 , ADP N:600 , HOH N:2016 , HOH N:2017 , HOH N:2019
BINDING SITE FOR RESIDUE MG N 601
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_ATPG_YEAST_001 (S174I, chain G/Q, )
2: VAR_ATPG_YEAST_002 (S275F, chain G/Q, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ATPG_YEAST_001
*
S
207
I
ATPG_YEAST
---
---
G/Q
S
174
I
2
UniProt
VAR_ATPG_YEAST_002
*
S
308
F
ATPG_YEAST
---
---
G/Q
S
275
F
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 14)
Info
All PROSITE Patterns/Profiles
1: ATPASE_GAMMA (G:263-276,Q:263-276)
2: ATPASE_ALPHA_BETA (D:346-355,E:346-355,F:346-355,N:34...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_GAMMA
PS00153
ATP synthase gamma subunit signature.
ATPG_YEAST
296-309
2
G:263-276
Q:263-276
2
ATPASE_ALPHA_BETA
PS00152
ATP synthase alpha and beta subunits signature.
ATPB_YEAST
379-388
6
D:346-355
E:346-355
F:346-355
N:346-355
O:346-355
P:346-355
ATPA_YEAST
400-409
6
A:365-374
B:365-374
C:365-374
K:365-374
L:365-374
M:365-374
[
close PROSITE info
]
Exons
(5, 18)
Info
All Exons
Exon 1.1 (A:26-509 | B:25-509 (gaps) | C:26-...)
Exon 2.1 (G:1-276 (gaps) | Q:1-276 (gaps))
Exon 3.1 (H:11-137 (gaps) | R:11-137 (gaps))
Exon 4.1 (D:6-475 | E:8-475 | F:7-475 | N:6-...)
Exon 5.1 (I:1-61 (gaps) | S:1-61 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
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
YBL099W
1
YBL099W.1
II:37050-38687
1638
ATPA_YEAST
1-545
545
6
A:26-509
B:25-509 (gaps)
C:26-509
K:26-509
L:25-509 (gaps)
M:26-509
484
485
484
484
485
484
2.1
YBR039W
1
YBR039W.1
II:315575-316510
936
ATPG_YEAST
1-311
311
2
G:1-276 (gaps)
Q:1-276 (gaps)
276
276
3.1
YDL004W
1
YDL004W.1
IV:443027-443509
483
ATPD_YEAST
1-160
160
2
H:11-137 (gaps)
R:11-137 (gaps)
127
127
4.1
YJR121W
1
YJR121W.1
X:647597-649132
1536
ATPB_YEAST
1-511
511
6
D:6-475
E:8-475
F:7-475
N:6-475
O:8-475
P:7-475
470
468
469
470
468
469
5.1
YPL271W
1
YPL271W.1
XVI:30079-30267
189
ATP5E_YEAST
1-62
62
2
I:1-61 (gaps)
S:1-61 (gaps)
61
61
[
close EXON info
]
SCOP Domains
(4, 20)
Info
All SCOP Domains
1a: SCOP_d3ziad3 (D:358-475)
1b: SCOP_d3ziae3 (E:358-475)
1c: SCOP_d3ziaf3 (F:358-475)
1d: SCOP_d3zian3 (N:358-475)
1e: SCOP_d3ziao3 (O:358-475)
1f: SCOP_d3ziap3 (P:358-475)
2a: SCOP_d3ziad1 (D:6-82)
2b: SCOP_d3ziae1 (E:8-82)
2c: SCOP_d3ziaf1 (F:7-82)
2d: SCOP_d3zian1 (N:6-82)
2e: SCOP_d3ziao1 (O:8-82)
2f: SCOP_d3ziap1 (P:7-82)
3a: SCOP_d3ziad2 (D:83-357)
3b: SCOP_d3ziae2 (E:83-357)
3c: SCOP_d3ziaf2 (F:83-357)
3d: SCOP_d3zian2 (N:83-357)
3e: SCOP_d3ziao2 (O:83-357)
3f: SCOP_d3ziap2 (P:83-357)
4a: SCOP_d3ziag_ (G:)
4b: SCOP_d3ziaq_ (Q:)
View:
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Protein Domains
(
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Organisms
(
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
Left-handed superhelix
(73)
Superfamily
:
C-terminal domain of alpha and beta subunits of F1 ATP synthase
(55)
Family
:
automated matches
(14)
Protein domain
:
automated matches
(14)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
1a
d3ziad3
D:358-475
1b
d3ziae3
E:358-475
1c
d3ziaf3
F:358-475
1d
d3zian3
N:358-475
1e
d3ziao3
O:358-475
1f
d3ziap3
P:358-475
Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
N-terminal domain of alpha and beta subunits of F1 ATP synthase
(55)
Family
:
automated matches
(14)
Protein domain
:
automated matches
(14)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
2a
d3ziad1
D:6-82
2b
d3ziae1
E:8-82
2c
d3ziaf1
F:7-82
2d
d3zian1
N:6-82
2e
d3ziao1
O:8-82
2f
d3ziap1
P:7-82
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
:
RecA protein-like (ATPase-domain)
(159)
Protein domain
:
automated matches
(32)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
3a
d3ziad2
D:83-357
3b
d3ziae2
E:83-357
3c
d3ziaf2
F:83-357
3d
d3zian2
N:83-357
3e
d3ziao2
O:83-357
3f
d3ziap2
P:83-357
Fold
:
Pyruvate kinase C-terminal domain-like
(59)
Superfamily
:
ATP synthase (F1-ATPase), gamma subunit
(29)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
4a
d3ziag_
G:
4b
d3ziaq_
Q:
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
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Asym.Unit (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (528 KB)
Header - Biol.Unit 1
Biol.Unit 2 (527 KB)
Header - Biol.Unit 2
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