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4B2Q
Asym. Unit
Info
Asym.Unit (1.2 MB)
Biol.Unit 1, α-C (1.2 MB)
Biol.Unit 1 (1.2 MB)
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(1)
Title
:
MODEL OF THE YEAST F1FO-ATP SYNTHASE DIMER BASED ON SUBTOMOGRAM AVERAGE
Authors
:
K. M. Davies, W. Kuehlbrandt
Date
:
17 Jul 12 (Deposition) - 29 Aug 12 (Release) - 24 Jul 13 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
37.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w (1x)
Keywords
:
Hydrolase, Subtomogram Average
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. M. Davies, C. Anselmi, I. Wittig, J. D. Faraldo-Gomez, W. Kuhlbrandt
Structure Of The Yeast F1Fo-Atp Synthase Dimer And Its Role In Shaping The Mitochondrial Cristae.
Proc. Natl. Acad. Sci. Usa V. 109 13602 2012
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
2d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
2e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
2f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ATP
6
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
MG
10
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:174 , THR A:175 , GLY A:176 , LYS A:177 , THR A:178 , ALA A:179 , GLU A:330 , GLN A:432 , GLN A:434 , MG A:1512 , SER D:355
BINDING SITE FOR RESIDUE ATP A1511
02
AC2
SOFTWARE
THR A:178 , ASP A:271 , ATP A:1511
BINDING SITE FOR RESIDUE MG A1512
03
AC3
SOFTWARE
GLN B:174 , THR B:175 , GLY B:176 , LYS B:177 , THR B:178 , ALA B:179 , ARG B:364 , GLN B:432 , GLN B:434 , MG B:1511
BINDING SITE FOR RESIDUE ATP B1510
04
AC4
SOFTWARE
LYS B:177 , THR B:178 , ASP B:271 , ATP B:1510
BINDING SITE FOR RESIDUE MG B1511
05
AC5
SOFTWARE
GLN C:174 , GLY C:176 , LYS C:177 , THR C:178 , ALA C:179 , ARG C:364 , GLN C:432 , GLN C:434 , MG C:1512 , SER F:355 , TYR F:368
BINDING SITE FOR RESIDUE ATP C1511
06
AC6
SOFTWARE
THR C:178 , ASP C:271 , ATP C:1511
BINDING SITE FOR RESIDUE MG C1512
07
AC7
SOFTWARE
ARG C:375 , GLY D:158 , ALA D:159 , GLY D:160 , VAL D:161 , GLY D:162 , LYS D:163 , THR D:164 , VAL D:165 , TYR D:345 , PHE D:418 , MG D:1477
BINDING SITE FOR RESIDUE ADP D1476
08
AC8
SOFTWARE
THR D:164 , GLU D:189 , ADP D:1476
BINDING SITE FOR RESIDUE MG D1477
09
AC9
SOFTWARE
VAL B:373 , SER B:374 , ARG B:375 , GLY F:160 , GLY F:162 , LYS F:163 , THR F:164 , VAL F:165 , TYR F:345 , PHE F:418 , MG F:1480
BINDING SITE FOR RESIDUE ADP F1479
10
BC1
SOFTWARE
THR F:164 , GLU F:189 , ASP F:256 , ADP F:1479
BINDING SITE FOR RESIDUE MG F1480
11
BC2
SOFTWARE
GLN a:174 , THR a:175 , GLY a:176 , LYS a:177 , THR a:178 , ALA a:179 , GLU a:330 , GLN a:432 , GLN a:434 , MG a:1512 , SER d:355
BINDING SITE FOR RESIDUE ATP a1511
12
BC3
SOFTWARE
THR a:178 , ASP a:271 , ATP a:1511
BINDING SITE FOR RESIDUE MG a1512
13
BC4
SOFTWARE
GLN b:174 , THR b:175 , GLY b:176 , LYS b:177 , THR b:178 , ALA b:179 , ARG b:364 , GLN b:432 , GLN b:434 , MG b:1511
BINDING SITE FOR RESIDUE ATP b1510
14
BC5
SOFTWARE
LYS b:177 , THR b:178 , ASP b:271 , ATP b:1510
BINDING SITE FOR RESIDUE MG b1511
15
BC6
SOFTWARE
GLN c:174 , GLY c:176 , LYS c:177 , THR c:178 , ALA c:179 , ARG c:364 , GLN c:432 , GLN c:434 , MG c:1512 , SER f:355 , TYR f:368
BINDING SITE FOR RESIDUE ATP c1511
16
BC7
SOFTWARE
THR c:178 , ASP c:271 , ATP c:1511
BINDING SITE FOR RESIDUE MG c1512
17
BC8
SOFTWARE
ARG c:375 , GLY d:158 , ALA d:159 , GLY d:160 , VAL d:161 , GLY d:162 , LYS d:163 , THR d:164 , VAL d:165 , TYR d:345 , PHE d:418 , MG d:1477
BINDING SITE FOR RESIDUE ADP d1476
18
BC9
SOFTWARE
THR d:164 , GLU d:189 , ADP d:1476
BINDING SITE FOR RESIDUE MG d1477
19
CC1
SOFTWARE
VAL b:373 , SER b:374 , ARG b:375 , GLY f:160 , GLY f:162 , LYS f:163 , THR f:164 , VAL f:165 , TYR f:345 , PHE f:418 , MG f:1480
BINDING SITE FOR RESIDUE ADP f1479
20
CC2
SOFTWARE
THR f:164 , GLU f:189 , ASP f:256 , ADP f:1479
BINDING SITE FOR RESIDUE MG f1480
[
close Site info
]
SAPs(SNPs)/Variants
(6, 84)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_ATP9_YEAST_001 (T46L, chain J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s, )
2: VAR_ATP9_YEAST_002 (L53F, chain J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s, )
3: VAR_ATP9_YEAST_003 (L57V, chain J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s, )
4: VAR_ATP9_YEAST_004 (C65S, chain J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s, )
5: VAR_ATPG_YEAST_001 (S174I, chain G/g, )
6: VAR_ATPG_YEAST_002 (S275F, chain G/g, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ATP9_YEAST_001
*
T
46
L
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s
T
46
L
2
UniProt
VAR_ATP9_YEAST_002
*
L
53
F
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s
L
53
F
3
UniProt
VAR_ATP9_YEAST_003
*
L
57
V
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s
L
57
V
4
UniProt
VAR_ATP9_YEAST_004
*
C
65
S
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S/j/k/l/m/n/o/p/q/r/s
C
65
S
5
UniProt
VAR_ATPG_YEAST_001
*
S
207
I
ATPG_YEAST
---
---
G/g
S
174
I
6
UniProt
VAR_ATPG_YEAST_002
*
S
308
F
ATPG_YEAST
---
---
G/g
S
275
F
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 34)
Info
All PROSITE Patterns/Profiles
1: ATPASE_C (J:38-59,K:38-59,L:38-59,M:38-59,N:...)
2: ATPASE_GAMMA (G:263-276,g:263-276)
3: ATPASE_ALPHA_BETA (D:346-355,E:346-355,F:346-355,d:34...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_C
PS00605
ATP synthase c subunit signature.
ATP9_YEAST
38-59
20
J:38-59
K:38-59
L:38-59
M:38-59
N:38-59
O:38-59
P:38-59
Q:38-59
R:38-59
S:38-59
j:38-59
k:38-59
l:38-59
m:38-59
n:38-59
o:38-59
p:38-59
q:38-59
r:38-59
s:38-59
2
ATPASE_GAMMA
PS00153
ATP synthase gamma subunit signature.
ATPG_YEAST
296-309
2
G:263-276
g:263-276
3
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
d:346-355
e:346-355
f:346-355
ATPA_YEAST
400-409
6
A:365-374
B:365-374
C:365-374
a:365-374
b:365-374
c:365-374
[
close PROSITE info
]
Exons
(20, 48)
Info
All Exons
Exon 1.4 (T:79-87 | t:79-87)
Exon 1.5 (T:88-129 | t:88-129)
Exon 1.6 (T:130-189 | t:130-189)
Exon 1.7 (T:190-207 | t:190-207)
Exon 2.3 (W:11-43 | w:11-43)
Exon 2.4 (W:44-87 | w:44-87)
Exon 2.5 (W:87-120 | w:87-120)
Exon 3.2 (U:4-40 | u:4-40)
Exon 3.3 (U:40-72 | u:40-72)
Exon 3.4 (U:73-96 | u:73-96)
Exon 3.5 (U:97-117 | u:97-117)
Exon 3.6 (U:118-123 | u:118-123)
Exon 4.2 (V:5-24 (gaps) | v:5-24 (gaps))
Exon 4.3 (V:24-66 | v:24-66)
Exon 4.4 (V:66-70 | v:66-70)
Exon 5.1 (A:26-510 | B:25-509 | C:26-510 | a...)
Exon 6.1 (G:1-278 (gaps) | g:1-278 (gaps))
Exon 7.1 (H:7-138 | h:7-138)
Exon 8.1 (D:6-475 | E:6-478 | F:7-478 | d:6-...)
Exon 9.1 (I:1-59 | i:1-59)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4
02: Boundary 1.4/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/-
06: Boundary 2.2/2.3
07: Boundary 2.3/2.4
08: Boundary 2.4/2.5
09: Boundary 2.5/2.6
10: Boundary 3.1/3.2
11: Boundary 3.2/3.3
12: Boundary 3.3/3.4
13: Boundary 3.4/3.5
14: Boundary 3.5/3.6
15: Boundary 3.6/-
16: Boundary 4.1/4.2
17: Boundary 4.2/4.3
18: Boundary 4.3/4.4
19: Boundary 4.4/-
20: Boundary -/5.1
21: Boundary 5.1/-
22: Boundary -/6.1
23: Boundary 6.1/-
24: Boundary -/7.1
25: Boundary 7.1/-
26: Boundary -/8.1
27: Boundary 8.1/-
28: Boundary -/9.1
29: Boundary 9.1/-
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
ENSBTAT00000008447
1
ENSBTAE00000366545
chr3:
34439903-34439828
76
AT5F1_BOVIN
1-14
14
0
-
-
1.2
ENSBTAT00000008447
2
ENSBTAE00000387804
chr3:
34439648-34439612
37
AT5F1_BOVIN
14-26
13
0
-
-
1.3
ENSBTAT00000008447
3
ENSBTAE00000428584
chr3:
34433047-34432902
146
AT5F1_BOVIN
26-75
50
0
-
-
1.4
ENSBTAT00000008447
4
ENSBTAE00000068331
chr3:
34429919-34429756
164
AT5F1_BOVIN
75-129
55
2
T:79-87
t:79-87
9
9
1.5
ENSBTAT00000008447
5
ENSBTAE00000068333
chr3:
34429411-34429286
126
AT5F1_BOVIN
130-171
42
2
T:88-129
t:88-129
42
42
1.6
ENSBTAT00000008447
6
ENSBTAE00000068340
chr3:
34425878-34425699
180
AT5F1_BOVIN
172-231
60
2
T:130-189
t:130-189
60
60
1.7
ENSBTAT00000008447
7
ENSBTAE00000068343
chr3:
34423268-34422853
416
AT5F1_BOVIN
232-256
25
2
T:190-207
t:190-207
18
18
2.1
ENSBTAT00000024326
1
ENSBTAE00000197898
chr1:
720699-720764
66
ATPO_BOVIN
1-12
12
0
-
-
2.2
ENSBTAT00000024326
2
ENSBTAE00000401349
chr1:
722101-722151
51
ATPO_BOVIN
13-29
17
0
-
-
2.3
ENSBTAT00000024326
3
ENSBTAE00000197900
chr1:
723098-723208
111
ATPO_BOVIN
30-66
37
2
W:11-43
w:11-43
33
33
2.4
ENSBTAT00000024326
4
ENSBTAE00000197901
chr1:
725362-725491
130
ATPO_BOVIN
67-110
44
2
W:44-87
w:44-87
44
44
2.5
ENSBTAT00000024326
5
ENSBTAE00000197902
chr1:
726174-726286
113
ATPO_BOVIN
110-147
38
2
W:87-120
w:87-120
34
34
2.6
ENSBTAT00000024326
6
ENSBTAE00000398411
chr1:
727512-727598
87
ATPO_BOVIN
148-176
29
0
-
-
2.7
ENSBTAT00000024326
7
ENSBTAE00000197904
chr1:
727876-728057
182
ATPO_BOVIN
177-213
37
0
-
-
3.1
ENSBTAT00000028282
1
ENSBTAE00000295799
chr19:
58014852-58014901
50
ATP5H_BOVIN
-
0
0
-
-
3.2
ENSBTAT00000028282
2
ENSBTAE00000231040
chr19:
58016320-58016449
130
ATP5H_BOVIN
1-41
41
2
U:4-40
u:4-40
37
37
3.3
ENSBTAT00000028282
3
ENSBTAE00000231042
chr19:
58016723-58016819
97
ATP5H_BOVIN
41-73
33
2
U:40-72
u:40-72
33
33
3.4
ENSBTAT00000028282
4
ENSBTAE00000231043
chr19:
58018243-58018314
72
ATP5H_BOVIN
74-97
24
2
U:73-96
u:73-96
24
24
3.5
ENSBTAT00000028282
5
ENSBTAE00000231044
chr19:
58019205-58019267
63
ATP5H_BOVIN
98-118
21
2
U:97-117
u:97-117
21
21
3.6
ENSBTAT00000028282
6
ENSBTAE00000231046
chr19:
58019418-58019617
200
ATP5H_BOVIN
119-161
43
2
U:118-123
u:118-123
6
6
4.1
ENSBTAT00000032427
1
ENSBTAE00000259413
chr1:
10042456-10042499
44
ATP5J_BOVIN
-
0
0
-
-
4.2
ENSBTAT00000032427
2
ENSBTAE00000006048
chr1:
10045981-10046151
171
ATP5J_BOVIN
1-55
55
2
V:5-24 (gaps)
v:5-24 (gaps)
20
20
4.3
ENSBTAT00000032427
3
ENSBTAE00000006056
chr1:
10048867-10048991
125
ATP5J_BOVIN
55-97
43
2
V:24-66
v:24-66
43
43
4.4
ENSBTAT00000032427
4
ENSBTAE00000006057
chr1:
10049596-10049771
176
ATP5J_BOVIN
97-108
12
2
V:66-70
v:66-70
5
5
5.1
YBL099W
1
YBL099W.1
II:37050-38687
1638
ATPA_YEAST
1-545
545
6
A:26-510
B:25-509
C:26-510
a:26-510
b:25-509
c:26-510
485
485
485
485
485
485
6.1
YBR039W
1
YBR039W.1
II:315575-316510
936
ATPG_YEAST
1-311
311
2
G:1-278 (gaps)
g:1-278 (gaps)
278
278
7.1
YDL004W
1
YDL004W.1
IV:443027-443509
483
ATPD_YEAST
1-160
160
2
H:7-138
h:7-138
132
132
8.1
YJR121W
1
YJR121W.1
X:647597-649132
1536
ATPB_YEAST
1-511
511
6
D:6-475
E:6-478
F:7-478
d:6-475
e:6-478
f:7-478
470
473
472
470
473
472
9.1
YPL271W
1
YPL271W.1
XVI:30079-30267
189
ATP5E_YEAST
1-62
62
2
I:1-59
i:1-59
59
59
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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)
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Nucleic
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Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain a
Chain b
Chain c
Chain d
Chain e
Chain f
Chain g
Chain h
Chain i
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Chain k
Chain l
Chain m
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Header - Biol.Unit 1
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