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2UX5
Asym. Unit
Info
Asym.Unit (172 KB)
Biol.Unit 1 (158 KB)
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(1)
Title
:
X-RAY HIGH RESOLUTION STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTER FROM RB. SPHAEROIDES AT PH 9 IN THE CHARGE-SEPARATED STATE
Authors
:
J. Koepke, R. Diehm, G. Fritzsch
Date
:
26 Mar 07 (Deposition) - 03 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.21
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Bacteriochlorophyll, Phosphatidylcholine, Chlorophyll, Cardiolipin, Metal-Binding, Transmembrane, Glucosylgalactosyl Diacylglycerol, Proton Translocation Pathways, Photosynthesis, Reaction Center, Electron Transport, Iron, Membrane, Transport, Magnesium, Chromophore, Binding Positions Of The Secondary Quinone Qb
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Koepke, E. M. Krammer, A. R. Klingen, P. Sebban, G. M. Ullmann, G. Fritzsch
Ph Modulates The Quinone Position In The Photosynthetic Reaction Center From Rhodobacter Sphaeroides In The Neutral And Charge Separated States.
J. Mol. Biol. V. 371 396 2007
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Hetero Components
(11, 29)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL A (BCLa)
01b: BACTERIOCHLOROPHYLL A (BCLb)
01c: BACTERIOCHLOROPHYLL A (BCLc)
01d: BACTERIOCHLOROPHYLL A (BCLd)
02a: BACTERIOPHEOPHYTIN A (BPHa)
02b: BACTERIOPHEOPHYTIN A (BPHb)
03a: CARDIOLIPIN (CDLa)
04a: FE (III) ION (FEa)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
05c: GLYCEROL (GOLc)
05d: GLYCEROL (GOLd)
05e: GLYCEROL (GOLe)
05f: GLYCEROL (GOLf)
05g: GLYCEROL (GOLg)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
07c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
07d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
07e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
07f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
07g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
07h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
07i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
08a: PHOSPHATE ION (PO4a)
09a: SPHEROIDENE (SPOa)
10a: UBIQUINONE-10 (U10a)
11a: UBIQUINONE-2 (UQ2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CDL
1
Ligand/Ion
CARDIOLIPIN
4
FE
1
Ligand/Ion
FE (III) ION
5
GOL
7
Ligand/Ion
GLYCEROL
6
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
LDA
9
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
PO4
1
Ligand/Ion
PHOSPHATE ION
9
SPO
1
Ligand/Ion
SPHEROIDENE
10
U10
1
Ligand/Ion
UBIQUINONE-10
11
UQ2
1
Ligand/Ion
UBIQUINONE-2
[
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Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , HOH L:2081 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1305 , LDA M:1312 , BPH M:1314 , SPO M:1316
BINDING SITE FOR RESIDUE BCL M1304
02
AC2
SOFTWARE
VAL L:157 , TYR L:162 , BCL L:1287 , MET M:122 , ALA M:153 , LEU M:156 , TRP M:157 , LEU M:160 , THR M:186 , ASN M:187 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:1304 , BPH M:1314
BINDING SITE FOR RESIDUE BCL M1305
03
AC3
SOFTWARE
TYR L:128 , PHE L:146 , HIS L:153 , LEU L:154 , BPH L:1285 , BCL L:1287 , HOH L:2112 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , LDA M:1306
BINDING SITE FOR RESIDUE BCL L1282
04
AC4
SOFTWARE
BCL L:1282 , PRO M:200 , GLY M:203 , LEU M:204 , PHE M:208 , LDA M:1308 , GOL M:1318 , HOH M:2121
BINDING SITE FOR RESIDUE LDA M1306
05
AC5
SOFTWARE
PHE M:7 , TRP M:41 , PHE M:42
BINDING SITE FOR RESIDUE LDA M1307
06
AC6
SOFTWARE
GLN H:32 , TYR H:40 , ARG M:253 , PHE M:258 , LDA M:1306 , LDA M:1309 , U10 M:1315
BINDING SITE FOR RESIDUE LDA M1308
07
AC7
SOFTWARE
PHE M:258 , LDA M:1308
BINDING SITE FOR RESIDUE LDA M1309
08
AC8
SOFTWARE
TYR L:148 , ILE L:150
BINDING SITE FOR RESIDUE LDA L1283
09
AC9
SOFTWARE
VAL L:220 , GLY L:221 , UQ2 L:1286 , VAL M:32 , GLY M:33 , LDA M:1311 , HOH M:2122
BINDING SITE FOR RESIDUE LDA M1310
10
BC1
SOFTWARE
LDA M:1310
BINDING SITE FOR RESIDUE LDA M1311
11
BC2
SOFTWARE
SER L:178 , BCL M:1304
BINDING SITE FOR RESIDUE LDA M1312
12
BC3
SOFTWARE
PHE L:179 , UQ2 L:1286 , HOH L:2113
BINDING SITE FOR RESIDUE LDA L1284
13
BC4
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M1313
14
BC5
SOFTWARE
PHE L:181 , LEU L:185 , LEU L:189 , LEU L:219 , GLY M:63 , ALA M:125 , VAL M:126 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:1304 , BCL M:1305
BINDING SITE FOR RESIDUE BPH M1314
15
BC6
SOFTWARE
ALA L:93 , ALA L:96 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , ALA L:124 , TYR L:148 , GLY L:149 , VAL L:241 , BCL L:1282 , BCL L:1287 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH L1285
16
BC7
SOFTWARE
PHE L:29 , GLY L:35 , TRP L:100 , ARG L:103 , MET M:218 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , PHE M:258 , ASN M:259 , ALA M:260 , ILE M:265 , TRP M:268 , LDA M:1308
BINDING SITE FOR RESIDUE U10 M1315
17
BC8
SOFTWARE
LEU L:189 , HIS L:190 , LEU L:193 , ASP L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LDA L:1284 , LEU M:47 , LDA M:1310 , HOH M:2100
BINDING SITE FOR RESIDUE UQ2 L1286
18
BC9
SOFTWARE
PHE L:97 , ALA L:124 , ILE L:125 , LEU L:131 , VAL L:157 , TYR L:162 , ASN L:166 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:1282 , BPH L:1285 , TYR M:210 , BCL M:1305
BINDING SITE FOR RESIDUE BCL L1287
19
CC1
SOFTWARE
PHE M:67 , ILE M:70 , GLY M:71 , TRP M:75 , SER M:119 , TRP M:157 , LEU M:160 , GLY M:161 , PHE M:162 , TRP M:171 , VAL M:175 , TYR M:177 , HIS M:182 , BCL M:1304
BINDING SITE FOR RESIDUE SPO M1316
20
CC2
SOFTWARE
ILE H:22 , PHE H:23 , TYR H:30 , GOL H:1252 , HOH H:2003 , ASN L:199 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , TRP M:271 , HOH M:2123 , HOH M:2124
BINDING SITE FOR RESIDUE CDL M1317
21
CC3
SOFTWARE
HIS H:126 , HOH H:2107 , GLU L:72 , TYR L:73 , LYS L:82 , THR M:21
BINDING SITE FOR RESIDUE PO4 L1288
22
CC4
SOFTWARE
GLN L:87 , THR L:90 , TRP L:142 , HOH L:2115
BINDING SITE FOR RESIDUE HTO L1289
23
CC5
SOFTWARE
GLU H:34 , LYS H:62 , HOH H:2003 , ASN L:199 , GOL L:1290 , ARG M:267 , CDL M:1317
BINDING SITE FOR RESIDUE GOL H1252
24
CC6
SOFTWARE
LYS H:62 , THR H:63 , PHE H:64 , GOL H:1252 , ALA L:198 , ASN L:199 , PRO L:200 , HOH L:2085
BINDING SITE FOR RESIDUE GOL L1290
25
CC7
SOFTWARE
GLY L:77 , ALA L:78 , LEU L:80 , GLN L:87
BINDING SITE FOR RESIDUE GOL L1291
26
CC8
SOFTWARE
LDA M:1306
BINDING SITE FOR RESIDUE GOL M1318
27
CC9
SOFTWARE
ALA H:25
BINDING SITE FOR RESIDUE GOL H1253
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,M:195-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOSH
167-193
1
L:166-192
RCEM_RHOSH
196-222
1
M:195-221
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 4)
Info
All SCOP Domains
1a: SCOP_d2ux5h2 (H:36-251)
2a: SCOP_d2ux5l_ (L:)
2b: SCOP_d2ux5m_ (M:)
3a: SCOP_d2ux5h1 (H:11-35)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PRC-barrel domain
(113)
Superfamily
:
PRC-barrel domain
(113)
Family
:
Photosynthetic reaction centre, H-chain, cytoplasmic domain
(108)
Protein domain
:
Photosynthetic reaction centre
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
1a
d2ux5h2
H:36-251
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Superfamily
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Family
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Protein domain
:
automated matches
(44)
Rhodobacter sphaeroides [TaxId: 1063]
(31)
2a
d2ux5l_
L:
2b
d2ux5m_
M:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Protein domain
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
3a
d2ux5h1
H:11-35
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2ux5H02 (H:117-249)
2a: CATH_2ux5H01 (H:12-116)
3a: CATH_2ux5M01 (M:1-143)
3b: CATH_2ux5M02 (M:144-303)
3c: CATH_2ux5L01 (L:1-163)
3d: CATH_2ux5L02 (L:164-263)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 2
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 2
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
1a
2ux5H02
H:117-249
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 1
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 1
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
2a
2ux5H01
H:12-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
3a
2ux5M01
M:1-143
3b
2ux5M02
M:144-303
3c
2ux5L01
L:1-163
3d
2ux5L02
L:164-263
[
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]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_2ux5H01 (H:141-212)
2a: PFAM_PRCH_2ux5H02 (H:11-137)
3a: PFAM_Photo_RC_2ux5L01 (L:29-272)
3b: PFAM_Photo_RC_2ux5M01 (M:50-303)
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Clans
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)
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Families
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(
)
Organisms
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(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-2ux5H01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-2ux5H02
H:11-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-2ux5L01
L:29-272
3b
Photo_RC-2ux5M01
M:50-303
[
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Asym.Unit (172 KB)
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