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3DUQ
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (150 KB)
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(1)
Title
:
E(L212)A, D(L213)A, N(M5)D TRIPLE MUTANT STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
Authors
:
P. R. Pokkuluri, M. Schiffer
Date
:
17 Jul 08 (Deposition) - 30 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Mutant Photosynthetic Reaction Center, Phenotypic Revertant, Proton Transfer, Membrane Protein, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. R. Pokkuluri, P. D. Laible, S. L. Ginell, D. K. Hanson, M. Schiffer
Structural Description Of Compensatory Mutations That Restore Proton Transfer Pathways To The L212A-L213A Mutant Bacterial Reaction Center
To Be Published
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Hetero Components
(7, 15)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
3a: CARDIOLIPIN (CDLa)
4a: FE (III) ION (FEa)
5a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
5b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
5c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
5d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
6a: SPEROIDENONE (SPNa)
7a: UBIQUINONE-10 (U10a)
7b: UBIQUINONE-10 (U10b)
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
LDA
4
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
6
SPN
1
Ligand/Ion
SPEROIDENONE
7
U10
2
Ligand/Ion
UBIQUINONE-10
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , TYR L:128 , LEU L:131 , TRP L:156 , VAL L:157 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , SER L:244 , CYS L:247 , MET L:248 , BCL L:501 , BPH L:503 , TYR M:210 , BCL M:502
BINDING SITE FOR RESIDUE BCL L 502
02
AC2
SOFTWARE
TYR L:128 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:502 , BPH L:503 , HOH L:1012 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BCL M:502 , U10 M:504 , LDA M:701
BINDING SITE FOR RESIDUE BCL L 501
03
AC3
SOFTWARE
PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , HIS L:153 , VAL L:241 , BCL L:501 , BCL L:502 , TYR M:210 , ALA M:213 , LEU M:214 , MET M:218 , TRP M:252 , MET M:256 , U10 M:504
BINDING SITE FOR RESIDUE BPH L 503
04
AC4
SOFTWARE
ILE L:175 , SER L:178 , PHE L:179 , HIS L:190 , LEU L:193 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229
BINDING SITE FOR RESIDUE U10 L 504
05
AC5
SOFTWARE
LDA H:703 , PRO L:28 , PHE L:29 , GLY M:257 , U10 M:504 , LDA M:701
BINDING SITE FOR RESIDUE LDA L 704
06
AC6
SOFTWARE
LEU L:75 , GLY L:76 , GLY L:77 , GLN L:87 , ILE L:91 , THR L:94 , TRP L:142
BINDING SITE FOR RESIDUE LDA L 709
07
AC7
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , LEU L:185 , HOH L:1013 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:502 , BPH M:503 , SPN M:600
BINDING SITE FOR RESIDUE BCL M 501
08
AC8
SOFTWARE
VAL L:157 , TYR L:162 , PHE L:181 , BCL L:501 , BCL L:502 , MET M:122 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:501 , BPH M:503
BINDING SITE FOR RESIDUE BCL M 502
09
AC9
SOFTWARE
PHE L:181 , LEU L:189 , LEU M:64 , TRP M:129 , THR M:146 , PHE M:150 , ALA M:273 , THR M:277 , BCL M:501 , BCL M:502
BINDING SITE FOR RESIDUE BPH M 503
10
BC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M 500
11
BC2
SOFTWARE
LDA H:703 , THR L:38 , TRP L:100 , BCL L:501 , BPH L:503 , LDA L:704 , MET M:218 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , MET M:262 , ILE M:265 , TRP M:268
BINDING SITE FOR RESIDUE U10 M 504
12
BC3
SOFTWARE
PHE M:67 , PHE M:68 , ILE M:70 , SER M:119 , TRP M:157 , GLY M:161 , TRP M:171 , VAL M:175 , GLY M:178 , HIS M:182 , BCL M:501
BINDING SITE FOR RESIDUE SPN M 600
13
BC4
SOFTWARE
TYR H:30 , HOH H:1130 , ASN L:199 , PRO L:200 , LYS M:144 , HIS M:145 , TRP M:148 , TRP M:155 , ARG M:267 , ILE M:270 , TRP M:271 , HOH M:1084
BINDING SITE FOR RESIDUE CDL M 800
14
BC5
SOFTWARE
LDA H:703 , BCL L:501 , LDA L:704 , PHE M:208
BINDING SITE FOR RESIDUE LDA M 701
15
BC6
SOFTWARE
TYR H:40 , LDA L:704 , U10 M:504 , LDA M:701
BINDING SITE FOR RESIDUE LDA H 703
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3duqh2 (H:36-250)
2a: SCOP_d3duql_ (L:)
3a: SCOP_d3duqm_ (M:)
4a: SCOP_d3duqh1 (H:11-35)
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)
(
)
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)
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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
d3duqh2
H:36-250
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
:
L (light) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
2a
d3duql_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d3duqm_
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)
4a
d3duqh1
H:11-35
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3duqH02 (H:117-249)
2a: CATH_3duqH01 (H:12-116)
3a: CATH_3duqM01 (M:5-143)
3b: CATH_3duqL01 (L:1-163)
3c: CATH_3duqL02 (L:164-263)
3d: CATH_3duqM02 (M:144-302)
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)
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)
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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)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(7)
1a
3duqH02
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)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(7)
2a
3duqH01
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)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(7)
3a
3duqM01
M:5-143
3b
3duqL01
L:1-163
3c
3duqL02
L:164-263
3d
3duqM02
M:144-302
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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