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1L9J
Biol. Unit 1
Info
Asym.Unit (329 KB)
Biol.Unit 1 (162 KB)
Biol.Unit 2 (161 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE CYTOCHROME-C(2)-PHOTOSYNTHETIC REACTION CENTER ELECTRON TRANSFER COMPLEX FROM RHODOBACTER SPHAEROIDES IN TYPE I CO-CRYSTALS
Authors
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Feher
Date
:
24 Mar 02 (Deposition) - 12 Jun 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.25
Chains
:
Asym. Unit : C,D,H,L,M,R,S,T
Biol. Unit 1: C,H,L,M (1x)
Biol. Unit 2: D,R,S,T (1x)
Keywords
:
Bacterial Photosynthesis, Electron Transfer Proteins, Protein-Protein Interactions, Membrane Proteins, Protein Complexes, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Fehe
X-Ray Structure Determination Of The Cytochrome C2: Reactio Center Electron Transfer Complex From Rhodobacter Sphaeroides.
J. Mol. Biol. V. 319 501 2002
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Hetero Components
(6, 11)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
1e: BACTERIOCHLOROPHYLL A (BCLe)
1f: BACTERIOCHLOROPHYLL A (BCLf)
1g: BACTERIOCHLOROPHYLL A (BCLg)
1h: BACTERIOCHLOROPHYLL A (BCLh)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
2c: BACTERIOPHEOPHYTIN A (BPHc)
2d: BACTERIOPHEOPHYTIN A (BPHd)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: FE (II) ION (FE2a)
4b: FE (II) ION (FE2b)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
6b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
6c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
6d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
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
CL
-1
Ligand/Ion
CHLORIDE ION
4
FE2
1
Ligand/Ion
FE (II) ION
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
LDA
2
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
1
Ligand/Ion
UBIQUINONE-10
[
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE2 M 1007
02
AC4
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , PHE L:181 , THR L:182 , BCL L:1002 , BPH L:1005 , TRP M:157 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1003 , LDA M:1011
BINDING SITE FOR RESIDUE BCL M 1001
03
AC5
SOFTWARE
PHE L:97 , ALA L:124 , TYR L:128 , LEU L:131 , VAL L:157 , TYR L:162 , PHE L:167 , HIS L:168 , HIS L:173 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:1004 , TYR M:210 , BCL M:1001 , BCL M:1003 , BPH M:1006
BINDING SITE FOR RESIDUE BCL L 1002
04
AC6
SOFTWARE
TYR L:162 , PHE L:181 , BCL L:1002 , BCL L:1004 , BPH L:1005 , TRP M:66 , ALA M:153 , LEU M:156 , TRP M:157 , THR M:186 , ASN M:187 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , GLY M:280 , GLY M:281 , ILE M:284 , BCL M:1001
BINDING SITE FOR RESIDUE BCL M 1003
05
AC7
SOFTWARE
ILE L:46 , ILE L:49 , TYR L:128 , LEU L:131 , ILE L:150 , TRP L:151 , HIS L:153 , LEU L:154 , BCL L:1002 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BCL M:1003 , BPH M:1006 , LDA M:1010 , HOH M:1025
BINDING SITE FOR RESIDUE BCL L 1004
06
AC8
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , LEU L:219 , GLY M:63 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , ALA M:273 , THR M:277 , BCL M:1001 , BCL M:1003
BINDING SITE FOR RESIDUE BPH L 1005
07
AC9
SOFTWARE
ILE L:46 , ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , TYR L:148 , HIS L:153 , LEU L:238 , VAL L:241 , BCL L:1002 , BCL L:1004 , TYR M:210 , ALA M:213 , LEU M:214 , MET M:218 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH M 1006
08
BC1
SOFTWARE
TRP L:100 , MET M:218 , HIS M:219 , THR M:222 , ILE M:223 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , THR M:261 , MET M:262 , ILE M:265 , TRP M:268
BINDING SITE FOR RESIDUE U10 M 1008
09
BC2
SOFTWARE
CYS C:15 , CYS C:18 , HIS C:19 , PRO C:38 , ARG C:46 , ALA C:48 , GLY C:49 , PHE C:54 , TYR C:57 , GLY C:58 , MET C:61 , TRP C:71 , PHE C:76 , TYR C:79 , VAL C:80 , LYS C:99 , MET C:100 , THR C:101 , PHE C:102 , LEU M:191
BINDING SITE FOR RESIDUE HEM C 1009
10
BC3
SOFTWARE
BCL L:1004 , LEU M:204 , MET M:272
BINDING SITE FOR RESIDUE LDA M 1010
11
BC4
SOFTWARE
PHE M:67 , PHE M:74 , MET M:122 , TRP M:157 , VAL M:175 , PRO M:176 , GLY M:178 , HIS M:182 , BCL M:1001
BINDING SITE FOR RESIDUE LDA M 1011
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: CYTC (C:3-121)
2: REACTION_CENTER (M:195-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CYC2_RHOSH
3-121
1
C:3-121
-
CYC2_RHOS4
24-142
1
C:3-121
-
2
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOS4
167-193
1
L:166-192
-
RCEL_RHOSH
167-193
1
L:166-192
-
RCEM_RHOS4
196-222
1
M:195-221
-
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1l9jc_ (C:)
1b: SCOP_d1l9jd_ (D:)
2a: SCOP_d1l9jh1 (H:36-253)
2b: SCOP_d1l9jt1 (T:36-253)
3a: SCOP_d1l9jl_ (L:)
3b: SCOP_d1l9jr_ (R:)
4a: SCOP_d1l9jm_ (M:)
4b: SCOP_d1l9js_ (S:)
5a: SCOP_d1l9jh2 (H:8-35)
5b: SCOP_d1l9jt2 (T:8-35)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
Cytochrome c2
(21)
Rhodobacter sphaeroides [TaxId: 1063]
(5)
1a
d1l9jc_
C:
1b
d1l9jd_
D:
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)
2a
d1l9jh1
H:36-253
2b
d1l9jt1
T:36-253
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)
3a
d1l9jl_
L:
3b
d1l9jr_
R:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
4a
d1l9jm_
M:
4b
d1l9js_
S:
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)
5a
d1l9jh2
H:8-35
5b
d1l9jt2
T:8-35
[
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CATH Domains
(4, 14)
Info
all CATH domains
1a: CATH_1l9jH02 (H:117-248)
1b: CATH_1l9jT02 (T:117-248)
2a: CATH_1l9jH01 (H:12-116)
2b: CATH_1l9jT01 (T:12-116)
3a: CATH_1l9jC00 (C:1-124)
3b: CATH_1l9jD00 (D:1-124)
4a: CATH_1l9jM02 (M:144-301)
4b: CATH_1l9jM01 (M:35-143)
4c: CATH_1l9jS01 (S:35-143)
4d: CATH_1l9jS02 (S:144-301)
4e: CATH_1l9jL01 (L:1-163)
4f: CATH_1l9jR01 (R:1-163)
4g: CATH_1l9jL02 (L:164-263)
4h: CATH_1l9jR02 (R:164-263)
View:
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)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
1a
1l9jH02
H:117-248
1b
1l9jT02
T:117-248
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. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
2a
1l9jH01
H:12-116
2b
1l9jT01
T:12-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
3a
1l9jC00
C:1-124
3b
1l9jD00
D:1-124
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. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
4a
1l9jM02
M:144-301
4b
1l9jM01
M:35-143
4c
1l9jS01
S:35-143
4d
1l9jS02
S:144-301
4e
1l9jL01
L:1-163
4f
1l9jR01
R:1-163
4g
1l9jL02
L:164-263
4h
1l9jR02
R:164-263
[
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]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_PRC_1l9jT01 (T:141-212)
1b: PFAM_PRC_1l9jT02 (T:141-212)
2a: PFAM_PRCH_1l9jT03 (T:8-137)
2b: PFAM_PRCH_1l9jT04 (T:8-137)
3a: PFAM_Photo_RC_1l9jR01 (R:29-272)
3b: PFAM_Photo_RC_1l9jR02 (R:29-272)
3c: PFAM_Photo_RC_1l9jS01 (S:50-301)
3d: PFAM_Photo_RC_1l9jS02 (S:50-301)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1l9jT01
T:141-212
1b
PRC-1l9jT02
T:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1l9jT03
T:8-137
2b
PRCH-1l9jT04
T:8-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1l9jR01
R:29-272
3b
Photo_RC-1l9jR02
R:29-272
3c
Photo_RC-1l9jS01
S:50-301
3d
Photo_RC-1l9jS02
S:50-301
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Asym.Unit (329 KB)
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Header - Biol.Unit 1
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