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1Q90
Biol. Unit 1
Info
Asym.Unit (170 KB)
Biol.Unit 1 (313 KB)
Biol.Unit 2 (621 KB)
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(1)
Title
:
STRUCTURE OF THE CYTOCHROME B6F (PLASTOHYDROQUINONE : PLASTOCYANIN OXIDOREDUCTASE) FROM CHLAMYDOMONAS REINHARDTII
Authors
:
D. Stroebel, Y. Choquet, J. -L. Popot, D. Picot
Date
:
22 Aug 03 (Deposition) - 09 Dec 03 (Release) - 25 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,G,L,M,N,R
Biol. Unit 1: A,B,C,D,G,L,M,N,R (2x)
Biol. Unit 2: A,B,C,D,G,L,M,N,R (4x)
Keywords
:
Membrane Protein Complex, Photosynthesis, Electron Transfer, Oxydoreductase, Chlorophyll, Beta-Carotene, Stigmatellin, Sulfoquinovosyldiacylglycerol, Monogalactosyldiacylglycerol
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Stroebel, Y. Choquet, J. -L. Popot, D. Picot
An Atypical Haem In The Cytochrome B6F Complex
Nature V. 426 413 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(8, 24)
Info
All Hetero Components
1a: BETA-CAROTENE (BCRa)
2a: CHLOROPHYLL A (CLAa)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
4d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
5a: EICOSANE (LFAa)
6a: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGL... (LMGa)
6b: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGL... (LMGb)
7a: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO... (SQDa)
8a: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2... (TDSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCR
2
Ligand/Ion
BETA-CAROTENE
2
CLA
2
Ligand/Ion
CHLOROPHYLL A
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
8
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
LFA
2
Ligand/Ion
EICOSANE
6
LMG
4
Ligand/Ion
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
7
SQD
2
Ligand/Ion
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
TDS
2
Ligand/Ion
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:1 , PRO A:2 , PHE A:4 , ALA A:5 , CYS A:21 , CYS A:24 , HIS A:25 , GLN A:59 , ALA A:62 , LEU A:69 , ASN A:70 , VAL A:71 , GLY A:72 , MET A:73 , ASN A:153 , GLY A:155 , ARG A:156 , GLY A:157 , VAL A:159 , TYR A:160 , PRO A:161
BINDING SITE FOR RESIDUE HEM A 900
02
AC2
SOFTWARE
VAL B:30 , TYR B:34 , CYS B:35 , GLY B:38 , PHE B:203 , ARG B:207 , GLY B:210 , ILE B:211 , HEM B:901 , HOH B:963 , ASN D:25 , PHE D:40 , ILE D:44
BINDING SITE FOR RESIDUE HEM B 903
03
AC3
SOFTWARE
TYR B:34 , GLY B:37 , GLY B:38 , THR B:40 , PHE B:41 , HIS B:100 , ARG B:103 , VAL B:104 , GLY B:109 , ARG B:114 , THR B:117 , TRP B:118 , GLY B:121 , VAL B:122 , MET B:124 , ALA B:125 , HIS B:202 , ILE B:206 , ILE B:211 , SER B:212 , HEM B:903 , HOH B:961 , HOH B:963
BINDING SITE FOR RESIDUE HEM B 901
04
AC4
SOFTWARE
GLN B:47 , GLY B:51 , PHE B:52 , MET B:54 , ARG B:83 , HIS B:86 , ARG B:87 , ALA B:90 , PHE B:131 , GLY B:135 , TYR B:136 , LEU B:138 , PRO B:139 , HIS B:187 , THR B:188 , PRO B:192
BINDING SITE FOR RESIDUE HEM B 902
05
AC5
SOFTWARE
CYS C:134 , HIS C:136 , LEU C:137 , GLY C:138 , CYS C:139 , CYS C:152 , HIS C:155 , GLY C:156 , SER C:157
BINDING SITE FOR RESIDUE FES C 210
06
AC6
SOFTWARE
TYR B:105 , ALA B:125 , SER B:130 , VAL B:133 , TYR D:80 , PHE D:81 , PRO D:83 , VAL D:104 , LEU D:132 , PHE D:133 , GLY D:136 , VAL D:139 , LMG D:953
BINDING SITE FOR RESIDUE CLA D 910
07
AC7
SOFTWARE
ILE B:32 , PHE B:33 , ILE B:39 , LEU B:99 , THR D:47 , VAL G:16 , GLY G:20 , VAL G:23 , THR M:77 , LEU M:81 , PHE N:84
BINDING SITE FOR RESIDUE BCR B 904
08
AC8
SOFTWARE
ALA B:147 , ILE B:150 , VAL B:151 , CYS C:154 , HIS C:155 , ILE D:75 , LEU D:76 , PRO D:77 , PHE D:85 , LEU D:88 , MET D:101
BINDING SITE FOR RESIDUE TDS D 920
09
AC9
SOFTWARE
LYS A:272 , PHE A:276 , TRP D:32 , ARG R:42 , ASN R:46
BINDING SITE FOR RESIDUE SQD R 950
10
BC1
SOFTWARE
ARG A:251 , LEU A:255 , LEU B:81 , GLY R:63 , TYR R:64
BINDING SITE FOR RESIDUE LFA B 960
11
BC2
SOFTWARE
GLN A:37 , ILE B:39 , CYS B:43 , MET B:92 , MET B:96 , THR D:47 , CYS D:50 , LEU D:54 , THR L:3 , ILE L:4 , TYR L:7 , PHE M:65 , THR M:69 , THR M:72 , MET M:76 , GLU N:69 , GLN N:74 , TRP N:77
BINDING SITE FOR RESIDUE LMG L 951
12
BC3
SOFTWARE
PHE B:102 , LEU D:134 , THR D:137 , ILE D:145 , THR D:148 , CLA D:910 , CYS G:7 , PRO G:15 , ILE G:18 , PHE G:22 , ALA M:63 , ILE M:66
BINDING SITE FOR RESIDUE LMG D 953
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_PETG_CHLRE_001 (L30R, chain G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PETG_CHLRE_001
*
L
30
R
PETG_CHLRE
---
---
G
L
30
R
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (B:4-215)
2: CYTB_CTER (D:17-159)
3: RIESKE (C:92-188)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_NTER
PS51002
Cytochrome b/b6 N-terminal region profile.
CYB6_CHLRE
4-215
2
B:4-215
2
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
PETD_CHLRE
17-160
2
D:17-159
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRIA_CHLRE
92-188
2
C:92-188
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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
(11, 11)
Info
All SCOP Domains
01a: SCOP_d1q90a2 (A:169-232)
02a: SCOP_d1q90a1 (A:1-168,A:233-247)
03a: SCOP_d1q90c_ (C:)
04a: SCOP_d1q90d_ (D:)
05a: SCOP_d1q90b_ (B:)
06a: SCOP_d1q90a3 (A:248-292)
07a: SCOP_d1q90r_ (R:)
08a: SCOP_d1q90g_ (G:)
09a: SCOP_d1q90l_ (L:)
10a: SCOP_d1q90m_ (M:)
11a: SCOP_d1q90n_ (N:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Rudiment single hybrid motif
(69)
Family
:
Cytochrome f, small domain
(12)
Protein domain
:
Cytochrome f, small domain
(12)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(6)
01a
d1q90a2
A:169-232
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Cytochrome f, large domain
(12)
Family
:
Cytochrome f, large domain
(12)
Protein domain
:
Cytochrome f, large domain
(12)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(6)
02a
d1q90a1
A:1-168,A:233-247
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
ISP subunit from the cytochrome b6f complex, soluble domain
(5)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
03a
d1q90c_
C:
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Superfamily
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Family
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(39)
Protein domain
:
Subunit IV of the cytochrome b6f complex
(8)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
04a
d1q90d_
D:
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Transmembrane di-heme cytochromes
(48)
Family
:
Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Protein domain
:
Cytochrome b6 subunit of the cytochrome b6f complex
(5)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
05a
d1q90b_
B:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Family
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Protein domain
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
06a
d1q90a3
A:248-292
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
ISP transmembrane anchor
(32)
Protein domain
:
ISP subunit from the cytochrome b6f complex, transmembrane anchor
(5)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
07a
d1q90r_
R:
Superfamily
:
PetG subunit of the cytochrome b6f complex
(8)
Family
:
PetG subunit of the cytochrome b6f complex
(8)
Protein domain
:
PetG subunit of the cytochrome b6f complex
(5)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
08a
d1q90g_
G:
Superfamily
:
PetL subunit of the cytochrome b6f complex
(7)
Family
:
PetL subunit of the cytochrome b6f complex
(7)
Protein domain
:
PetL subunit of the cytochrome b6f complex
(7)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
09a
d1q90l_
L:
Superfamily
:
PetM subunit of the cytochrome b6f complex
(9)
Family
:
PetM subunit of the cytochrome b6f complex
(9)
Protein domain
:
PetM subunit of the cytochrome b6f complex
(8)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
10a
d1q90m_
M:
Superfamily
:
PetN subunit of the cytochrome b6f complex
(9)
Family
:
PetN subunit of the cytochrome b6f complex
(9)
Protein domain
:
PetN subunit of the cytochrome b6f complex
(5)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(1)
11a
d1q90n_
N:
[
close SCOP info
]
CATH Domains
(6, 6)
Info
all CATH domains
1a: CATH_1q90D01 (D:11-66)
2a: CATH_1q90D02 (D:67-159)
3a: CATH_1q90B00 (B:4-215)
4a: CATH_1q90C00 (C:80-206)
5a: CATH_1q90A02 (A:171-230)
6a: CATH_1q90A01 (A:1-170,A:231-248)
View:
Select:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome C Oxidase; Chain M
(30)
Homologous Superfamily
:
Cytochrome C Oxidase, chain M
(29)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
1a
1q90D01
D:11-66
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
plastocyanin oxidoreductase
(7)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
2a
1q90D02
D:67-159
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
3a
1q90B00
B:4-215
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
4a
1q90C00
C:80-206
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
5a
1q90A02
A:171-230
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Chlamydomonas reinhardtii. Organism_taxid: 3055. Strain: h6f5.
(1)
6a
1q90A01
A:1-170,A:231-248
[
close CATH info
]
Pfam Domains
(8, 8)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_1q90B01 (B:91-215)
2a: PFAM_Apocytochr_F_C_1q90A01 (A:167-286)
3a: PFAM_Rieske_1q90C01 (C:95-183)
4a: PFAM_CytB6_F_Fe_S_1q90R01 (R:34-71)
5a: PFAM_Cytochrom_B_C_1q90D01 (D:65-157)
6a: PFAM_PetG_1q90G01 (G:1-30)
7a: PFAM_PetL_1q90L01 (L:1-32)
8a: PFAM_PetM_1q90M01 (M:62-95)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
1a
Cytochrom_B_N_2-1q90B01
B:91-215
Clan
:
Hybrid
(58)
Family
:
Apocytochr_F_C
(5)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
2a
Apocytochr_F_C-1q90A01
A:167-286
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
3a
Rieske-1q90C01
C:95-183
Clan
:
no clan defined [family: CytB6-F_Fe-S]
(3)
Family
:
CytB6-F_Fe-S
(3)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
4a
CytB6-F_Fe-S-1q90R01
R:34-71
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
5a
Cytochrom_B_C-1q90D01
D:65-157
Clan
:
no clan defined [family: PetG]
(3)
Family
:
PetG
(3)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
6a
PetG-1q90G01
G:1-30
Clan
:
no clan defined [family: PetL]
(2)
Family
:
PetL
(2)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
7a
PetL-1q90L01
L:1-32
Clan
:
no clan defined [family: PetM]
(3)
Family
:
PetM
(3)
Chlamydomonas reinhardtii (Chlamydomonas smithii)
(1)
8a
PetM-1q90M01
M:62-95
[
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