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2E76
Biol. Unit 1
Info
Asym.Unit (186 KB)
Biol.Unit 1 (333 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CYTOCHROME B6F COMPLEX WITH TRIDECYL-STIGMATELLIN (TDS) FROM M.LAMINOSUS
Authors
:
W. A. Cramer, E. Yamashita, H. Zhang
Date
:
05 Jan 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.41
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (2x)
Keywords
:
Photosynthesis, Cytochrome F, Rieske Iron-Sulfur Protein, Heme Cn
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Yamashita, H. Zhang, W. A. Cramer
Structure Of The Cytochrome B(6)F Complex: Quinone Analogue Inhibitors As Ligands Of Heme C(N)
J. Mol. Biol. V. 370 39 2007
[
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Hetero Components
(8, 32)
Info
All Hetero Components
1a: BETA-CAROTENE (BCRa)
2a: CADMIUM ION (CDa)
3a: CHLOROPHYLL A (CLAa)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
5d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
6a: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCa)
6b: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCb)
7a: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO... (SQDa)
8a: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2... (TDSa)
8b: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2... (TDSb)
9a: UNDECYL-MALTOSIDE (UMQa)
9b: UNDECYL-MALTOSIDE (UMQb)
9c: UNDECYL-MALTOSIDE (UMQc)
9d: UNDECYL-MALTOSIDE (UMQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCR
2
Ligand/Ion
BETA-CAROTENE
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CLA
2
Ligand/Ion
CHLOROPHYLL A
4
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
HEM
8
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
OPC
4
Ligand/Ion
(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
7
SQD
2
Ligand/Ion
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
TDS
4
Ligand/Ion
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
9
UMQ
8
Ligand/Ion
UNDECYL-MALTOSIDE
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Sites
(17, 17)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:75 , HIS C:143 , HOH C:302
BINDING SITE FOR RESIDUE CD A 216
02
AC2
SOFTWARE
GLN A:47 , PHE A:48 , GLY A:51 , PHE A:52 , MET A:54 , ARG A:83 , HIS A:86 , ARG A:87 , PHE A:131 , GLY A:132 , GLY A:135 , TYR A:136 , LEU A:138 , PRO A:139 , HIS A:187 , PHE A:189
BINDING SITE FOR RESIDUE HEM A 301
03
AC3
SOFTWARE
TYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , MET A:97 , HIS A:100 , VAL A:101 , ARG A:103 , VAL A:104 , GLY A:109 , ARG A:114 , THR A:117 , TRP A:118 , GLY A:121 , VAL A:122 , LEU A:124 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:1106
BINDING SITE FOR RESIDUE HEM A 302
04
AC4
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , LEU A:41 , PHE A:203 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , HOH A:1106 , ASN B:25 , PHE B:40 , VAL B:43 , ILE B:44 , TDS B:1202
BINDING SITE FOR RESIDUE HEM A 303
05
AC5
SOFTWARE
MET A:92 , CYS B:50 , PRO C:37 , GLN C:38 , ALA E:5 , TYR F:7 , LEU G:5 , LEU G:9 , BCR G:101 , TRP H:8 , LEU H:12 , PHE H:15
BINDING SITE FOR RESIDUE OPC A 1002
06
AC6
SOFTWARE
MET A:73 , ASN A:74 , VAL A:76 , SER A:77 , PHE A:78 , TRP A:80 , HOH A:1105 , VAL B:52 , ASP C:251 , ARG C:254 , TRP C:257 , PHE C:261 , ALA D:34
BINDING SITE FOR RESIDUE UMQ A 1101
07
AC7
SOFTWARE
LEU A:12 , LEU A:17 , ASP A:20
BINDING SITE FOR RESIDUE UMQ A 1102
08
AC8
SOFTWARE
ASP A:6 , GLN A:15 , UMQ A:1104
BINDING SITE FOR RESIDUE UMQ A 1103
09
AC9
SOFTWARE
VAL A:21 , THR A:22 , UMQ A:1103 , TRP B:32 , SQD D:201
BINDING SITE FOR RESIDUE UMQ A 1104
10
BC1
SOFTWARE
ILE A:98 , TYR A:105 , TYR B:80 , PRO B:83 , VAL B:84 , ILE B:87 , VAL B:104 , LEU B:106 , LEU B:108 , ILE B:132 , PHE B:133 , GLY B:136 , THR B:140 , HOH B:211 , OPC B:1001
BINDING SITE FOR RESIDUE CLA B 201
11
BC2
SOFTWARE
TYR A:105 , LEU B:100 , GLU B:115 , ASN B:118 , ARG B:126 , PRO B:127 , VAL B:128 , ALA B:129 , CLA B:201
BINDING SITE FOR RESIDUE OPC B 1001
12
BC3
SOFTWARE
TYR A:136 , VAL A:143 , ALA A:147 , ILE A:150 , PRO A:155 , ILE B:75 , LEU B:76 , PRO B:77 , LEU B:81 , PHE B:85 , LEU B:88 , CYS D:128 , HIS D:129
BINDING SITE FOR RESIDUE TDS B 1201
13
BC4
SOFTWARE
ARG A:207 , HEM A:303 , LEU B:36 , PHE B:40 , PHE D:24
BINDING SITE FOR RESIDUE TDS B 1202
14
BC5
SOFTWARE
TYR C:1 , PRO C:2 , TRP C:4 , CYS C:22 , CYS C:25 , HIS C:26 , GLN C:60 , LEU C:70 , ASN C:71 , VAL C:72 , GLY C:73 , ALA C:74 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , ILE C:160 , TYR C:161
BINDING SITE FOR RESIDUE HEM C 301
15
BC6
SOFTWARE
CYS D:108 , HIS D:110 , LEU D:111 , GLY D:112 , CYS D:126 , CYS D:128 , HIS D:129 , GLY D:130 , SER D:131
BINDING SITE FOR RESIDUE FES D 200
16
BC7
SOFTWARE
UMQ A:1104 , TRP B:32 , PRO B:33 , LYS C:275 , VAL C:279 , ARG D:16 , ASN D:20 , LEU D:21 , GLY D:25
BINDING SITE FOR RESIDUE SQD D 201
17
BC8
SOFTWARE
ILE A:39 , OPC A:1002 , ILE F:16 , TRP F:20 , ALA G:16 , GLY G:19 , GLY G:20 , PHE H:15
BINDING SITE FOR RESIDUE BCR G 101
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (A:4-215)
2: CYTB_CTER (B:35-160)
3: RIESKE (D:61-162)
;
View:
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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_MASLA
4-215
2
A:4-215
2
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
PETD_MASLA
35-160
2
B:35-160
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_MASLA
61-162
2
D:61-162
[
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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
(8, 8)
Info
All SCOP Domains
1a: SCOP_d2e76d1 (D:46-179)
2a: SCOP_d2e76b1 (B:1-160)
3a: SCOP_d2e76a1 (A:13-214)
4a: SCOP_d2e76d2 (D:12-45)
5a: SCOP_d2e76g1 (G:9-35)
6a: SCOP_d2e76e1 (E:1-32)
7a: SCOP_d2e76f1 (F:1-32)
8a: SCOP_d2e76h1 (H:3-29)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
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)
Mastigocladus laminosus [TaxId: 83541]
(4)
1a
d2e76d1
D:46-179
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)
Mastigocladus laminosus [TaxId: 83541]
(7)
2a
d2e76b1
B:1-160
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)
Mastigocladus laminosus [TaxId: 83541]
(4)
3a
d2e76a1
A:13-214
Fold
:
Single transmembrane helix
(568)
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
ISP transmembrane anchor
(32)
Protein domain
:
ISP subunit from the cytochrome b6f complex, transmembrane anchor
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
4a
d2e76d2
D:12-45
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)
Mastigocladus laminosus [TaxId: 83541]
(4)
5a
d2e76g1
G:9-35
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)
Mastigocladus laminosus [TaxId: 83541]
(6)
6a
d2e76e1
E:1-32
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)
Mastigocladus laminosus [TaxId: 83541]
(7)
7a
d2e76f1
F:1-32
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)
Mastigocladus laminosus [TaxId: 83541]
(4)
8a
d2e76h1
H:3-29
[
close SCOP info
]
CATH Domains
(7, 7)
Info
all CATH domains
1a: CATH_2e76B01 (B:9-66)
2a: CATH_2e76B02 (B:67-160)
3a: CATH_2e76A00 (A:1-215)
4a: CATH_2e76C03 (C:255-288)
5a: CATH_2e76D02 (D:48-179)
6a: CATH_2e76C02 (C:172-233)
7a: CATH_2e76C01 (C:1-171,C:234-254)
View:
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(
)
(
)
Architectures
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)
(
)
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)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
1a
2e76B01
B:9-66
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
plastocyanin oxidoreductase
(7)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
2a
2e76B02
B:67-160
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
3a
2e76A00
A:1-215
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(6)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
4a
2e76C03
C:255-288
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
5a
2e76D02
D:48-179
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
6a
2e76C02
C:172-233
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
7a
2e76C01
C:1-171,C:234-254
[
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Pfam Domains
(0, 0)
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all PFAM domains
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