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2ZT9
Asym. Unit
Info
Asym.Unit (174 KB)
Biol.Unit 1 (317 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CYTOCHROME B6F COMPLEX FROM NOSTOC SP. PCC 7120
Authors
:
W. A. Craner, Baniulis D. , Yamashita E.
Date
:
27 Sep 08 (Deposition) - 10 Feb 09 (Release) - 11 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
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 B6F Complex, Heme B, 2Fe-2S Protein, Cytochrome F
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Baniulis, E. Yamashita, J. P. Whitelegge, A. I. Zatsman, M. P. Hendrich, S. S. Hasan, C. M. Ryan, W. A. Cramer
Structure-Function, Stability, And Chemical Modification Of The Cyanobacterial Cytochrome B6F Complex From Nostoc Sp. Pcc 7120
J. Biol. Chem. V. 284 9861 2009
[
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Hetero Components
(7, 13)
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: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCa)
5b: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCb)
6a: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO... (SQDa)
7a: UNDECYL-MALTOSIDE (UMQa)
7b: UNDECYL-MALTOSIDE (UMQb)
7c: UNDECYL-MALTOSIDE (UMQc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCR
1
Ligand/Ion
BETA-CAROTENE
2
CLA
1
Ligand/Ion
CHLOROPHYLL A
3
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
OPC
2
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
6
SQD
1
Ligand/Ion
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
7
UMQ
3
Ligand/Ion
UNDECYL-MALTOSIDE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:47 , PHE A:48 , GLY A:51 , MET A:54 , ARG A:83 , HIS A:86 , ARG A:87 , ALA A:90 , MET A:93 , PHE A:131 , GLY A:135 , PRO A:139 , HIS A:187 , PHE A:189
BINDING SITE FOR RESIDUE HEM A 301
02
AC2
SOFTWARE
TYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , LEU A:41 , MET A:93 , HIS A:100 , VAL A:101 , ARG A:103 , VAL A:104 , GLY A:109 , TRP A:118 , GLY A:121 , VAL A:122 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:401
BINDING SITE FOR RESIDUE HEM A 302
03
AC3
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , LEU A:41 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , HOH A:401 , VAL B:39 , PHE B:40 , ARG H:26
BINDING SITE FOR RESIDUE HEM A 303
04
AC4
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 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , VAL C:160 , TYR C:161 , PRO C:162
BINDING SITE FOR RESIDUE HEM C 301
05
AC5
SOFTWARE
CYS D:108 , HIS D:110 , LEU D:111 , CYS D:126 , HIS D:129 , SER D:131
BINDING SITE FOR RESIDUE FES D 200
06
AC6
SOFTWARE
ILE A:98 , PHE A:102 , TYR A:105 , TYR B:80 , VAL B:84 , ILE B:87 , MET B:101 , PHE B:133 , GLY B:136 , THR B:140 , OPC B:202 , HOH B:211
BINDING SITE FOR RESIDUE CLA B 201
07
AC7
SOFTWARE
ILE A:32 , PHE A:33 , ILE A:39 , LEU A:99 , ILE F:16 , TRP F:20 , VAL G:16 , ALA G:19 , GLY G:20 , TYR G:23 , PHE H:15 , ILE H:19 , OPC H:30
BINDING SITE FOR RESIDUE BCR G 101
08
AC8
SOFTWARE
SER B:103 , VAL B:111 , ILE B:114 , GLU B:115 , ASN B:118 , ARG B:126 , VAL B:128 , ALA B:129 , CLA B:201
BINDING SITE FOR RESIDUE OPC B 202
09
AC9
SOFTWARE
MET A:92 , PRO C:37 , GLN C:38 , TYR E:7 , ILE E:8 , SER F:12 , LEU G:5 , BCR G:101 , MET H:1 , TRP H:8 , LEU H:12
BINDING SITE FOR RESIDUE OPC H 30
10
BC1
SOFTWARE
GLU A:75 , VAL A:76 , ASN A:77 , PHE A:78 , TRP A:80 , ASN C:253 , ARG C:254 , TRP C:257
BINDING SITE FOR RESIDUE UMQ A 304
11
BC2
SOFTWARE
ASN A:3 , TYR A:5 , UMQ A:306 , SQD B:203
BINDING SITE FOR RESIDUE UMQ A 305
12
BC3
SOFTWARE
GLN A:15 , ALA A:18 , GLU A:19 , THR A:22 , UMQ A:305 , TRP B:32 , SQD B:203 , ASN C:288
BINDING SITE FOR RESIDUE UMQ A 306
13
BC4
SOFTWARE
UMQ A:305 , UMQ A:306 , TRP B:32 , PRO B:33 , LYS C:275 , ARG D:16 , ASN D:20 , THR D:28
BINDING SITE FOR RESIDUE SQD B 203
[
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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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (A:4-215)
2: CYTB_CTER (B:35-160)
3: RIESKE (D:61-162)
;
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_NOSS1
4-215
1
A:4-215
2
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
PETD_NOSS1
35-160
1
B:35-160
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRIA_NOSS1
61-162
1
D:61-162
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d2zt9b_ (B:)
2a: SCOP_d2zt9a_ (A:)
3a: SCOP_d2zt9f_ (F:)
4a: SCOP_d2zt9h_ (H:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
automated matches
(1)
Nostoc sp. [TaxId: 103690]
(1)
1a
d2zt9b_
B:
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
:
automated matches
(11)
Nostoc sp. [TaxId: 103690]
(1)
2a
d2zt9a_
A:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
PetM subunit of the cytochrome b6f complex
(9)
Family
:
PetM subunit of the cytochrome b6f complex
(9)
Protein domain
:
automated matches
(1)
Nostoc sp. [TaxId: 103690]
(1)
3a
d2zt9f_
F:
Superfamily
:
PetN subunit of the cytochrome b6f complex
(9)
Family
:
PetN subunit of the cytochrome b6f complex
(9)
Protein domain
:
automated matches
(4)
Nostoc sp. [TaxId: 103690]
(1)
4a
d2zt9h_
H:
[
close SCOP info
]
CATH Domains
(7, 7)
Info
all CATH domains
1a: CATH_2zt9B01 (B:9-66)
2a: CATH_2zt9B02 (B:67-160)
3a: CATH_2zt9A00 (A:1-215)
4a: CATH_2zt9C03 (C:255-289)
5a: CATH_2zt9D02 (D:48-179)
6a: CATH_2zt9C02 (C:172-233)
7a: CATH_2zt9C01 (C:1-171,C:234-254)
View:
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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)
Pcc 7120 (Nostoc sp)
(1)
1a
2zt9B01
B:9-66
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
plastocyanin oxidoreductase
(7)
Pcc 7120 (Nostoc sp)
(1)
2a
2zt9B02
B:67-160
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Pcc 7120 (Nostoc sp)
(1)
3a
2zt9A00
A:1-215
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(6)
Pcc 7120 (Nostoc sp)
(1)
4a
2zt9C03
C:255-289
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Pcc 7120 (Nostoc sp)
(1)
5a
2zt9D02
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)
Pcc 7120 (Nostoc sp)
(1)
6a
2zt9C02
C:172-233
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Pcc 7120 (Nostoc sp)
(1)
7a
2zt9C01
C:1-171,C:234-254
[
close CATH info
]
Pfam Domains
(9, 9)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_2zt9A01 (A:91-215)
2a: PFAM_Apocytochr_F_C_2zt9C01 (C:168-289)
3a: PFAM_Rieske_2zt9D01 (D:67-158)
4a: PFAM_CytB6_F_Fe_S_2zt9D02 (D:9-46)
5a: PFAM_Cytochrom_B_C_2zt9B01 (B:65-158)
6a: PFAM_PetG_2zt9G01 (G:1-37)
7a: PFAM_PetL_2zt9E01 (E:1-31)
8a: PFAM_PetM_2zt9F01 (F:3-32)
9a: PFAM_PetN_2zt9H01 (H:1-29)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
1a
Cytochrom_B_N_2-2zt9A01
A:91-215
Clan
:
Hybrid
(58)
Family
:
Apocytochr_F_C
(5)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(2)
2a
Apocytochr_F_C-2zt9C01
C:168-289
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
3a
Rieske-2zt9D01
D:67-158
Clan
:
no clan defined [family: CytB6-F_Fe-S]
(3)
Family
:
CytB6-F_Fe-S
(3)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
4a
CytB6-F_Fe-S-2zt9D02
D:9-46
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
5a
Cytochrom_B_C-2zt9B01
B:65-158
Clan
:
no clan defined [family: PetG]
(3)
Family
:
PetG
(3)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
6a
PetG-2zt9G01
G:1-37
Clan
:
no clan defined [family: PetL]
(2)
Family
:
PetL
(2)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
7a
PetL-2zt9E01
E:1-31
Clan
:
no clan defined [family: PetM]
(3)
Family
:
PetM
(3)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
8a
PetM-2zt9F01
F:3-32
Clan
:
no clan defined [family: PetN]
(2)
Family
:
PetN
(2)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
9a
PetN-2zt9H01
H:1-29
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