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1NTM
Biol. Unit 1
Info
Asym.Unit (357 KB)
Biol.Unit 1 (681 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MITOCHONDRIAL CYTOCHROME BC1 COMPLEX AT 2.4 ANGSTROM
Authors
:
X. Gao, X. Wen, L. Esser, B. Quinn, L. Yu, C. Yu, D. Xia
Date
:
30 Jan 03 (Deposition) - 07 Oct 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K (2x)
Keywords
:
Bc1, Qcr, Membrane Protein, Proton Translocation, Electron Transfer, Protease, Mpp, Mitochondrial Processing Peptidase, Cytochrome C1, Cytochrome B, Rieske, Iron Sulfur Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Gao, X. Wen, L. Esser, B. Quinn, L. Yu, C. -A. Yu, D. Xia
Structural Basis For The Quinone Reduction In The Bc(1) Complex: A Comparative Analysis Of Crystal Structures Of Mitochondrial Cytochrome Bc(1) With Bound Substrate And Inhibitors At The Q(I) Site
Biochemistry V. 42 9067 2003
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN C:44 , ILE C:45 , GLY C:48 , LEU C:49 , TYR C:55 , ARG C:80 , HIS C:83 , ALA C:84 , ALA C:87 , PHE C:90 , THR C:126 , GLY C:130 , TYR C:131 , LEU C:133 , PRO C:134 , PHE C:179 , HIS C:182 , PHE C:183 , PRO C:186
BINDING SITE FOR RESIDUE HEM C 381
2
AC2
SOFTWARE
TRP C:31 , GLY C:34 , LEU C:37 , HIS C:97 , VAL C:98 , ARG C:100 , SER C:106 , TRP C:113 , GLY C:116 , VAL C:117 , LEU C:119 , HIS C:196 , SER C:205 , ASN C:206 , HOH C:1044
BINDING SITE FOR RESIDUE HEM C 382
3
AC3
SOFTWARE
CYS D:37 , CYS D:40 , HIS D:41 , ASN D:105 , LEU D:109 , PRO D:110 , PRO D:111 , ARG D:120 , TYR D:126 , ILE D:158 , GLY D:159 , MET D:160 , PRO D:163 , ILE D:164
BINDING SITE FOR RESIDUE HEM D 242
4
AC4
SOFTWARE
CYS E:139 , HIS E:141 , LEU E:142 , CYS E:158 , CYS E:160 , HIS E:161 , SER E:163
BINDING SITE FOR RESIDUE FES E 197
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_QCR2_BOVIN_001 (T27R, chain B, )
2: VAR_CYB_BOVIN_001 (F90V, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_QCR2_BOVIN_001
*
T
41
R
QCR2_BOVIN
---
---
B
T
27
R
2
UniProt
VAR_CYB_BOVIN_001
*
F
90
V
CYB_BOVIN
---
---
C
F
90
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: INSULINASE (B:54-77)
2: CYTC (D:24-125)
3: RIESKE (E:109-194)
4: CYTB_CTER (C:210-379)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INSULINASE
PS00143
Insulinase family, zinc-binding region signature.
QCR2_BOVIN
68-91
2
B:54-77
2
CYTC
PS51007
Cytochrome c family profile.
CY1_BOVIN
108-209
2
D:24-125
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_BOVIN
187-272
2
E:109-194
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_BOVIN
210-379
2
C:210-379
[
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Exons
(0, 0)
Info
All Exons
View:
Select:
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
(14, 16)
Info
All SCOP Domains
01a: SCOP_d1ntmd1 (D:1-195)
02a: SCOP_d1ntme1 (E:70-196)
03a: SCOP_d1ntma1 (A:1-233)
03b: SCOP_d1ntma2 (A:234-446)
04a: SCOP_d1ntmb1 (B:17-235)
04b: SCOP_d1ntmb2 (B:236-439)
05a: SCOP_d1ntmi_ (I:)
06a: SCOP_d1ntmf_ (F:)
07a: SCOP_d1ntmc1 (C:261-379)
08a: SCOP_d1ntmc2 (C:2-260)
09a: SCOP_d1ntmh_ (H:)
10a: SCOP_d1ntmd2 (D:196-241)
11a: SCOP_d1ntme2 (E:1-69)
12a: SCOP_d1ntmj_ (J:)
13a: SCOP_d1ntmk_ (K:)
14a: SCOP_d1ntmg_ (G:)
View:
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Classes
(
)
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Folds
(
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Superfamilies
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
Cytochrome bc1 domain
(36)
Protein domain
:
Cytochrome bc1 domain
(27)
Cow (Bos taurus) [TaxId: 9913]
(17)
01a
d1ntmd1
D:1-195
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
(28)
Cow (Bos taurus) [TaxId: 9913]
(18)
02a
d1ntme1
E:70-196
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LuxS/MPP-like metallohydrolase
(89)
Superfamily
:
LuxS/MPP-like metallohydrolase
(89)
Family
:
MPP-like
(65)
Protein domain
:
Cytochrome bc1 core subunit 1
(27)
Cow (Bos taurus) [TaxId: 9913]
(17)
03a
d1ntma1
A:1-233
03b
d1ntma2
A:234-446
Protein domain
:
Cytochrome bc1 core subunit 2
(27)
Cow (Bos taurus) [TaxId: 9913]
(17)
04a
d1ntmb1
B:17-235
04b
d1ntmb2
B:236-439
Fold
:
Non-globular alpha+beta subunits of globular proteins
(21)
Superfamily
:
Non-globular alpha+beta subunits of globular proteins
(21)
Family
:
Ubiquinol-cytochrome c reductase 8 kDa protein
(17)
Protein domain
:
Ubiquinol-cytochrome c reductase 8 kDa protein
(14)
Cow (Bos taurus) [TaxId: 9913]
(14)
05a
d1ntmi_
I:
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(21)
Cow (Bos taurus) [TaxId: 9913]
(14)
06a
d1ntmf_
F:
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
:
Mitochondrial cytochrome b subunit, C-terminal domain
(30)
Cow (Bos taurus) [TaxId: 9913]
(17)
07a
d1ntmc1
C:261-379
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
:
Mitochondrial cytochrome b subunit, N-terminal domain
(30)
Cow (Bos taurus) [TaxId: 9913]
(17)
08a
d1ntmc2
C:2-260
Fold
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(20)
Cow (Bos taurus) [TaxId: 9913]
(12)
09a
d1ntmh_
H:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(36)
Family
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(27)
Protein domain
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(27)
Cow (Bos taurus) [TaxId: 9913]
(17)
10a
d1ntmd2
D:196-241
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
ISP transmembrane anchor
(32)
Protein domain
:
Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
(27)
Cow (Bos taurus) [TaxId: 9913]
(17)
11a
d1ntme2
E:1-69
Superfamily
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(25)
Cow (Bos taurus) [TaxId: 9913]
(18)
12a
d1ntmj_
J:
Superfamily
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(15)
Family
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(15)
Protein domain
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(12)
Cow (Bos taurus) [TaxId: 9913]
(12)
13a
d1ntmk_
K:
Superfamily
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(28)
Cow (Bos taurus) [TaxId: 9913]
(18)
14a
d1ntmg_
G:
[
close SCOP info
]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_1ntmA02 (A:239-442)
01b: CATH_1ntmB01 (B:17-227)
01c: CATH_1ntmB02 (B:239-439)
01d: CATH_1ntmA01 (A:14-227)
02a: CATH_1ntmD02 (D:1-196)
03a: CATH_1ntmF00 (F:6-110)
04a: CATH_1ntmH00 (H:12-78)
05a: CATH_1ntmC00 (C:2-379)
06a: CATH_1ntmD01 (D:197-241)
07a: CATH_1ntmG00 (G:1-75)
08a: CATH_1ntmK00 (K:1-51)
09a: CATH_1ntmJ00 (J:1-60)
10a: CATH_1ntmE01 (E:2-65)
11a: CATH_1ntmE02 (E:66-196)
12a: CATH_1ntmI00 (I:1-57)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Cattle (Bos taurus)
(17)
01a
1ntmA02
A:239-442
01b
1ntmB01
B:17-227
01c
1ntmB02
B:239-439
01d
1ntmA01
A:14-227
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Cattle (Bos taurus)
(18)
02a
1ntmD02
D:1-196
Topology
:
Cytochrome Bc1 Complex; Chain F
(39)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain F
(39)
Cattle (Bos taurus)
(17)
03a
1ntmF00
F:6-110
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.20, no name defined]
(39)
Cattle (Bos taurus)
(17)
04a
1ntmH00
H:12-78
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Cattle (Bos taurus)
(17)
05a
1ntmC00
C:2-379
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.100, no name defined]
(56)
Cattle (Bos taurus)
(17)
06a
1ntmD01
D:197-241
Homologous Superfamily
:
[code=1.20.5.210, no name defined]
(39)
Cattle (Bos taurus)
(17)
07a
1ntmG00
G:1-75
Homologous Superfamily
:
[code=1.20.5.220, no name defined]
(20)
Cattle (Bos taurus)
(14)
08a
1ntmK00
K:1-51
Homologous Superfamily
:
[code=1.20.5.260, no name defined]
(39)
Cattle (Bos taurus)
(17)
09a
1ntmJ00
J:1-60
Homologous Superfamily
:
[code=1.20.5.270, no name defined]
(39)
Cattle (Bos taurus)
(17)
10a
1ntmE01
E:2-65
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Cattle (Bos taurus)
(18)
11a
1ntmE02
E:66-196
Architecture
:
Ribbon
(789)
Topology
:
Cytochrome Bc1 Complex; Chain I
(29)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain I
(29)
Cattle (Bos taurus)
(17)
12a
1ntmI00
I:1-57
[
close CATH info
]
Pfam Domains
(13, 15)
Info
all PFAM domains
01a: PFAM_Cytochrom_B_N_2_1ntmC01 (C:88-253)
02a: PFAM_Cytochrom_C1_1ntmD01 (D:12-230)
03a: PFAM_Rieske_1ntmE01 (E:77-188)
04a: PFAM_Peptidase_M16_1ntmA01 (A:24-171)
04b: PFAM_Peptidase_M16_1ntmB01 (B:34-180)
05a: PFAM_Peptidase_M16_C_1ntmA02 (A:176-361)
05b: PFAM_Peptidase_M16_C_1ntmB02 (B:185-364)
06a: PFAM_UcrQ_1ntmG01 (G:1-75)
07a: PFAM_Cytochrom_B_C_1ntmC02 (C:258-359)
08a: PFAM_UCR_14kD_1ntmF01 (F:6-106)
09a: PFAM_UCR_6_4kD_1ntmK01 (K:1-51)
10a: PFAM_UCR_TM_1ntmE02 (E:1-67)
11a: PFAM_UCR_UQCRX_QCR9_1ntmJ01 (J:6-60)
12a: PFAM_UCR_hinge_1ntmH01 (H:14-78)
13a: PFAM_Ubiq_Cytc_red_N_1ntmI01 (I:1-57)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Bos taurus (Bovine)
(13)
01a
Cytochrom_B_N_2-1ntmC01
C:88-253
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Bos taurus (Bovine)
(13)
02a
Cytochrom_C1-1ntmD01
D:12-230
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Bos taurus (Bovine)
(13)
03a
Rieske-1ntmE01
E:77-188
Clan
:
Peptidase_ME
(35)
Family
:
Peptidase_M16
(29)
Bos taurus (Bovine)
(13)
04a
Peptidase_M16-1ntmA01
A:24-171
04b
Peptidase_M16-1ntmB01
B:34-180
Family
:
Peptidase_M16_C
(29)
Bos taurus (Bovine)
(13)
05a
Peptidase_M16_C-1ntmA02
A:176-361
05b
Peptidase_M16_C-1ntmB02
B:185-364
Clan
:
UcrQ-like
(20)
Family
:
UcrQ
(20)
Bos taurus (Bovine)
(13)
06a
UcrQ-1ntmG01
G:1-75
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Bos taurus (Bovine)
(13)
07a
Cytochrom_B_C-1ntmC02
C:258-359
Clan
:
no clan defined [family: UCR_14kD]
(20)
Family
:
UCR_14kD
(20)
Bos taurus (Bovine)
(13)
08a
UCR_14kD-1ntmF01
F:6-106
Clan
:
no clan defined [family: UCR_6-4kD]
(11)
Family
:
UCR_6-4kD
(11)
Bos taurus (Bovine)
(11)
09a
UCR_6-4kD-1ntmK01
K:1-51
Clan
:
no clan defined [family: UCR_TM]
(20)
Family
:
UCR_TM
(20)
Bos taurus (Bovine)
(13)
10a
UCR_TM-1ntmE02
E:1-67
Clan
:
no clan defined [family: UCR_UQCRX_QCR9]
(20)
Family
:
UCR_UQCRX_QCR9
(20)
Bos taurus (Bovine)
(13)
11a
UCR_UQCRX_QCR9-1ntmJ01
J:6-60
Clan
:
no clan defined [family: UCR_hinge]
(20)
Family
:
UCR_hinge
(20)
Bos taurus (Bovine)
(13)
12a
UCR_hinge-1ntmH01
H:14-78
Clan
:
no clan defined [family: Ubiq-Cytc-red_N]
(17)
Family
:
Ubiq-Cytc-red_N
(17)
Bos taurus (Bovine)
(13)
13a
Ubiq-Cytc-red_N-1ntmI01
I:1-57
[
close Pfam info
]
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (357 KB)
Header - Asym.Unit
Biol.Unit 1 (681 KB)
Header - Biol.Unit 1
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