[English] 日本語
Yorodumi
- PDB-4d6t: Cytochrome bc1 bound to the 4(1H)-pyridone GW844520 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d6t
TitleCytochrome bc1 bound to the 4(1H)-pyridone GW844520
Components
  • (CYTOCHROME B-C1 COMPLEX SUBUNIT ...) x 9
  • CYTOCHROME B
  • CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
KeywordsELECTRON TRANSPORT / CYTOCHROME BC1 / PYRIDONE / MEMBRANE PROTEIN / COMPLEX
Function / homology
Function and homology information


Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / : / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 ...Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4X9 / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 ...Chem-4X9 / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsCapper, M.J. / O'Neill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome Bc1.
Authors: Capper, M.J. / O'Neill, P.M. / Fisher, N. / Strange, R.W. / Moss, D. / Ward, S.A. / Berry, N.G. / Lawrenson, A.S. / Hasnain, S.S. / Biagini, G.A. / Antonyuk, S.V.
History
DepositionNov 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
B: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
C: CYTOCHROME B
D: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
E: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
F: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
G: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
H: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
I: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
J: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
N: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
O: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
P: CYTOCHROME B
Q: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
R: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
S: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
T: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
U: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
V: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
W: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)561,76849
Polymers547,10020
Non-polymers14,66729
Water00
1
A: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
B: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
C: CYTOCHROME B
D: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
E: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
F: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
G: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
H: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
I: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
J: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,80424
Polymers273,55710
Non-polymers7,24714
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
N: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
O: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
P: CYTOCHROME B
Q: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
R: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
S: CYTOCHROME B-C1 COMPLEX SUBUNIT 7
T: CYTOCHROME B-C1 COMPLEX SUBUNIT 8
U: CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
V: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
W: CYTOCHROME B-C1 COMPLEX SUBUNIT 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,96425
Polymers273,54410
Non-polymers7,42015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.896, 129.896, 722.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21N
12B
22O
13C
23P
14D
24Q
15E
25R
16F
26S
17G
27T
18H
28U
19I
29V
110J
210W

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA2 - 44536 - 479
21ALAALAARGARGNK2 - 44536 - 479
12PROPROGLUGLUBB21 - 43835 - 452
22PROPROGLUGLUOL21 - 43835 - 452
13LEULEULYSLYSCC10 - 37810 - 378
23LEULEULYSLYSPM10 - 37810 - 378
14ASPASPPROPRODD2 - 24026 - 264
24ASPASPPROPROQN2 - 24026 - 264
15SERSERSERSEREE1 - 7279 - 150
25SERSERSERSERRO1 - 7279 - 150
16TRPTRPALAALAFF12 - 10813 - 109
26TRPTRPALAALASP12 - 10813 - 109
17ARGARGPROPROGG2 - 743 - 75
27ARGARGPROPROTQ2 - 743 - 75
18LEULEUSERSERHH13 - 7626 - 89
28LEULEUSERSERUR13 - 7626 - 89
19LEULEUVALVALII64 - 7664 - 76
29VALVALVALVALVS64 - 7664 - 76
110PROPROTYRTYRJJ3 - 594 - 60
210PROPROTYRTYRWT3 - 594 - 60

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.04838, 0.156426, -0.986504), (0.153975, -0.974687, -0.162104), (-0.98689, -0.159739, 0.02307)48.14476, 28.70022, 51.05802
3given(1), (1), (1)
4given(-0.048608, 0.157809, -0.986273), (0.157234, -0.973919, -0.163582), (-0.986364, -0.163027, 0.022528)48.17714, 28.44029, 51.13189
5given(1), (1), (1)
6given(-0.057766, 0.143855, -0.987911), (0.155616, -0.97617, -0.151245), (-0.986127, -0.162471, 0.034004)49.16862, 28.68466, 51.38012
7given(1), (1), (1)
8given(-0.058711, 0.144368, -0.987781), (0.160021, -0.975331, -0.15206), (-0.985366, -0.166994, 0.03416)49.18262, 28.6318, 51.60391
9given(1), (1), (1)
10given(-0.059782, 0.145979, -0.98748), (0.15591, -0.975743, -0.153682), (-0.98596, -0.163146, 0.035572)49.1147, 28.71913, 51.46771
11given(1), (1), (1)
12given(-0.060541, 0.134082, -0.989119), (0.164573, -0.976034, -0.142381), (-0.984505, -0.171402, 0.037024)49.29145, 28.77032, 51.66734
13given(1), (1), (1)
14given(-0.065678, 0.152337, -0.986144), (0.160908, -0.973727, -0.161135), (-0.984782, -0.169262, 0.03944)49.01892, 28.30037, 51.72233
15given(1), (1), (1)
16given(-0.037816, 0.128234, -0.991023), (0.177894, -0.975027, -0.132953), (-0.983323, -0.181325, 0.014059)49.92825, 28.83717, 52.67122
17given(1), (1), (1)
18given(-0.227653, 0.102518, -0.968331), (0.0732, -0.989827, -0.122003), (-0.970987, -0.098656, 0.217833)67.69967, 37.74205, 49.65176
19given(1), (1), (1)
20given(-0.060552, 0.155257, -0.986017), (0.144845, -0.976007, -0.162576), (-0.9876, -0.152664, 0.036611)48.75871, 29.05512, 50.88627

-
Components

-
CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 9 types, 16 molecules ANBEIRFSGTHUJWOV

#1: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL / COMPLEX III SUBUNIT 1 / CORE PROTEIN I / UBIQUINOL-CYTOCHROME -C REDUCTASE COMPLEX CORE PROTEIN 1


Mass: 52796.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P31800
#2: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL / COMPLEX III SUBUNIT 2 / CORE PROTEIN II / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P23004
#5: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / ...COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / COMPLEX III SUBUNIT IX / UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN


Mass: 29586.842 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13272
#6: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 7 / COMPLEX III SUBUNIT 7 / COMPLEX III SUBUNIT VII / QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ...COMPLEX III SUBUNIT 7 / COMPLEX III SUBUNIT VII / QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN


Mass: 13502.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00129
#7: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 8 / COMPLEX III SUBUNIT 8 / COMPLEX III SUBUNIT VIII / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 9.5 KDA ...COMPLEX III SUBUNIT 8 / COMPLEX III SUBUNIT VIII / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 9.5 KDA PROTEIN / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C


Mass: 9737.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13271
#8: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL / COMPLEX III SUBUNIT 6 / COMPLEX III SUBUNIT VIII / CYTOCHROME C1 NON-HEME 11 KDA PROTEIN / ...COMPLEX III SUBUNIT 6 / COMPLEX III SUBUNIT VIII / CYTOCHROME C1 NON-HEME 11 KDA PROTEIN / MITOCHONDRIAL HINGE PROTEIN / UBIQUINO L- CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN


Mass: 10638.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00126
#9: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 9 / COMPLEX III SUBUNIT 9 / COMPLEX III SUBUNIT X / CYTOCHROME C1 NON-HEME 7 KDA PROTEIN / UBIQUINOL- ...COMPLEX III SUBUNIT 9 / COMPLEX III SUBUNIT X / CYTOCHROME C1 NON-HEME 7 KDA PROTEIN / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN


Mass: 7469.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00130
#10: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL / COMPLEX III SUBUNIT 2 / CORE PROTEIN II / UBIQUINOL-CYTOCHROME -C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 48204.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P23004
#11: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / ...COMPLEX III SUBUNIT 5 / CYTOCHROME B-C1 COMPLEX SUBUNIT 5 / RIESKE IRON-SULFUR PROTEIN / RISP / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / COMPLEX III SUBUNIT IX / UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN


Mass: 29572.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase

-
Protein , 2 types, 4 molecules CPDQ

#3: Protein CYTOCHROME B / COMPLEX III SUBUNIT 3 / COMPLEX III SUBUNIT III / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / UBIQUINOL- ...COMPLEX III SUBUNIT 3 / COMPLEX III SUBUNIT III / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME B SUBUNIT


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00157
#4: Protein CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL / COMPLEX III SUBUNIT 4 / COMPLEX III SUBUNIT IV / CYTOCHROME B -C1 COMPLEX SUBUNIT 4 / UBIQUINOL- ...COMPLEX III SUBUNIT 4 / COMPLEX III SUBUNIT IV / CYTOCHROME B -C1 COMPLEX SUBUNIT 4 / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX TOCCYHROME C1 SUBUNIT / CYTOCHROME C-1


Mass: 29414.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P00125

-
Non-polymers , 8 types, 29 molecules

#12: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-4X9 / 3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol


Mass: 409.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15ClF3NO3
#14: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#15: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#16: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#17: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#19: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 38.01 % / Description: NONE
Crystal growpH: 6.8
Details: 50 MM POTASSIUM PHOSPHATE BUFFER PH 6.8, 12% P4000, 1.4% HECAMEG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2013 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.56→42.1 Å / Num. obs: 81351 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 7
Reflection shellResolution: 3.55→3.68 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPJ

1ppj


Resolution: 3.57→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25156 3953 4.9 %RANDOM
Rwork0.206 ---
obs0.2083 77417 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 133.886 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.69 Å20 Å2
2--1.37 Å20 Å2
3----4.45 Å2
Refinement stepCycle: LAST / Resolution: 3.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30326 0 725 0 31051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01931812
X-RAY DIFFRACTIONr_bond_other_d00.0230188
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.98143214
X-RAY DIFFRACTIONr_angle_other_deg3.635369363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46753839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38323.3911386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.625155128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81715207
X-RAY DIFFRACTIONr_chiral_restr0.0810.24706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02135568
X-RAY DIFFRACTIONr_gen_planes_other0.0110.027437
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.0213.33415419
X-RAY DIFFRACTIONr_mcbond_other8.0213.33415418
X-RAY DIFFRACTIONr_mcangle_it12.52119.98619237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.56713.69616393
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A549tight positional0.030.05
11A549tight positional0.030.05
12N3949tight thermal12.520.5
12N3949tight thermal12.520.5
21B3661tight thermal11.510.5
22O3661tight thermal11.510.5
31C3436tight thermal8.630.5
32P3436tight thermal8.630.5
41D2176tight thermal11.770.5
42Q2176tight thermal11.770.5
51E627tight thermal11.170.5
52R627tight thermal11.170.5
61F988tight thermal9.270.5
62S988tight thermal9.270.5
71G715tight thermal9.940.5
72T715tight thermal9.940.5
81H608tight thermal20.590.5
82U608tight thermal20.590.5
91I101tight thermal22.490.5
92V101tight thermal22.490.5
101J549tight thermal10.620.5
102W549tight thermal10.620.5
LS refinement shellResolution: 3.567→3.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 268 -
Rwork0.312 5651 -
obs--98.63 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more