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- PDB-3o20: Electron transfer complexes:experimental mapping of the Redox-dep... -

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Basic information

Entry
Database: PDB / ID: 3o20
TitleElectron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / globular protein / electron carrier / MITOCHONDRIAL RESPIRATION / Electron trasport chain
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / lipid binding / apoptotic process / heme binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / NITRATE ION / Cytochrome c
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDe March, M. / De Zorzi, R. / Casini, A. / Messori, L. / Geremia, S. / Demitri, N. / Gabbiani, C. / Guerri, A.
Citation
Journal: J. Inorg. Biochem. / Year: 2014
Title: Nitrate as a probe of cytochrome c surface: crystallographic identification of crucial "hot spots" for protein-protein recognition.
Authors: De March, M. / Demitri, N. / De Zorzi, R. / Casini, A. / Gabbiani, C. / Guerri, A. / Messori, L. / Geremia, S.
#1: Journal: Biochemistry / Year: 2007
Title: Three-dimensional structure of the respiratory chain supercomplex I1III2IV1 from bovine heart mitochondria.
Authors: Eva Schäfer / Norbert A Dencher / Janet Vonck / David N Parcej /
Abstract: The respiratory chain complexes can arrange into multienzyme assemblies, so-called supercomplexes. We present the first 3D map of a respiratory chain supercomplex. It was determined by random conical ...The respiratory chain complexes can arrange into multienzyme assemblies, so-called supercomplexes. We present the first 3D map of a respiratory chain supercomplex. It was determined by random conical tilt electron microscopy analysis of a bovine supercomplex consisting of complex I, dimeric complex III, and complex IV (I1III2IV1). Within this 3D map the positions and orientations of all the individual complexes in the supercomplex were determined unambiguously. Furthermore, the ubiquinone and cytochrome c binding sites of each complex in the supercomplex could be located. The mobile electron carrier binding site of each complex was found to be in proximity to the binding site of the succeeding complex in the respiratory chain. This provides structural evidence for direct substrate channeling in the supercomplex assembly with short diffusion distances for the mobile electron carriers.
#2: Journal: J. Biol. Chem. / Year: 2007
Title: A structural model of the cytochrome C reductase/oxidase supercomplex from yeast mitochondria.
Authors: Heinemeyer, J. / Braun, H.P. / Boekema, E.J. / Kouril, R.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,22724
Polymers35,2553
Non-polymers2,97221
Water6,575365
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8049
Polymers11,7521
Non-polymers1,0538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,86610
Polymers11,7521
Non-polymers1,1159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5565
Polymers11,7521
Non-polymers8054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.092, 52.029, 77.749
Angle α, β, γ (deg.)90.00, 123.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C
15A
25B
35C
16A
26B
36C
17A
27B
37C
18A
28B
38C
19A
29B
39C
110A
210B
310C
111A
211B
311C
112A
212B
312C
113A
213B
313C
114A
214B
314C
115A
215B
315C
116A
216B
316C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS1AA1 - 72 - 8
21GLYGLYLYSLYS1BB1 - 72 - 8
31GLYGLYLYSLYS1CC1 - 72 - 8
12LYSLYSLYSLYS3AA89
22LYSLYSLYSLYS3BB89
32LYSLYSLYSLYS3CC89
13ILEILEVALVAL1AA9 - 1110 - 12
23ILEILEVALVAL1BB9 - 1110 - 12
33ILEILEVALVAL1CC9 - 1110 - 12
14GLNGLNGLNGLN3AA1213
24GLNGLNGLNGLN3BB1213
34GLNGLNGLNGLN3CC1213
15LYSLYSALAALA1AA13 - 1514 - 16
25LYSLYSALAALA1BB13 - 1514 - 16
35LYSLYSALAALA1CC13 - 1514 - 16
16GLNGLNGLNGLN3AA1617
26GLNGLNGLNGLN3BB1617
36GLNGLNGLNGLN3CC1617
17CYSCYSGLYGLY1AA17 - 2418 - 25
27CYSCYSGLYGLY1BB17 - 2418 - 25
37CYSCYSGLYGLY1CC17 - 2418 - 25
18LYSLYSLYSLYS3AA2526
28LYSLYSLYSLYS3BB2526
38LYSLYSLYSLYS3CC2526
19HISHISLEULEU1AA26 - 6827 - 69
29HISHISLEULEU1BB26 - 6827 - 69
39HISHISLEULEU1CC26 - 6827 - 69
110GLUGLUGLUGLU3AA6970
210GLUGLUGLUGLU3BB6970
310GLUGLUGLUGLU3CC6970
111ASNASNILEILE1AA70 - 8571 - 86
211ASNASNILEILE1BB70 - 8571 - 86
311ASNASNILEILE1CC70 - 8571 - 86
112LYSLYSLYSLYS3AA86 - 8887 - 89
212LYSLYSLYSLYS3BB86 - 8887 - 89
312LYSLYSLYSLYS3CC86 - 8887 - 89
113THRTHRLYSLYS1AA89 - 9990 - 100
213THRTHRLYSLYS1BB89 - 9990 - 100
313THRTHRLYSLYS1CC89 - 9990 - 100
114LYSLYSLYSLYS3AA100101
214LYSLYSLYSLYS3BB100101
314LYSLYSLYSLYS3CC100101
115ALAALATHRTHR1AA101 - 102102 - 103
215ALAALATHRTHR1BB101 - 102102 - 103
315ALAALATHRTHR1CC101 - 102102 - 103
116ASNASNGLUGLU3AA103 - 104104 - 105
216ASNASNGLUGLU3BB103 - 104104 - 105
316ASNASNGLUGLU3CC103 - 104104 - 105

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16

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Components

#1: Protein Cytochrome c /


Mass: 11751.635 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→65.09 Å / Num. obs: 21667

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HRC

1hrc


Resolution: 1.9→65.09 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.863 / SU B: 4.879 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27616 1166 5.1 %RANDOM
Rwork0.19285 ---
obs0.19712 21667 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å21.36 Å2
2---1.31 Å20 Å2
3---2.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 201 365 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222748
X-RAY DIFFRACTIONr_angle_refined_deg1.7942.143682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06125.294102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.403156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022038
X-RAY DIFFRACTIONr_nbd_refined0.2070.21503
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.259
X-RAY DIFFRACTIONr_mcbond_it1.0851.51665
X-RAY DIFFRACTIONr_mcangle_it1.47122478
X-RAY DIFFRACTIONr_scbond_it2.37931296
X-RAY DIFFRACTIONr_scangle_it3.3024.51197
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A50tight positional0.080.05
12B50tight positional0.060.05
13C50tight positional0.080.05
21A3tight positional0.010.05
22B3tight positional0.010.05
23C3tight positional0.010.05
31A26tight positional0.050.05
32B26tight positional0.050.05
33C26tight positional0.050.05
41A4tight positional0.020.05
42B4tight positional0.020.05
43C4tight positional0.020.05
51A20tight positional0.070.05
52B20tight positional0.070.05
53C20tight positional0.070.05
61A4tight positional0.040.05
62B4tight positional0.040.05
63C4tight positional0.020.05
71A56tight positional0.060.05
72B56tight positional0.050.05
73C56tight positional0.050.05
81A4tight positional0.020.05
82B4tight positional0.020.05
83C4tight positional0.020.05
91A342tight positional0.060.05
92B342tight positional0.060.05
93C342tight positional0.060.05
101A4tight positional0.010.05
102B4tight positional0.030.05
103C4tight positional0.020.05
111A124tight positional0.060.05
112B124tight positional0.060.05
113C124tight positional0.060.05
121A12tight positional0.040.05
122B12tight positional0.060.05
123C12tight positional0.050.05
131A94tight positional0.070.05
132B94tight positional0.070.05
133C94tight positional0.070.05
141A4tight positional0.030.05
142B4tight positional0.030.05
143C4tight positional0.010.05
151A12tight positional0.050.05
152B12tight positional0.040.05
153C12tight positional0.040.05
161A8tight positional0.080.05
162B8tight positional0.070.05
163C8tight positional0.040.05
41A5loose positional1.615
42B5loose positional2.525
43C5loose positional1.75
61A5loose positional0.645
62B5loose positional1.365
63C5loose positional0.745
81A5loose positional1.155
82B5loose positional1.215
83C5loose positional1.925
101A5loose positional0.995
102B5loose positional0.485
103C5loose positional0.535
121A15loose positional0.425
122B15loose positional0.545
123C15loose positional0.435
141A5loose positional1.245
142B5loose positional0.655
143C5loose positional0.845
161A10loose positional0.615
162B10loose positional0.425
163C10loose positional0.425
11A50tight thermal0.190.5
12B50tight thermal0.210.5
13C50tight thermal0.250.5
21A3tight thermal0.130.5
22B3tight thermal0.450.5
23C3tight thermal0.390.5
31A26tight thermal0.390.5
32B26tight thermal0.310.5
33C26tight thermal0.430.5
41A4tight thermal0.160.5
42B4tight thermal0.220.5
43C4tight thermal0.110.5
51A20tight thermal0.350.5
52B20tight thermal0.210.5
53C20tight thermal0.460.5
61A4tight thermal0.350.5
62B4tight thermal0.40.5
63C4tight thermal0.130.5
71A56tight thermal0.220.5
72B56tight thermal0.250.5
73C56tight thermal0.240.5
81A4tight thermal0.190.5
82B4tight thermal0.170.5
83C4tight thermal0.230.5
91A342tight thermal0.250.5
92B342tight thermal0.260.5
93C342tight thermal0.310.5
101A4tight thermal0.190.5
102B4tight thermal0.210.5
103C4tight thermal0.110.5
111A124tight thermal0.280.5
112B124tight thermal0.280.5
113C124tight thermal0.360.5
121A12tight thermal0.210.5
122B12tight thermal0.260.5
123C12tight thermal0.250.5
131A94tight thermal0.270.5
132B94tight thermal0.260.5
133C94tight thermal0.280.5
141A4tight thermal0.350.5
142B4tight thermal0.210.5
143C4tight thermal0.470.5
151A12tight thermal0.190.5
152B12tight thermal0.30.5
153C12tight thermal0.230.5
161A8tight thermal0.120.5
162B8tight thermal0.140.5
163C8tight thermal0.10.5
41A5loose thermal2.7610
42B5loose thermal4.2110
43C5loose thermal2.1310
61A5loose thermal1.4610
62B5loose thermal1.210
63C5loose thermal2.2710
81A5loose thermal2.3110
82B5loose thermal2.9310
83C5loose thermal1.710
101A5loose thermal3.9410
102B5loose thermal5.7810
103C5loose thermal1.910
121A15loose thermal2.4110
122B15loose thermal3.6610
123C15loose thermal2.7510
141A5loose thermal1.4910
142B5loose thermal0.510
143C5loose thermal1.8410
161A10loose thermal2.410
162B10loose thermal0.8610
163C10loose thermal2.7210
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 73 -
Rwork0.228 1311 -
obs--77.93 %

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