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Basic information

Entry
Database: PDB / ID: 5iy5
TitleElectron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution
Components
  • (Cytochrome c oxidase subunit ...) x 13
  • Cytochrome c
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV ...cytochrome c-heme linkage / cytochrome complex / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / positive regulation of cysteine-type endopeptidase activity / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ATP synthesis coupled electron transport / enzyme regulator activity / respirasome / central nervous system development / mitochondrial intermembrane space / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / positive regulation of apoptotic process / copper ion binding / lipid binding / apoptotic process / heme binding / mitochondrion / nucleoplasm / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain J / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c, class IA/ IB / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HEME C / Chem-PEK / PEROXIDE ION / Chem-PGV / Chem-PSC ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HEME C / Chem-PEK / PEROXIDE ION / Chem-PGV / Chem-PSC / TRISTEAROYLGLYCEROL / Unknown ligand / Cytochrome c / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShimada, S. / Baba, J. / Aoe, S. / Shimada, A. / Yamashita, E. / Tsukihara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: EMBO J. / Year: 2017
Title: Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
Authors: Shimada, S. / Shinzawa-Itoh, K. / Baba, J. / Aoe, S. / Shimada, A. / Yamashita, E. / Kang, J. / Tateno, M. / Yoshikawa, S. / Tsukihara, T.
History
DepositionMar 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 2.0Oct 9, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
1: Cytochrome c
2: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,565102
Polymers427,79628
Non-polymers28,76874
Water40,3002237
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
1: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,19651
Polymers213,89814
Non-polymers15,29737
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
2: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,36951
Polymers213,89814
Non-polymers13,47137
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.290, 183.872, 148.929
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number4
Space group name H-MP1211
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
111K
211X
112L
212Y
113M
213Z
1141
2142

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 526
2116N1 - 526
1126B1 - 229
2126O1 - 229
1136C1 - 272
2136P1 - 272
1146D4 - 147
2146Q4 - 147
1156E5 - 109
2156R5 - 109
1166F1 - 99
2166S1 - 99
1176G1 - 85
2176T1 - 85
1186H7 - 85
2186U7 - 85
1196I1 - 73
2196V1 - 73
11106J1 - 59
21106W1 - 59
11116K6 - 54
21116X6 - 54
11126L2 - 47
21126Y2 - 47
11136M1 - 43
21136Z1 - 43
1114610 - 105
2114620 - 105

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.831972, -0.010747, -0.554713), (-0.007647, -0.99994, 0.007905), (-0.554765, -0.002335, -0.832004)40.340462, -0.83419, 132.57309
3given(1), (1), (1)
4given(0.83133, -0.003219, -0.55577), (-0.0026, -0.999995, 0.001903), (-0.555773, -0.000137, -0.831334)40.307961, -0.35593, 132.498322
5given(1), (1), (1)
6given(0.832054, -0.010883, -0.554587), (-0.010091, -0.999939, 0.004483), (-0.554602, 0.001866, -0.832114)40.277721, -0.51278, 132.604248
7given(1), (1), (1)
8given(0.836256, -0.021573, -0.547914), (-0.015942, -0.99976, 0.015033), (-0.548107, -0.003837, -0.836399)39.459751, -1.30309, 132.800507
9given(1), (1), (1)
10given(0.833846, -0.029407, -0.551213), (-0.019535, -0.999526, 0.023773), (-0.551651, -0.009055, -0.834026)40.22459, -2.48523, 132.649017
11given(1), (1), (1)
12given(0.821611, -0.008057, -0.569992), (0.000334, -0.999893, 0.014616), (-0.570048, -0.012199, -0.821521)42.050598, -1.31192, 131.525681
13given(1), (1), (1)
14given(0.831893, -0.034914, -0.553837), (-0.022329, -0.999317, 0.029458), (-0.554487, -0.012139, -0.832104)39.3965, -1.81845, 132.51799
15given(1), (1), (1)
16given(0.79982, 0.022778, -0.599808), (0.020668, -0.999732, -0.010405), (-0.599885, -0.004075, -0.800076)45.554569, -0.59304, 132.288742
17given(1), (1), (1)
18given(0.83598, -0.019898, -0.548399), (-0.007473, -0.999663, 0.024879), (-0.548709, -0.0167, -0.835847)39.527012, -2.57625, 133.019135
19given(1), (1), (1)
20given(0.825431, 0.005776, -0.564474), (0.003982, -0.999982, -0.004409), (-0.564489, 0.001391, -0.825439)41.866268, 0.43834, 131.759918
21given(1), (1), (1)
22given(0.834354, -0.021583, -0.550807), (-0.011835, -0.999704, 0.021245), (-0.551103, -0.011207, -0.834362)39.91309, -2.22789, 132.753418
23given(1), (1), (1)
24given(0.832704, -0.009258, -0.553641), (-0.007505, -0.999957, 0.005432), (-0.553667, -0.000368, -0.832738)40.26115, -0.47406, 132.631439
25given(1), (1), (1)
26given(0.829286, -0.035633, -0.557687), (-0.011914, -0.998865, 0.046107), (-0.558697, -0.031591, -0.82877)40.648491, -5.73668, 131.899734
27given(1), (1), (1)
28given(0.830096, -0.03594, -0.556461), (-0.049126, -0.998754, -0.008776), (-0.555452, 0.034621, -0.830827)40.14864, 3.66861, 132.950516

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Components

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Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I


Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530
#3: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 29725.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415
#4: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 16913.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / / Cytochrome c oxidase polypeptide Va


Mass: 12083.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428
#7: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9532.667 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 9411.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6553.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470
#11: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 5442.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5362.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4738.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175

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Protein / Sugars , 2 types, 4 molecules 12

#14: Protein Cytochrome c /


Mass: 11751.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004
#30: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 17 types, 2309 molecules

#15: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#18: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#19: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#20: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#21: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C57H110O6
#22: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#23: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#24: Chemical
ChemComp-CHD / CHOLIC ACID / Cholic acid


Mass: 408.571 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H40O5
#25: Chemical ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 768.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#26: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#27: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 15 / Source method: obtained synthetically
#28: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE / Phosphatidylcholine


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#29: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#31: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#32: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2237 / 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: 3.55 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 8
Details: 15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 397399 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.044 / Rrim(I) all: 0.105 / Χ2: 1.36 / Net I/av σ(I): 17.007 / Net I/σ(I): 8.8 / Num. measured all: 1960373
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2-2.023.798850.6230.5990.72499.5
2.02-2.033.799620.6640.5570.72499.40.933
2.03-2.053.898510.6790.4980.74699.50.8390.982
2.05-2.073.898960.740.4690.74299.30.7890.925
2.07-2.093.899460.7350.4240.75699.50.7160.838
2.09-2.113.898440.7420.4130.75999.40.7010.819
2.11-2.133.899240.7860.3720.77999.40.6340.74
2.13-2.153.898530.8140.3450.76299.40.590.688
2.15-2.183.999520.8440.3190.79899.40.5480.638
2.18-2.23.998320.8460.2940.899.30.5090.592
2.2-2.233.999420.8650.2740.8299.30.4740.551
2.23-2.253.998420.8740.250.84599.20.4360.506
2.25-2.28498250.8820.2360.91599.20.4120.478
2.28-2.31499040.9010.2130.84999.20.3760.435
2.31-2.344.198390.9090.1980.85399.10.350.405
2.34-2.374.199260.930.180.852990.3240.373
2.37-2.414.198590.9340.1660.86698.90.2990.344
2.41-2.444.298430.9460.150.885990.2740.315
2.44-2.484.3100140.9320.1440.93399.70.2590.299
2.48-2.524.599270.9320.1390.96499.90.2510.289
2.52-2.564.699570.9380.131.00499.90.2380.273
2.56-2.614.798970.9420.121.08499.80.2210.253
2.61-2.664.899500.9480.1081.12799.70.2020.231
2.66-2.714.999110.9490.11.18299.70.1880.214
2.71-2.774.999730.9590.0911.24399.60.1720.196
2.77-2.84599370.9620.0851.28599.50.1620.184
2.84-2.915.199380.9670.0751.29399.60.1450.165
2.91-2.995.299080.9750.0671.32899.40.1310.148
2.99-3.085.399490.9810.0611.36999.60.1220.137
3.08-3.175.499370.9830.0551.45499.70.1110.124
3.17-3.295.699610.9870.0491.57599.80.1040.115
3.29-3.425.899820.9890.0451.77999.80.0980.109
3.42-3.586.199630.9890.0462.18199.90.1040.114
3.58-3.766.7100240.9920.0442.4411000.1040.113
3.76-46.9100180.9940.0372.4141000.0910.098
4-4.317.199730.9950.0322.2541000.0790.085
4.31-4.747.3100250.9960.0282.0481000.0710.077
4.74-5.437.5100430.9960.0271.811000.0670.072
5.43-6.837.6100550.9970.0241.5171000.0620.066
6.83-507.3101320.9960.0251.75699.30.0610.066

-
Processing

Software
NameVersionClassification
REFMAC5.8.0048refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYR and 1HRC

2dyr

1hrc


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2045 / WRfactor Rwork: 0.162 / FOM work R set: 0.7862 / SU B: 9.054 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1297 / SU Rfree: 0.1284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 19990 5 %RANDOM
Rwork0.1665 ---
obs0.1686 377338 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 166.2 Å2 / Biso mean: 48.152 Å2 / Biso min: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20.24 Å2
2--3.62 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30158 0 2183 2237 34578
Biso mean--71.26 55.59 -
Num. residues----3768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02633567
X-RAY DIFFRACTIONr_angle_refined_deg2.2052.01745237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58453776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55823.0781303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.469155100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.90815131
X-RAY DIFFRACTIONr_chiral_restr0.150.24770
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02924471
X-RAY DIFFRACTIONr_mcbond_it3.2043.41515126
X-RAY DIFFRACTIONr_mcangle_it4.4855.08518884
X-RAY DIFFRACTIONr_scbond_it4.65118441
X-RAY DIFFRACTIONr_sphericity_bonded7.5452
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4373LOOSE POSITIONAL0.165
1A4373LOOSE THERMAL3.0410
2B1866LOOSE POSITIONAL0.295
2B1866LOOSE THERMAL5.2410
3C2573LOOSE POSITIONAL0.425
3C2573LOOSE THERMAL3.3810
4D1187LOOSE POSITIONAL0.665
4D1187LOOSE THERMAL4.5810
5E852LOOSE POSITIONAL0.265
5E852LOOSE THERMAL2.2210
6F749LOOSE POSITIONAL0.785
6F749LOOSE THERMAL4.4810
7G704LOOSE POSITIONAL0.715
7G704LOOSE THERMAL4.5710
8H662LOOSE POSITIONAL0.585
8H662LOOSE THERMAL8.6110
9I601LOOSE POSITIONAL0.685
9I601LOOSE THERMAL6.310
10J489LOOSE POSITIONAL0.675
10J489LOOSE THERMAL5.1110
11K384LOOSE POSITIONAL0.235
11K384LOOSE THERMAL6.710
12L380LOOSE POSITIONAL0.315
12L380LOOSE THERMAL2.5610
13M335LOOSE POSITIONAL0.425
13M335LOOSE THERMAL4.7310
14869LOOSE POSITIONAL0.545
14869LOOSE THERMAL8.1210
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 1459 -
Rwork0.313 27295 -
all-28754 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36420.0095-0.07440.13750.0750.40920.00470.04430.0499-0.0374-0.00240.0074-0.0395-0.052-0.00230.04540.02480.01110.02340.01310.0159-2.46810.920333.7561
20.5142-0.0779-0.18130.15190.07980.453-0.01530.042-0.0321-0.03680.023-0.05080.02320.1012-0.00760.0550.03030.0220.0623-0.00970.024823.9593-9.914827.2901
30.2143-0.1037-0.10020.20820.15190.54220.0145-0.07220.10710.02510.0171-0.0318-0.15030.0157-0.03160.0980.00570.02010.0315-0.03370.06055.311319.098562.0657
40.58020.008-0.0810.09920.0360.18440.01370.1452-0.0466-0.0585-0.02470.031-0.0029-0.05880.0110.07080.0263-0.00020.0522-0.0120.0271-14.9622-11.296316.9191
51.7936-0.4925-0.44541.06940.46481.1455-0.056-0.2158-0.23160.0657-0.01270.06210.223-0.01380.06870.0675-0.0290.01430.05760.01540.0943-38.62-31.059935.1935
60.70780.44750.42280.84640.55290.55550.0934-0.15010.0280.1519-0.13050.14540.0568-0.25020.03710.04690.0070.04810.17750.00860.0622-31.6217-0.876960.3435
70.690.0329-0.47660.1818-0.12681.08470.0651-0.18070.10020.0590.0218-0.0722-0.17730.2234-0.08690.1308-0.04440.00770.0767-0.05980.109721.490923.153567.5275
80.7139-0.80530.09451.69240.30030.5459-0.0131-0.15050.11690.07340.1688-0.33240.02640.2499-0.15570.01020.0045-0.00170.2612-0.06940.135347.89642.56844.703
92.950.719-0.53750.2651-0.28030.3478-0.0298-0.0771-0.4549-0.0494-0.0484-0.1090.08660.07810.07830.15680.03930.04750.0699-0.05250.181212.3357-27.82721.1523
100.8109-0.0806-0.32110.37970.06181.23560.14230.11740.2593-0.0680.0010.0093-0.42-0.2542-0.14330.22360.10750.02090.06950.01070.2083-11.322232.595147.7737
110.3462-0.2777-0.17380.23110.10470.43170.0860.1764-0.1454-0.0804-0.09940.12850.052-0.22410.01340.20110.0177-0.00890.2631-0.00650.09820.7476-7.27062.1483
121.15650.1945-0.38750.16150.12781.0173-0.02050.12320.096-0.1291-0.01070.0659-0.2086-0.08310.03120.16280.0721-0.00020.06950.05290.0907-12.366217.524723.0532
132.34650.8792-1.0150.3915-0.2481.59160.03260.0930.1266-0.09160.00280.0701-0.1763-0.0531-0.03540.18160.0852-0.01820.11560.0630.0768-11.287412.281612.3375
140.3129-0.0542-0.15330.14620.09590.5813-0.0223-0.08810.01590.09850.0663-0.03290.08120.124-0.0440.08990.0463-0.01860.0636-0.01840.009319.2947-0.9429105.6131
150.42060.0634-0.12490.2071-0.0520.50420.0009-0.12640.1140.05640.0732-0.1087-0.05030.2877-0.07410.0226-0.0031-0.03220.2444-0.12460.120744.90929.626696.5361
160.29520.03220.07670.26160.13430.5018-0.00430.0402-0.06940.02620.0261-0.0160.22060.0185-0.02170.13270.020.00010.0257-0.01110.01679.8022-19.353678.1938
170.4774-0.1356-0.24860.17710.09970.4745-0.015-0.18550.11840.16310.0963-0.04710.00820.1707-0.08130.19120.0326-0.02520.1353-0.03510.040818.150711.6181126.6039
182.39840.2562-0.25030.91730.19480.85680.05670.09320.32280.01930.04950.0815-0.1254-0.1025-0.10620.18340.06410.07270.03150.03990.0711-11.426931.7685124.0653
190.1772-0.0976-0.21320.86350.99631.5618-0.03140.02980.00080.0226-0.12290.2251-0.002-0.35450.15420.08050.01780.01450.18540.01710.0858-19.94651.0314100.4757
201.23880.0120.42890.2829-0.11140.5699-0.01140.2675-0.1415-0.03850.048-0.02650.13190.1311-0.03650.18130.07320.00980.1206-0.0580.056220.5906-23.527564.7265
210.74330.0289-0.89850.48060.59512.47410.01970.0522-0.0283-0.01910.0653-0.1311-0.08580.2743-0.08490.01760.00090.01470.2729-0.07580.128554.4694-2.722968.6443
222.3-0.6683-0.79660.4629-0.00170.54660.1483-0.02410.46670.06180.0319-0.1896-0.19140.1306-0.18030.1635-0.0946-0.01710.283-0.16020.266538.860827.6905107.7976
231.04810.28670.28130.30940.18521.08280.0793-0.1862-0.38420.1370.0104-0.04840.4486-0.063-0.08970.3659-0.02930.02170.06260.07260.16433.5854-32.523299.3213
242.32430.2862-1.16380.2991-0.24471.22620.0894-0.4040.18210.19020.0464-0.0653-0.03180.2276-0.13580.18670.0606-0.08430.3957-0.10890.06739.34567.3514130.4352
250.43190.09250.19530.2360.20160.5051-0.1227-0.0252-0.06510.16620.1107-0.00730.28490.14190.0120.35770.12640.0170.13630.04750.067116.7001-17.481120.495
263.1927-1.4902-1.02180.77720.48881.5808-0.1619-0.2958-0.02140.22290.1374-0.03440.26180.28680.02450.33230.1065-0.0690.19220.01860.027323.5186-12.3533128.8741
273.1276-0.13530.01783.5780.39263.1804-0.26750.03430.9187-0.17660.1084-0.1501-0.9610.27290.15910.4372-0.1223-0.02050.0396-0.00290.375541.278426.997519.8774
284.34491.21770.83882.27741.22372.6393-0.0156-0.1238-0.6420.1413-0.1013-0.42061.01620.30310.11690.54230.29250.02760.3395-0.06790.434562.6153-27.245593.1504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 608
2X-RAY DIFFRACTION2B1 - 303
3X-RAY DIFFRACTION3C3 - 311
4X-RAY DIFFRACTION4D4 - 201
5X-RAY DIFFRACTION5E5 - 202
6X-RAY DIFFRACTION6F1 - 102
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H7 - 85
9X-RAY DIFFRACTION9I1 - 101
10X-RAY DIFFRACTION10J1 - 102
11X-RAY DIFFRACTION11K6 - 54
12X-RAY DIFFRACTION12L2 - 102
13X-RAY DIFFRACTION13M1 - 101
14X-RAY DIFFRACTION14N1 - 614
15X-RAY DIFFRACTION15O1 - 301
16X-RAY DIFFRACTION16P3 - 310
17X-RAY DIFFRACTION17Q4 - 201
18X-RAY DIFFRACTION18R5 - 109
19X-RAY DIFFRACTION19S1 - 102
20X-RAY DIFFRACTION20T1 - 103
21X-RAY DIFFRACTION21U7 - 85
22X-RAY DIFFRACTION22V1 - 73
23X-RAY DIFFRACTION23W1 - 102
24X-RAY DIFFRACTION24X6 - 54
25X-RAY DIFFRACTION25Y2 - 101
26X-RAY DIFFRACTION26Z1 - 101
27X-RAY DIFFRACTION2710 - 201
28X-RAY DIFFRACTION2820 - 201

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