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- PDB-5b3s: Bovine heart cytochrome c oxidase in the carbon monoxide-bound mi... -

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Basic information

Entry
Database: PDB / ID: 5b3s
TitleBovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / PROTON PUMP / HEME / RESPIRATORY CHAIN
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding
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 / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / 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 VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / 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 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / CARBON MONOXIDE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC ...CARDIOLIPIN / CHOLIC ACID / CARBON MONOXIDE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsShimada, A. / Shinzawa-Ito, K. / Yoshikawa, S. / Tsukihara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06092 Japan
CitationJournal: To Be Published
Title: Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)
Authors: Shimada, A. / Muramoto, K. / Shinzawa-Ito, K. / Yoshikawa, S. / Tsukihara, T.
History
DepositionMar 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 2, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation_author / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_end_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_planes.rmsd / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_rejects / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: Multiple structures were assigned in the residues 380-385 of subunits A and N.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,590196
Polymers403,39226
Non-polymers48,198170
Water50,9642829
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,123103
Polymers201,69613
Non-polymers24,42790
Water23413
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,46793
Polymers201,69613
Non-polymers23,77180
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.491, 203.303, 177.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.993132, -0.004598, 0.116908), (-0.000582, -0.999021, -0.04424), (0.116997, -0.044004, 0.992157)165.076614, 623.951172, 4.15898
3given(1), (1), (1)
4given(-0.993491, -0.000372, 0.113907), (-0.005274, -0.998772, -0.049258), (0.113786, -0.049538, 0.992269)164.204727, 625.395386, 6.3826
5given(1), (1), (1)
6given(-0.993049, 0.00158, 0.117694), (-0.006588, -0.999089, -0.042173), (0.11752, -0.042656, 0.992154)163.074463, 624.238403, 3.67299
7given(1), (1), (1)
8given(-0.993524, -0.003245, 0.113572), (-0.000765, -0.999378, -0.035251), (0.113616, -0.035109, 0.992904)165.297165, 622.454651, 1.78843
9given(1), (1), (1)
10given(-0.990455, -0.056842, 0.12557), (0.049966, -0.997109, -0.057246), (0.128461, -0.050425, 0.990432)179.964844, 619.684387, 5.32225
11given(1), (1), (1)
12given(-0.994349, -0.002938, 0.106117), (-0.001097, -0.999279, -0.037946), (0.106152, -0.037848, 0.993629)167.169846, 622.699524, 3.23326
13given(1), (1), (1)
14given(-0.992965, -0.001635, 0.118393), (-0.003904, -0.998909, -0.046534), (0.11834, -0.046669, 0.991876)163.861267, 624.793701, 4.84214
15given(1), (1), (1)
16given(-0.993547, 0.007646, 0.113161), (-0.012654, -0.998969, -0.043601), (0.112711, -0.044751, 0.99262)161.85231, 625.263062, 4.80743
17given(1), (1), (1)
18given(-0.993773, -0.03402, 0.106101), (0.030182, -0.998838, -0.037568), (0.107255, -0.034132, 0.993645)176.823029, 618.61554, 1.93165
19given(1), (1), (1)
20given(-0.992995, 0.002355, 0.11813), (-0.00797, -0.998859, -0.047083), (0.117884, -0.047695, 0.991881)162.811478, 625.320618, 5.21324
21given(1), (1), (1)
22given(-0.993676, 0.000684, 0.112285), (-0.004293, -0.999482, -0.031899), (0.112205, -0.032179, 0.993164)164.2789, 622.54541, 0.99365
23given(1), (1), (1)
24given(-0.9933, -0.014449, 0.11466), (0.009558, -0.999026, -0.043085), (0.115171, -0.0417, 0.99247)168.506332, 622.228027, 3.6115
25given(1), (1), (1)
26given(-0.992728, -0.021363, 0.11847), (0.015705, -0.9987, -0.048488), (0.119352, -0.046275, 0.991773)169.746307, 622.218628, 4.39374

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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 (domestic 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 (domestic cattle) / References: UniProt: P68530, cytochrome-c oxidase
#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 (domestic cattle) / References: UniProt: P00415, cytochrome-c oxidase
#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 (domestic 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 (domestic cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10233.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic 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 (domestic cattle) / References: UniProt: P10175

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Sugars , 1 types, 23 molecules

#27: Sugar...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 16 types, 2976 molecules

#14: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical ChemComp-CU / COPPER (II) ION


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.: 2 / Source method: obtained synthetically / Formula: Na
#18: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#19: 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


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#20: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: C2H6O2
#21: Chemical
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL


Mass: 891.480 Da / Num. of mol.: 6 / 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-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


Mass: 759.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM
#24: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 9 / 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


Mass: 768.055 Da / Num. of mol.: 6 / 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


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#28: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#29: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#30: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2829 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.8
Details: 40mM Sodium phosphate, 0.2% decylmaltoside, 2% EG, PEG 4000

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→200 Å / Num. obs: 737777 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.028 / Rrim(I) all: 0.094 / Χ2: 1.582 / Net I/av σ(I): 31.952 / Net I/σ(I): 9.7 / Num. measured all: 7497834
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.698.91.132184270.8320.3971.2011.113100
1.69-1.718.91.035182670.8630.3631.0981.113100
1.71-1.728.90.954183270.8710.3351.0121.126100
1.72-1.7490.899184330.880.3150.9531.13100
1.74-1.7690.797183100.9060.2790.8461.137100
1.76-1.7790.728183180.9210.2550.7731.139100
1.77-1.7990.658183300.9380.230.6981.146100
1.79-1.819.10.615183810.9410.2140.6521.148100
1.81-1.839.10.568183770.9450.1980.6021.158100
1.83-1.859.10.525184160.9570.1830.5571.158100
1.85-1.879.10.479183450.9610.1660.5081.162100
1.87-1.899.20.454183820.9590.1580.4821.179100
1.89-1.929.20.397183250.9710.1370.421.199100
1.92-1.949.20.362183780.9740.1250.3831.222100
1.94-1.969.30.341183790.9770.1180.3611.249100
1.96-1.999.30.316183980.9790.1090.3341.3100
1.99-2.029.30.289183930.9810.0990.3061.368100
2.02-2.059.40.272183600.9820.0930.2871.468100
2.05-2.089.40.249183960.9820.0850.2641.5999.9
2.08-2.129.50.236184170.9840.080.2491.6499.9
2.12-2.159.50.22183820.9850.0740.2321.72899.9
2.15-2.199.60.197183730.9870.0660.2081.73999.8
2.19-2.239.60.178183380.990.060.1881.70999.8
2.23-2.289.70.158184030.9910.0530.1671.65799.9
2.28-2.339.70.139184800.9940.0460.1461.55299.9
2.33-2.389.80.125183810.9950.0410.1321.47999.9
2.38-2.449.80.113184480.9950.0370.1191.473100
2.44-2.519.80.104184680.9960.0340.111.501100
2.51-2.589.90.1184780.9960.0330.1051.568100
2.58-2.679.90.101184720.9960.0330.1061.74100
2.67-2.7611.80.114184980.9950.0340.1192.114100
2.76-2.8712.90.117185020.9950.0330.1212.441100
2.87-3130.106185210.9950.030.1112.445100
3-3.1613.10.092185340.9960.0260.0962.202100
3.16-3.3613.20.08185770.9970.0230.0832.037100
3.36-3.6213.30.073186130.9980.0210.0762.058100
3.62-3.98130.066186360.9970.0190.0692.125100
3.98-4.5612.30.055187070.9980.0170.0581.78199.9
4.56-5.7512.20.054188130.9980.0160.0571.61699.9
5.75-20011.30.05187940.9970.0170.0531.39597

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
REFMAC5.8.0048phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1A

5b1a


Resolution: 1.68→39.624 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 37025 5.03 %RANDOM
Rwork0.1526 ---
obs0.1538 736437 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→39.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28449 0 3148 2829 34426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01532902
X-RAY DIFFRACTIONf_angle_d1.72244248
X-RAY DIFFRACTIONf_dihedral_angle_d18.52419338
X-RAY DIFFRACTIONf_chiral_restr0.0994748
X-RAY DIFFRACTIONf_plane_restr0.015152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.271412510.25323089X-RAY DIFFRACTION100
1.6991-1.71910.259812390.236823188X-RAY DIFFRACTION100
1.7191-1.740.251612230.226923236X-RAY DIFFRACTION100
1.74-1.76210.241111920.213523182X-RAY DIFFRACTION100
1.7621-1.78530.219411730.203423233X-RAY DIFFRACTION100
1.7853-1.80970.211712290.194623246X-RAY DIFFRACTION100
1.8097-1.83560.220112020.186823216X-RAY DIFFRACTION100
1.8356-1.8630.204211940.179123267X-RAY DIFFRACTION100
1.863-1.89210.19812320.170523238X-RAY DIFFRACTION100
1.8921-1.92310.189212080.163323212X-RAY DIFFRACTION100
1.9231-1.95630.184112120.160223244X-RAY DIFFRACTION100
1.9563-1.99180.180712260.157823251X-RAY DIFFRACTION100
1.9918-2.03010.17712190.153723238X-RAY DIFFRACTION100
2.0301-2.07160.180111840.150423303X-RAY DIFFRACTION100
2.0716-2.11660.171811790.145823327X-RAY DIFFRACTION100
2.1166-2.16580.171912290.144623220X-RAY DIFFRACTION100
2.1658-2.220.171712320.143723247X-RAY DIFFRACTION100
2.22-2.280.168312740.141223196X-RAY DIFFRACTION100
2.28-2.34710.168312400.142323324X-RAY DIFFRACTION100
2.3471-2.42290.169612880.142923245X-RAY DIFFRACTION100
2.4229-2.50940.1712340.143923362X-RAY DIFFRACTION100
2.5094-2.60990.16712290.142723352X-RAY DIFFRACTION100
2.6099-2.72860.162412510.140623398X-RAY DIFFRACTION100
2.7286-2.87250.172612250.145423378X-RAY DIFFRACTION100
2.8725-3.05240.174413130.148723356X-RAY DIFFRACTION100
3.0524-3.28790.169712190.147223522X-RAY DIFFRACTION100
3.2879-3.61860.168612720.144923466X-RAY DIFFRACTION100
3.6186-4.14180.164313100.138123516X-RAY DIFFRACTION100
4.1418-5.21630.165413250.137123625X-RAY DIFFRACTION100
5.2163-39.6240.194712210.175423735X-RAY DIFFRACTION98
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)
10.22540.0154-0.08290.10430.00710.26750.00510.04770.02090.00780.00780.01650.0121-0.05510.00020.09940.0019-0.00750.10520.01060.091660.895304.7638197.5296
20.34690.09190.05140.1997-0.03870.38530.02450.1016-0.06770.00950.0172-0.072-0.03350.10370.07570.0724-0.0061-0.00020.0725-0.03010.1194126.1774310.8876193.7561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1 through 514) or (chain B and resid 1 through 227) or (chain C and resid 3 through 261) or (chain D and resid 4 through 147) or (chain E and resid 5 through 109) or (chain F and resid 1 through 94) or (chain G and resid 1 through 84) or (chain H and resid 7 through 85) or (chain I and resid 1 through 73) or (chain J and resid 1 through 58) or (chain K and resid 6 through 54) or (chain L and resid 2 through 47) or (chain M and resid 1 through 43)
2X-RAY DIFFRACTION2(chain N and resid 1 through 514) or (chain O and resid 1 through 227) or (chain P and resid 3 through 261) or (chain Q and resid 4 through 147) or (chain R and resid 5 through 109) or (chain S and resid 1 through 94) or (chain T and resid 1 through 84) or (chain U and resid 7 through 85) or (chain V and resid 1 through 73) or (chain W and resid 1 through 58) or (chain X and resid 6 through 54) or (chain Y and resid 2 through 47) or (chain Z and resid 1 through 43)

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